September 2008 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] galaxy-dev Digest, Vol 33, Issue 21
by Ross 06 Oct '08

06 Oct '08

I may be missing something, but right now, and without any changes to Galaxy, there's no reason why a new tool should not wrap an existing (or new) command line executable program that uses web services to do something interesting! I have an rgenetics tool that uses the Haploview java executable in command line mode to prepare image files of LD patterns in the Hapmap populations with an inhouse sample over a region, and then stitches them together into a single image so they can be visually compared - Galaxy doesn't know or care if the tool executable uses web services - the job runner sets up the call and then deals with the resulting tool outputs correctly - as long as the cluster node executing the tool has internet access, it can interact with the web services transparently - as Greg says, the tool will be fragile to changes in the web service call syntax but that's always a problem in the long term. I agree with Greg that bringing web services interfaces *directly* into the existing Galaxy framework does not appear to have a high priority at this time and I'm not even sure that it makes an awful lot of sense in the long term - especially since we can let web service interaction live out in tool space where it already works? Is there a specific use-case anyone has in mind where the web services interface really needs to be brought inside the framework itself? On Tue, Sep 30, 2008 at 2:00 AM, <galaxy-dev-request(a)bx.psu.edu> wrote: > > Today's Topics: > > 1. Re: Galaxy with web services (Greg Von Kuster) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 29 Sep 2008 09:52:39 -0400 > From: Greg Von Kuster <ghv2(a)psu.edu> > Subject: Re: [galaxy-dev] Galaxy with web services > To: Praveen Agrawal <praveen(a)scfbio-iitd.res.in> > Cc: galaxy-dev(a)bx.psu.edu > Message-ID: <48E0DDA7.1090200(a)psu.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hello Praveen, > > Currently web-based interaction is only used for external data sources > (biomart, UCSC table browser, most other things under "Get Data"). For > the other tools, we generate a command line based on the user input, > which Galaxy then runs. The motivation for this is control and trust. > One of our major goals with Galaxy is to ensure reproducibility, and > relying on web services which can change their interfaces or behavior > makes this very challenging. We are certainly interested in supporting > web services in the Galaxy framework, but implementation is not yet > under way. Several of the methods currently in ~/tools/__init__.py ( > among others ) will need to evolve and grow in order to support a web > services interface for remote tools. We'll certainly keep you informed > as we begin to support this, but it may be a while... > > Greg Von Kuster > Galaxy Development Team > > > Praveen Agrawal wrote: >> Hi, >> I am trying to use Galaxy at my site and cann't figure out Galaxy with web >> services. I understand that it's possible to integrate a data source using >> WSDL/SOAP. Is the same possible for a remote tool as well? -- python -c "foo = map(None,'moc.liamg(a)surazal.ssor'); foo.reverse(); print ''.join(foo)"

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[hg] galaxy 1534: Fix for disk usage report in the webapps syste...
by Greg Von Kuster 30 Sep '08

30 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/1706aadf16b2 changeset: 1534:1706aadf16b2 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Sep 29 10:37:54 2008 -0400 description: Fix for disk usage report in the webapps system controller. 1 file(s) affected in this change: lib/galaxy/webapps/reports/controllers/system.py diffs (20 lines): diff -r 3830fefb07da -r 1706aadf16b2 lib/galaxy/webapps/reports/controllers/system.py --- a/lib/galaxy/webapps/reports/controllers/system.py Fri Sep 26 14:22:37 2008 -0400 +++ b/lib/galaxy/webapps/reports/controllers/system.py Mon Sep 29 10:37:54 2008 -0400 @@ -157,13 +157,15 @@ disk_usage = self.get_disk_usage( file_path ) min_file_size = 2**32 # 4 Gb file_size_str = nice_size( min_file_size ) + hda = trans.model.HistoryDatasetAssociation d = trans.model.Dataset datasets = [] where = ( d.table.c.file_size > min_file_size ) dataset_rows = d.query().filter( where ).order_by( desc( d.table.c.file_size ) ) for dataset in dataset_rows: - datasets.append( ( dataset.id, str( dataset.update_time )[0:10], dataset.history_id, dataset.deleted, dataset.file_size ) ) + history_dataset_assoc = hda.filter_by( dataset_id=dataset.id ).order_by( desc( hda.table.c.history_id ) ).all()[0] + datasets.append( ( dataset.id, str( dataset.update_time )[0:10], history_dataset_assoc.history_id, dataset.deleted, dataset.file_size ) ) return file_path, disk_usage, datasets, file_size_str def nice_size( size ):

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[hg] galaxy 1535: Modified the way biomart tool runs: output gen...
by Greg Von Kuster 30 Sep '08

30 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/931d6ca549d3 changeset: 1535:931d6ca549d3 user: guru date: Tue Sep 30 15:30:57 2008 -0400 description: Modified the way biomart tool runs: output generation will be completed before exec_afer_process hook is called. 4 file(s) affected in this change: tools/data_source/biomart.py tools/data_source/biomart.xml tools/data_source/biomart_filter.py tools/data_source/biomart_test.xml diffs (148 lines): diff -r 1706aadf16b2 -r 931d6ca549d3 tools/data_source/biomart.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/biomart.py Tue Sep 30 15:30:57 2008 -0400 @@ -0,0 +1,55 @@ +#!/usr/bin/env python +#Retreives data from BIOMART and stores in a file. Biomart parameters are provided in the input/output file. +#guruprasad Ananda + +import urllib, sys, os, gzip, tempfile, shutil +from galaxy import eggs + +assert sys.version_info[:2] >= ( 2, 4 ) + +def stop_err( msg ): + sys.stderr.write( msg ) + sys.exit() + +def __main__(): + filename = sys.argv[1] + params = {} + for line in open(filename, 'r'): + try: + line = line.strip() + fields = line.split('\t') + params[fields[0]] = fields[1] + except: + continue + + URL = params.get( 'URL', None ) + if not URL: + open( filename, 'w' ).write( "" ) + stop_err( 'Datasource has not sent back a URL parameter.' ) + URL = URL + '&_export=1&GALAXY_URL=0' + CHUNK_SIZE = 2**20 # 1Mb + MAX_SIZE = CHUNK_SIZE * 100 + try: + page = urllib.urlopen(URL) + except Exception, exc: + stop_err('Problems connecting to %s (%s)' % (URL, exc) ) + + fp = open(filename, 'w') + size = 0 + max_size_exceeded = False + while 1: + chunk = page.read(CHUNK_SIZE) + if not chunk: + break + size += len(chunk) + if size > MAX_SIZE: + max_size_exceeded = True + break + fp.write(chunk) + fp.close() + + if max_size_exceeded: + print 'Maximum data size of 100 MB exceeded, incomplete data retrieval.' + +if __name__ == "__main__": + __main__() diff -r 1706aadf16b2 -r 931d6ca549d3 tools/data_source/biomart.xml --- a/tools/data_source/biomart.xml Mon Sep 29 10:37:54 2008 -0400 +++ b/tools/data_source/biomart.xml Tue Sep 30 15:30:57 2008 -0400 @@ -1,14 +1,14 @@ <?xml version="1.0"?> <tool name="BioMart" id="biomart"> - <description>Central server</description> - - <command/> - + <command interpreter="python"> + biomart.py + $output + </command> <inputs action="http://www.biomart.org/biomart/martview" check_values="false" method="get" target="_top"> <display>go to BioMart Central $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" /> - </inputs> + </inputs> <uihints minwidth="800"/> diff -r 1706aadf16b2 -r 931d6ca549d3 tools/data_source/biomart_filter.py --- a/tools/data_source/biomart_filter.py Mon Sep 29 10:37:54 2008 -0400 +++ b/tools/data_source/biomart_filter.py Tue Sep 30 15:30:57 2008 -0400 @@ -14,41 +14,16 @@ data_type = sniff.guess_ext( data.file_name, sniff_order=app.datatypes_registry.sniff_order ) data = app.datatypes_registry.change_datatype(data, data_type) data.name = data_name + #store BIOMART parameters temporarily in output file + out = open(data.file_name,'w') + for key, value in param_dict.items(): + print >> out, "%s\t%s" % (key,value) + out.close() out_data[name] = data + def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): - """Verifies the data after the run""" - URL = param_dict.get( 'URL', None ) - if not URL: - raise Exception('Datasource has not sent back a URL parameter') - URL = URL + '&_export=1&GALAXY_URL=0' - CHUNK_SIZE = 2**20 # 1Mb - MAX_SIZE = CHUNK_SIZE * 100 - try: - page = urllib.urlopen(URL) - except Exception, exc: - raise Exception('Problems connecting to %s (%s)' % (URL, exc) ) name, data = out_data.items()[0] - fp = open(data.file_name, 'wb') - size = 0 - max_size_exceeded = False - - while 1: - chunk = page.read(CHUNK_SIZE) - if not chunk: - break - size += len(chunk) - if size > MAX_SIZE: - max_size_exceeded = True - break - fp.write(chunk) - fp.close() - - if max_size_exceeded: - data.info = 'Maximum data size of 100 MB exceeded, incomplete data retrieval.' - else: - data.info = data.name - if not isinstance(data.datatype, datatypes.interval.Bed) and isinstance(data.datatype, datatypes.interval.Interval): #Set meta data, format file to be valid interval type data.set_meta(first_line_is_header=True) diff -r 1706aadf16b2 -r 931d6ca549d3 tools/data_source/biomart_test.xml --- a/tools/data_source/biomart_test.xml Mon Sep 29 10:37:54 2008 -0400 +++ b/tools/data_source/biomart_test.xml Tue Sep 30 15:30:57 2008 -0400 @@ -3,7 +3,10 @@ <description>Test server</description> - <command/> + <command interpreter="python"> + biomart.py + $output + </command> <inputs action="http://test.biomart.org/biomart/martview" check_values="false" method="get" target="_top"> <display>go to BioMart Central $GALAXY_URL</display>

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[hg] galaxy 1533: Update to implicit converter discovery. Will n...
by Greg Von Kuster 30 Sep '08

30 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/3830fefb07da changeset: 1533:3830fefb07da user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Sep 26 14:22:37 2008 -0400 description: Update to implicit converter discovery. Will now allow the use of converters that create datatypes that are a subclass of what is needed by the tool. i.e. If tool input requires 'interval', and a datatype has a BED converter available but no interval converter, the BED converter can now be used. 5 file(s) affected in this change: lib/galaxy/datatypes/data.py lib/galaxy/datatypes/registry.py lib/galaxy/model/__init__.py lib/galaxy/tools/actions/__init__.py lib/galaxy/tools/parameters/basic.py diffs (138 lines): diff -r 3b6771227a43 -r 3830fefb07da lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Fri Sep 26 09:10:04 2008 -0400 +++ b/lib/galaxy/datatypes/data.py Fri Sep 26 14:22:37 2008 -0400 @@ -185,6 +185,10 @@ """Returns available converters by type for this dataset""" return datatypes_registry.get_converters_by_datatype(original_dataset.ext) + def find_conversion_destination( self, dataset, accepted_formats, datatypes_registry, **kwd ): + """Returns ( target_ext, exisiting converted dataset )""" + return datatypes_registry.find_conversion_destination_for_dataset_by_extensions( dataset, accepted_formats, **kwd ) + def convert_dataset(self, trans, original_dataset, target_type, return_output = False, visible = True ): """This function adds a job to the queue to convert a dataset to another type. Returns a message about success/failure.""" converter = trans.app.datatypes_registry.get_converter_by_target_type( original_dataset.ext, target_type ) diff -r 3b6771227a43 -r 3830fefb07da lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Fri Sep 26 09:10:04 2008 -0400 +++ b/lib/galaxy/datatypes/registry.py Fri Sep 26 14:22:37 2008 -0400 @@ -233,3 +233,16 @@ if target_ext in converters.keys(): return converters[target_ext] return None + def find_conversion_destination_for_dataset_by_extensions( self, dataset, accepted_formats, converter_safe = True ): + """Returns ( target_ext, exisiting converted dataset )""" + for convert_ext in self.get_converters_by_datatype( dataset.ext ): + if isinstance( self.get_datatype_by_extension( convert_ext ), accepted_formats ): + datasets = dataset.get_converted_files_by_type( convert_ext ) + if datasets: + ret_data = datasets[0] + elif not converter_safe: + continue + else: + ret_data = None + return ( convert_ext, ret_data ) + return ( None, None ) \ No newline at end of file diff -r 3b6771227a43 -r 3830fefb07da lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Fri Sep 26 09:10:04 2008 -0400 +++ b/lib/galaxy/model/__init__.py Fri Sep 26 14:22:37 2008 -0400 @@ -254,6 +254,10 @@ def get_converter_types(self): return self.datatype.get_converter_types( self, datatypes_registry) + + def find_conversion_destination( self, accepted_formats, **kwd ): + """Returns ( target_ext, exisiting converted dataset )""" + return self.datatype.find_conversion_destination( self, accepted_formats, datatypes_registry, **kwd ) def copy( self, copy_children = False, parent_id = None ): des = HistoryDatasetAssociation( hid=self.hid, name=self.name, info=self.info, blurb=self.blurb, peek=self.peek, extension=self.extension, dbkey=self.dbkey, metadata=self._metadata, dataset = self.dataset, visible=self.visible, deleted=self.deleted, parent_id=parent_id, copied_from_history_dataset_association = self ) diff -r 3b6771227a43 -r 3830fefb07da lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Fri Sep 26 09:10:04 2008 -0400 +++ b/lib/galaxy/tools/actions/__init__.py Fri Sep 26 14:22:37 2008 -0400 @@ -29,22 +29,21 @@ def visitor( prefix, input, value, parent = None ): def process_dataset( data ): if data and not isinstance( data.datatype, input.formats ): - for target_ext in input.extensions: - if target_ext in data.get_converter_types(): - data.refresh() #need to refresh incase this conversion just took place, i.e. input above in tool performed the same conversion - datasets = data.get_converted_files_by_type( target_ext ) - if datasets: data = datasets[0] - elif input.converter_safe( param_values, trans ): - #run converter here - assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, metadata_safe = False ) - new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output = True, visible = False ).values()[0] - new_data.hid = data.hid - new_data.name = data.name - new_data.flush() - assoc.dataset = new_data - assoc.flush() - data = new_data - break + data.refresh() #need to refresh in case this conversion just took place, i.e. input above in tool performed the same conversion + target_ext, converted_dataset = data.find_conversion_destination( input.formats, converter_safe = input.converter_safe( param_values, trans ) ) + if target_ext: + if converted_dataset: + data = converted_dataset + else: + #run converter here + assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, metadata_safe = False ) + new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output = True, visible = False ).values()[0] + new_data.hid = data.hid + new_data.name = data.name + new_data.flush() + assoc.dataset = new_data + assoc.flush() + data = new_data return data if isinstance( input, DataToolParameter ): if isinstance( value, list ): diff -r 3b6771227a43 -r 3830fefb07da lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Fri Sep 26 09:10:04 2008 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Fri Sep 26 14:22:37 2008 -0400 @@ -1059,16 +1059,12 @@ selected = ( value and ( data in value ) ) field.add_option( "%s: %s" % ( hid, data.name[:30] ), data.id, selected ) else: - for target_ext in self.extensions: - if target_ext in data.get_converter_types(): - datasets = data.get_converted_files_by_type( target_ext ) - if datasets: - data = datasets[0] - elif not self.converter_safe( other_values, trans ): - continue - selected = ( value and ( data in value ) ) - field.add_option( "%s: (as %s) %s" % ( hid, target_ext, data.name[:30] ), data.id, selected ) - break #we only report the first valid converter, assume self.extensions is a priority list + target_ext, converted_dataset = data.find_conversion_destination( self.formats, converter_safe = self.converter_safe( other_values, trans ) ) + if target_ext: + if converted_dataset: + data = converted_dataset + selected = ( value and ( data in value ) ) + field.add_option( "%s: (as %s) %s" % ( hid, target_ext, data.name[:30] ), data.id, selected ) # Also collect children via association object dataset_collector( data.children, hid ) dataset_collector( history.datasets, None ) @@ -1111,9 +1107,9 @@ pass #no valid options def dataset_collector( datasets ): def is_convertable( dataset ): - for target_ext in self.extensions: - if target_ext in data.get_converter_types(): - return True + target_ext, converted_dataset = dataset.find_conversion_destination( self.formats, converter_safe = True ) #need to assume converter_safe = True, since we don't know about other parameter values here + if target_ext is not None: + return True return False for i, data in enumerate( datasets ): if data.visible and not data.deleted and data.state not in [data.states.ERROR] and ( isinstance( data.datatype, self.formats) or is_convertable( data ) ): @@ -1184,7 +1180,7 @@ return [] def converter_safe( self, other_values, trans ): - if trans.workflow_building_mode: + if not hasattr( trans, 'workflow_building_mode' ) or trans.workflow_building_mode: return False converter_safe = [True] def visitor( prefix, input, value, parent = None ):

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Galaxy with web services
by Praveen Agrawal 29 Sep '08

29 Sep '08

Hi, I am trying to use Galaxy at my site and cann't figure out Galaxy with web services. I understand that it's possible to integrate a data source using WSDL/SOAP. Is the same possible for a remote tool as well? Regards, Praveen ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ http://www.scfbio-iitd.res.in ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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[hg] galaxy 1531: Enhance the way dataset.set_meta() behaves, by...
by Greg Von Kuster 26 Sep '08

26 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/aa1088e4c6c6 changeset: 1531:aa1088e4c6c6 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Sep 25 15:03:05 2008 -0400 description: Enhance the way dataset.set_meta() behaves, by adding a flag 'overwrite', which when False will only overwrite metadata values that are not previously set or are not accessable for user modification. 7 file(s) affected in this change: lib/galaxy/datatypes/data.py lib/galaxy/datatypes/interval.py lib/galaxy/datatypes/metadata.py lib/galaxy/datatypes/registry.py lib/galaxy/datatypes/sequence.py lib/galaxy/datatypes/tabular.py lib/galaxy/jobs/__init__.py diffs (269 lines): diff -r 58ea8585bd88 -r aa1088e4c6c6 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Thu Sep 25 10:19:56 2008 -0400 +++ b/lib/galaxy/datatypes/data.py Thu Sep 25 15:03:05 2008 -0400 @@ -81,7 +81,7 @@ # flag the object as modified for SQLAlchemy. if copy_from: dataset.metadata = copy_from.metadata - def set_meta( self, dataset, **kwd ): + def set_meta( self, dataset, overwrite = True, **kwd ): """Unimplemented method, allows guessing of metadata from contents of file""" return True def set_readonly_meta( self, dataset ): diff -r 58ea8585bd88 -r aa1088e4c6c6 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Thu Sep 25 10:19:56 2008 -0400 +++ b/lib/galaxy/datatypes/interval.py Thu Sep 25 15:03:05 2008 -0400 @@ -64,8 +64,8 @@ else: dataset.blurb = "%s regions" % util.commaify( str( line_count ) ) - def set_meta( self, dataset, first_line_is_header=False, **kwd ): - Tabular.set_meta( self, dataset, skip=0 ) + def set_meta( self, dataset, overwrite = True, first_line_is_header = False, **kwd ): + Tabular.set_meta( self, dataset, overwrite = overwrite, skip = 0 ) """Tries to guess from the line the location number of the column for the chromosome, region start-end and strand""" if dataset.has_data(): @@ -80,7 +80,8 @@ for index, col_name in enumerate( elems ): if col_name in valid: meta_name = valid[col_name] - setattr( dataset.metadata, meta_name, index+1 ) + if overwrite or not dataset.metadata.element_is_set( meta_name ): + setattr( dataset.metadata, meta_name, index+1 ) values = alias_spec[ meta_name ] start = values.index( col_name ) for lower in values[ start: ]: @@ -94,26 +95,32 @@ if len( elems ) > 2: for str in data.col1_startswith: if line.lower().startswith( str ): - dataset.metadata.chromCol = 1 + if overwrite or not dataset.metadata.element_is_set( 'chromCol' ): + dataset.metadata.chromCol = 1 try: int( elems[1] ) - dataset.metadata.startCol = 2 + if overwrite or not dataset.metadata.element_is_set( 'startCol' ): + dataset.metadata.startCol = 2 except: pass # Metadata default will be used try: int( elems[2] ) - dataset.metadata.endCol = 3 + if overwrite or not dataset.metadata.element_is_set( 'endCol' ): + dataset.metadata.endCol = 3 except: pass # Metadata default will be used if len( elems ) > 3: try: int( elems[3] ) except: - dataset.metadata.nameCol = 4 + if overwrite or not dataset.metadata.element_is_set( 'nameCol' ): + dataset.metadata.nameCol = 4 if len( elems ) < 6 or elems[5] not in data.valid_strand: - dataset.metadata.strandCol = 0 + if overwrite or not dataset.metadata.element_is_set( 'strandCol' ): + dataset.metadata.strandCol = 0 else: - dataset.metadata.strandCol = 6 + if overwrite or not dataset.metadata.element_is_set( 'strandCol' ): + dataset.metadata.strandCol = 6 metadata_is_set = True break if metadata_is_set: @@ -286,8 +293,9 @@ MetadataElement( name="endCol", default=3, desc="End column", param=metadata.ColumnParameter ) MetadataElement( name="strandCol", desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0 ) MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True, visible=False ) + ###do we need to repeat these? they are the same as should be inherited from interval type - def set_meta( self, dataset, **kwd ): + def set_meta( self, dataset, overwrite = True, **kwd ): """Sets the metadata information for datasets previously determined to be in bed format.""" i = 0 if dataset.has_data(): @@ -300,15 +308,18 @@ for startswith in data.col1_startswith: if line.lower().startswith( startswith ): if len( elems ) > 3: - dataset.metadata.nameCol = 4 + if overwrite or not dataset.metadata.element_is_set( 'nameCol' ): + dataset.metadata.nameCol = 4 if len(elems) < 6: - dataset.metadata.strandCol = 0 + if overwrite or not dataset.metadata.element_is_set( 'strandCol' ): + dataset.metadata.strandCol = 0 else: - dataset.metadata.strandCol = 6 + if overwrite or not dataset.metadata.element_is_set( 'strandCol' ): + dataset.metadata.strandCol = 6 metadata_set = True break if metadata_set: break - Tabular.set_meta( self, dataset, skip=i ) + Tabular.set_meta( self, dataset, overwrite = overwrite, skip = i ) def as_ucsc_display_file( self, dataset, **kwd ): """Returns file contents with only the bed data. If bed 6+, treat as interval.""" @@ -443,7 +454,7 @@ Tabular.__init__(self, **kwd) self.add_display_app ( 'elegans', 'display in GBrowse', 'as_gbrowse_display_file', 'gbrowse_links' ) - def set_meta( self, dataset, **kwd ): + def set_meta( self, dataset, overwrite = True, **kwd ): i = 0 for i, line in enumerate( file ( dataset.file_name ) ): line = line.rstrip('\r\n') @@ -456,7 +467,7 @@ break except: pass - Tabular.set_meta( self, dataset, skip=i ) + Tabular.set_meta( self, dataset, overwrite = overwrite, skip = i ) def make_html_table( self, dataset, skipchars=[] ): """Create HTML table, used for displaying peek""" @@ -589,7 +600,7 @@ """Initialize datatype, by adding GBrowse display app""" Gff.__init__(self, **kwd) - def set_meta( self, dataset, **kwd ): + def set_meta( self, dataset, overwrite = True, **kwd ): i = 0 for i, line in enumerate( file ( dataset.file_name ) ): line = line.rstrip('\r\n') @@ -614,7 +625,7 @@ phase = elems[7] if valid_start and valid_end and start < end and strand in self.valid_gff3_strand and phase in self.valid_gff3_phase: break - Tabular.set_meta( self, dataset, skip=i ) + Tabular.set_meta( self, dataset, overwrite = overwrite, skip = i ) def sniff( self, filename ): """ @@ -692,7 +703,7 @@ def make_html_table( self, dataset ): return Tabular.make_html_table( self, dataset, skipchars=['track', '#'] ) - def set_meta( self, dataset, **kwd ): + def set_meta( self, dataset, overwrite = True, **kwd ): i = 0 for i, line in enumerate( file ( dataset.file_name ) ): line = line.rstrip('\r\n') @@ -705,7 +716,7 @@ for str in data.col1_startswith: if elems[0].lower().startswith(str): break - Tabular.set_meta( self, dataset, skip=i ) + Tabular.set_meta( self, dataset, overwrite = overwrite, skip = i ) def sniff( self, filename ): """ @@ -746,8 +757,8 @@ """Initialize interval datatype, by adding UCSC display app""" Tabular.__init__(self, **kwd) self.add_display_app ( 'ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links' ) - def set_meta( self, dataset, **kwd ): - Tabular.set_meta( self, dataset, skip=1 ) + def set_meta( self, dataset, overwrite = True, **kwd ): + Tabular.set_meta( self, dataset, overwrite = overwrite, skip = 1 ) def display_peek( self, dataset ): """Returns formated html of peek""" return Tabular.make_html_table( self, dataset, skipchars=['track', '#'] ) @@ -858,8 +869,8 @@ Tabular.__init__(self, **kwd) self.add_display_app ('elegans', 'display in GBrowse', 'as_gbrowse_display_file', 'gbrowse_links' ) - def set_meta( self, dataset, **kwd ): - Tabular.set_meta( self, dataset, skip=1 ) + def set_meta( self, dataset, overwrite = True, **kwd ): + Tabular.set_meta( self, dataset, overwrite = overwrite, skip = 1 ) def make_html_table( self, dataset ): return Tabular.make_html_table( self, dataset, skipchars=['track', '#'] ) diff -r 58ea8585bd88 -r aa1088e4c6c6 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py Thu Sep 25 10:19:56 2008 -0400 +++ b/lib/galaxy/datatypes/metadata.py Thu Sep 25 15:03:05 2008 -0400 @@ -185,6 +185,8 @@ self.parent._metadata = value else: self.bunch[name] = value + def element_is_set( self, name ): + return bool( self.bunch.get( name, False ) ) MetadataElement = Statement(MetadataElementSpec) diff -r 58ea8585bd88 -r aa1088e4c6c6 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Thu Sep 25 10:19:56 2008 -0400 +++ b/lib/galaxy/datatypes/registry.py Thu Sep 25 15:03:05 2008 -0400 @@ -190,8 +190,7 @@ # initialization. if data.has_data(): data.init_meta( copy_from=data ) - if isinstance( data.datatype, tabular.Tabular ): - data.set_readonly_meta() + data.set_meta( overwrite = False ) data.set_peek() return data diff -r 58ea8585bd88 -r aa1088e4c6c6 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Thu Sep 25 10:19:56 2008 -0400 +++ b/lib/galaxy/datatypes/sequence.py Thu Sep 25 15:03:05 2008 -0400 @@ -164,7 +164,7 @@ def init_meta( self, dataset, copy_from=None ): Alignment.init_meta( self, dataset, copy_from=copy_from ) - def set_meta( self, dataset, first_line_is_header=False, **kwd ): + def set_meta( self, dataset, overwrite = True, **kwd ): """ Parses and sets species and chromosomes from MAF files. """ @@ -190,6 +190,7 @@ if i > 100000: break except: pass + #these metadata values are not accessable by users, always overwrite dataset.metadata.species = species dataset.metadata.species_chromosomes = species_chromosomes diff -r 58ea8585bd88 -r aa1088e4c6c6 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py Thu Sep 25 10:19:56 2008 -0400 +++ b/lib/galaxy/datatypes/tabular.py Thu Sep 25 15:03:05 2008 -0400 @@ -26,8 +26,8 @@ data.Text.init_meta( self, dataset, copy_from=copy_from ) def set_readonly_meta( self, dataset, skip=1, **kwd ): """Resets the values of readonly metadata elements.""" - Tabular.set_meta( self, dataset, skip=skip ) - def set_meta( self, dataset, skip=1, **kwd ): + Tabular.set_meta( self, dataset, overwrite = True, skip = skip ) + def set_meta( self, dataset, overwrite = True, skip = 1, **kwd ): """ Tries to determine the number of columns as well as those columns that contain numerical values in the dataset. A skip parameter is @@ -35,6 +35,7 @@ their data type classes are responsible to determine how many invalid comment lines should be skipped. """ + #we treat 'overwrite' as always True (we always want to set tabular metadata when called) if dataset.has_data(): column_types = [] diff -r 58ea8585bd88 -r aa1088e4c6c6 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Thu Sep 25 10:19:56 2008 -0400 +++ b/lib/galaxy/jobs/__init__.py Thu Sep 25 15:03:05 2008 -0400 @@ -409,12 +409,7 @@ dataset.blurb = "error" elif dataset.has_data(): # Only set metadata values if they are missing... - if dataset.missing_meta(): - dataset.set_meta() - else: - # ...however, some tools add / remove columns, - # so we have to reset the readonly metadata values - dataset.set_readonly_meta() + dataset.set_meta( overwrite_exisiting = False ) dataset.set_peek() else: dataset.blurb = "empty"

1 0

[hg] galaxy 1532: Fix for interval to bed converter.
by Greg Von Kuster 26 Sep '08

26 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/3b6771227a43 changeset: 1532:3b6771227a43 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Sep 26 09:10:04 2008 -0400 description: Fix for interval to bed converter. 1 file(s) affected in this change: lib/galaxy/datatypes/converters/interval_to_bed_converter.py diffs (11 lines): diff -r aa1088e4c6c6 -r 3b6771227a43 lib/galaxy/datatypes/converters/interval_to_bed_converter.py --- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.py Thu Sep 25 15:03:05 2008 -0400 +++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.py Fri Sep 26 09:10:04 2008 -0400 @@ -38,6 +38,7 @@ skipped_lines = 0 first_skipped_line = 0 out = open( output_name,'w' ) + count = 0 for count, region in enumerate( bx.intervals.io.NiceReaderWrapper( open( input_name, 'r' ), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False ) ): try: if nameCol >= 0:

1 0

[hg] galaxy 1530: Update check_galaxy for new twill.
by Nate Coraor 25 Sep '08

25 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/58ea8585bd88 changeset: 1530:58ea8585bd88 user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Sep 25 10:19:56 2008 -0400 description: Update check_galaxy for new twill. 1 file(s) affected in this change: scripts/check_galaxy.py diffs (21 lines): diff -r ad3f61801a82 -r 58ea8585bd88 scripts/check_galaxy.py --- a/scripts/check_galaxy.py Wed Sep 24 18:20:39 2008 -0400 +++ b/scripts/check_galaxy.py Thu Sep 25 10:19:56 2008 -0400 @@ -190,7 +190,7 @@ tc.fv("1", "password", pw) tc.submit("Login") tc.code(200) - if len(tc.get_browser()._browser.forms()) > 0: + if len(tc.get_browser().get_all_forms()) > 0: # uh ohs, fail p = userParser() p.feed(tc.browser.get_html()) @@ -210,7 +210,7 @@ tc.fv("1", "confirm", pw) tc.submit("Create") tc.code(200) - if len(tc.get_browser()._browser.forms()) > 0: + if len(tc.get_browser().get_all_forms()) > 0: p = userParser() p.feed(tc.browser.get_html()) if p.already_exists:

1 0

[hg] galaxy 1527: Some metadata updates.
by greg＠scofield.bx.psu.edu 24 Sep '08

24 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/b6420d2f247c changeset: 1527:b6420d2f247c user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Sep 24 13:52:01 2008 -0400 description: Some metadata updates. 3 file(s) affected in this change: lib/galaxy/datatypes/metadata.py lib/galaxy/model/__init__.py lib/galaxy/tools/__init__.py diffs (84 lines): diff -r 38e533287df4 -r b6420d2f247c lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py Wed Sep 24 11:14:44 2008 -0400 +++ b/lib/galaxy/datatypes/metadata.py Wed Sep 24 13:52:01 2008 -0400 @@ -155,11 +155,8 @@ else: self.spec = spec #set default metadata values - if not self.parent._metadata: + if self.parent._metadata is None: self.parent._metadata = {} - for name, value in self.spec.items(): - if name not in self.bunch: - self.bunch[name] = value.default def __iter__(self): return self.bunch.__iter__() @@ -177,12 +174,10 @@ def __getattr__(self, name): if name == "bunch": return self.parent._metadata - rval = self.bunch.get( name ) - if rval is None: - rval = self.spec.get( name, None ) - if rval: - rval = rval.no_value - return rval + if name in self.bunch: + return self.bunch[name] + if name in self.spec: + return self.spec[name].default def __setattr__(self, name, value): if name in ["parent","spec"]: self.__dict__[name] = value diff -r 38e533287df4 -r b6420d2f247c lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Wed Sep 24 11:14:44 2008 -0400 +++ b/lib/galaxy/model/__init__.py Wed Sep 24 13:52:01 2008 -0400 @@ -5,7 +5,7 @@ the relationship cardinalities are obvious (e.g. prefer Dataset to Data) """ -import os.path, os, errno +import os.path, os, errno, copy import sha import galaxy.datatypes from galaxy.util.bunch import Bunch @@ -114,7 +114,8 @@ self.extension = extension self.designation = designation self.metadata = metadata or dict() - self.dbkey = dbkey + if dbkey: #dbkey is stored in metadata, only set if non-zero, or else we could clobber one supplied by input 'metadata' + self.dbkey = dbkey self.deleted = deleted self.visible = visible # Relationships @@ -164,7 +165,7 @@ return self._metadata_collection def set_metadata( self, bunch ): # Needs to accept a MetadataCollection, a bunch, or a dict - self._metadata = dict( bunch.items() ) + self._metadata = dict( [ ( key, copy.deepcopy( value ) ) for key, value in bunch.items() ] ) metadata = property( get_metadata, set_metadata ) """ diff -r 38e533287df4 -r b6420d2f247c lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed Sep 24 11:14:44 2008 -0400 +++ b/lib/galaxy/tools/__init__.py Wed Sep 24 13:52:01 2008 -0400 @@ -1185,6 +1185,7 @@ primary_data.info = dataset.info primary_data.state = primary_data.states.OK primary_data.init_meta( copy_from=dataset ) + primary_data.set_meta() primary_data.set_peek() primary_data.set_size() primary_data.flush() @@ -1245,6 +1246,8 @@ def __getattr__( self, name ): rval = self.metadata.get( name, None ) if name in self.metadata.spec: + if rval is None: + rval = self.metadata.spec[name].no_value rval = self.metadata.spec[name].wrap( rval, self.metadata.parent ) return rval def __nonzero__( self ):

1 0

[hg] galaxy 1529: Adding tools to fetch microsatellites and esti...
by greg＠scofield.bx.psu.edu 24 Sep '08

24 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/ad3f61801a82 changeset: 1529:ad3f61801a82 user: guru date: Wed Sep 24 18:20:39 2008 -0400 description: Adding tools to fetch microsatellites and estimate their mutabilities. 9 file(s) affected in this change: test-data/2way.maf test-data/ortho_ms.tab test-data/ortho_ms_mut.tab tool_conf.xml.sample tools/regVariation/getIndelRates_3way.xml tools/regVariation/microsats_alignment_level.py tools/regVariation/microsats_alignment_level.xml tools/regVariation/microsats_mutability.py tools/regVariation/microsats_mutability.xml diffs (1641 lines): diff -r 447c74d98fe5 -r ad3f61801a82 test-data/2way.maf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2way.maf Wed Sep 24 18:20:39 2008 -0400 @@ -0,0 +1,401 @@ +##maf version=1 +a score=51988 +s hg18.chr1 464 785 + 247249719 ccctcgcggtaccctcagccggcccgcccgcccgggtctgacctgaggagaactgtgctccgccttcagagtaccaccgaaatctgtgcagaggacaacgcagctccgccctcgcggtgctctccgggtctgtgctgaggagaacgcaactccgccggcgcaggcgcagagaggcgcgccgcgccggcgcaggcgcagacacatgctagcgcgtcggggtggaggcgtggcgcaggcgcagagaggcgcgccgcgccggcgcaggcgcagagacacatgctaccgcgtccaggggtggaggcgtggcgcaggcgcagagaggcgcaccgcgccggcgcaggcgcagagacacatgctagcgcgtccaggggtggaggcgtggcgcaggcgcagagacgcaagcctacgggcgggggttgggggggcgtgtgttgcaggagcaaagtcgcacggcgccgggctggggcggggggagggtggcgccgtgcacgcgcagaaactcacgtcacggtggcgcggcgcagagacgggtagaacctcagtaatccgaaaagccgggatcgaccgccccttgcttgcagccgggcactacaggacccgcttgctcacggtgctgtgccagggcgccccctgctggcgactagggcaactgcagggctctcttgcttagagtggtggccagcgccccctgctggcgccggggcactgcagggccctcttgcttactgtatagtggtggcacgccgcctgctggcagctagggacattgcagggtcctcttgctc +s panTro2.chr15 13361 700 - 100063422 ccctcgcagtaccctcagcccgcccgcccgcccgggtctgacctgaggagaactctgctccgccttcgcagtaccaccgaaatctgtgcagaggagaactcagctccaccctcgcggtgctctccgggtctgtgctgaggagaacgcaactccgccgtcgtaaacgc----------gccgcgccggcgcacgcgcaga----------------------gaggcg------------------gcgcgccgcgccggcgcacgcgcagagacacatgctagcgcgtctcgggg---------------------gagaggcgcaccgcgccggcgcag------agacacatactagcgcgtcctgggg-ggaggtgcggcgctgtcgccgagac-cacgcctatgggcgggggttgcgggg-cgcgtggtgcaggagcaaagtcgcacggagcctgtctgggg-----gcaggtgggctccgtgcaggcgcagaaacgcacgtcgcggcggcgcggcgcagagacgggtggaacctcagtaatcagaaaagccgggctggaccgccccctgcttgcagccgggcactacaggacccgcttgctcacggtgctctgccagtgcgccccctgctggcaactagggcaactgcagggctctcttgcttagagtggtggccagcgggggctgctggctccggggcactgcagggccctcttgcttactgtatagtggtggcacgccgcctgctggcagctagggacattgcagggtcctcttgctc + +a score=5767 +s hg18.chr1 1249 62 + 247249719 aaggtgtagtggcagcacgcccacctgctggcagctggggacactgccgggccctcttgctC +s panTro2.chr9_random 4665776 62 + 7733331 aaagtgtagtggcagcacgcccgcctgctggcagctggggacactgccgggccctcttgctc + +a score=108196 +s hg18.chr1 1311 1227 + 247249719 CAACAGTACTGGCGG-ATTATAGGGAAACACCCGGAGcatatgctgtttggtctcagtagactcctaaatatgggattcctgggtttaaaagtaaaaaataaatatgtttaatttgtgaactgattaccatcagaattgtactgttctgtatcccaccagcaatgtctaggaatgcctgtttctccacaaagtgtttacttttggatttttgccagtctaacaggtgaAGccctggagattcttattagtgatttgggctggggcctggccatgtgtatttttttaaatttccactgatgattttgctgcatggccggtgttgagaatgactgCGCAAATTTGCCGGATTTCCTTTGCTGTTCCTGCATGTAGTTTAAACGAGATTGCCAGCACCGGGTATCATTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAGGCATAGGGGAAAGATTGGAGGAAAGAT------------GAGTGAGAGCATCAACTTCTCTCACAACCTAGGCCAGTAAGTAGTGCTTGTGCTCATCTCCTTGGCTGTGATACGTGGCCGGCCCTCGCTCCAGCAGCTGGACCCCTACCTGCCGTCTGCTGCCATCGGAGCCCAAAGCCGGGCTGTGACTGCTCAGACCAGCCGGCTGGAGGGAGGGGCTCAGCAGGTCTGGC TTTGGCCCTGGGAGAGCAGGTGGAAGATCAGGCAGGCCATCGCTGCCACAGAACCCAGTGGATTGGCCTAGGTGGGATCTCTGAGCTCAACAAGCCCTCTCTGGGTGGTAGGTGCAGAGACGGGAGGGGCAGAGCCGCAGGCACAGCCAAGAGGGCTGAAGAAATGGTAGAACGGAGCAGCTGGTGATGTGTGGGCCCACCGGCCCCAGGCTCCTGTCTCCCCCCAGGTGTGTGGTGATGCCAGGCATGCCCTTCCCCAGCATCAGGTCTCCAGAGCTGCAGAAGACGAC +s panTro2.chr15 14061 1233 - 100063422 caacagtagtggcggGATTATGGGGAAACACCCGGAGCATATGCTGTTTGGTCTCAgtaggctcctaaatatgggattcctggatttaaaagtataaaataaatatgtttaatttgttaactgattaccatcagaattgtactgttctgtaccccaccagcaatgtctaggaatgcctgtttctccacaaagtgtttacttttggatttttgccagtctaacaggtgaAGccctggagattcttattagtgatttgggctggggcctggccatgtgtatttttttaaatttccactgatgattttgctgcatggccggtgttgagaatgactgTGCAAATTTGCCGGATTTCCTTTGCTGTTCCTGCATGTCGTTTAAACGACATTGCCAGCACCGGGTATCGTTCACCATTTTTCTTTTT-----CTTGCCGTCAGCCTTTTCTTTGACCTCTTCTCTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGGGAGGTCACAGGGTCTTGATGCTGTGGTCTTGGTCTGCAGGTGTCTGACTTTCAGCAACTGCTGGCCTGTGCCAGGGTGGAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATATTCTGGCCCCTGTTGTCTGCATGTAACCTAATACCACAACCAGGCATGGGGGAAAGACTGGAGGAAAGATTGGAGAAAAGATGAGTGAGAGGATCAACTTCTCTGACAGCCTAGGCCAGTAAGTAGTGCTTCTGCTCATCTCCTTGGCTGTGATACGTGGCCGGCCCTCGCTCCAGCAGCTGGACCCCTACCTGCCGTCTGCTGCCATCGGAGCCCAAATCCGGGCTGTGACTGCTCAGACCAGCCGGCTGGAGGGAGGGGCTCAGCAGCTCTGGC TTTGGCCTTGGGATAGCAGGTGGAAGATCAGGCAGGCCATCGCTGCCGCAGAACCCAGTGAATTGGCCTAGGTGGGATCTCTGAGCTGAACAAGCCCTCTCCGGGTGGTAGGTGCAGAGAGGGGAGGGGCAGAGCCGCAGGCACAGCCAAGAGGGCTGAGGAAATGGTAGAACGGAGCAGCTGGTGATGTCTGGGCCCACCGGCCCCAGGCTCCTGTCTCCCCCCAG--GTGTGGTGATGCCAGGCATGCCCTTCCTCAGCATCAGGTCTCCAGAGCTGCAGAAGACGAC + +a score=179761 +s hg18.chr1 2538 2022 + 247249719 GGCCGACTTGGATCACACTCTTGTGAGTGTCCCCAGTGTTGCAGAGGTG-AGAGGAGAGTAG-ACAGTGAGTGGGAGTGG-CGTCGCCCCTAGGGCTCTACGGGGCCGGCGTCTCCTGTCTCCTGGAGAGGCTTCGATGCCCCTCCACACCCTCTTGATCTTCCCTGTGATGTCATCTGGAGCCCTGCTGCTTGCGGTGGCCTATAAAGCCTCCTAGTCTGGCTCCAAGGCCTGGCAGAGTCTTTCCCAGGGAAAGCTACAAGCAGCAAACAGTCTGCATGGGTCATCCCCTTCACTCCCAGCTCAGAGCCCAGGCCAGGGGCCCCCAAGAAAGGCTCTGGTGGAGAACCTGTGCATGAAGGCTGTCAACCAGTCCATAGGCAAGCCTGGCTGCCTCCAGCTGGGTCGACAGACAGGGGCTGGAGAAGGGGAGAAGAGGAAAGTGAGGTTGCCTGCCCTGTCTCCTACCTGAGGCTGAGGAAGGAGAAGGGGATGCACTGTTGGGGAGGCAGCTGTAACTCAAAGCCTTAGCCTCTGTTCCCACGAAGGCAGGGCCATCAGGCACCAAAGGGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACACGCTGTTGGCCTGGATCTGAGCCCTGGTGGAGGTCAAAGCCACCTTTGGTTCTGCCATTGCTGCTGTGTGGAAGTTCACTCCTGCCTTTTCCTTTCCCTAGAGCCTCCACCACCCCGAGATCACATTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGGCGCTGTGCCCTTCCTTTGCTCTGCCCGCTGGAGACGGTGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTGTGGAGTCCAGAGTGTTGCCAGGAC CCAGGCACAGGCATTAGTGCCCGTTGGAGAAAACAGGGGAATCCCGAAGAAATGGTGGGTCCTGGCCATCCGTGAGATCTTCCCAGGGCAGCTCCCCTCTGTGGAATCCAATCTGTCTTCCATCCTGCGTGGCCGAGGGCCAGGCTTCTCACTGGGCCTCTGCAGGAGGCTGCCATT--TGTCCTGCCCACCTTCTTAGAAGCGAGACGGAGCAGACCCATCTGCTACTGCCCTTTCTATAATAACTAAAGTTAGCTGCCCTGGACTATTCACCCCCTAGTCTCAATTTAAGAAGATCCCCATGGCCACAGGGCCCCTGCCTGGGGGCTTGTCACCTCCCCCACCTTCTTCCTGAGTCATTCCTGCAGCCTTGCTCCCTAACCTGCCCCACAGCCTTGCCTGGATTTCTATCTCCCTGGCTTGGTGCCAGTTCCTCCAAGTCGATGGCACCTCCCTCCCTCTCAACCACTTGAGCAAACTCCAAGACATCTTCTACCCCAACACCAGCAATTGTGCCAAGGGCCATTAGGCTCTCAGCATGACTATTTTTAGAGACCCCGTGTCTGTCACTGAAACCTTTTTTGTGGGAGACTATTCCTCCCATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTCTCCTCCCTCTCATCCCAGAGAAACAGGTCAGCTGGGAGCTTCTGCCCCCACTGCCTAGGGACCAACAGGGGCAGGAGGCAGTCACTGACCCCGAGACGTTTGCATCCTGCACAGCTAGAGATCCTTTATTAAAAGCACACTGTTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTT-----AAGAACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCAA GGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACGGCCCAAGTCTGGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCT +s panTro2.chr15 15769 2032 - 100063422 GGCCAACTTGGATCACACTCTAATGAGTGTCCCCAGTATTGCAGTGGTGCAGAGGAGAGTAGTACGGTGAGTGGGAGTGGTCGTCTCCCCTAGGGATGTGCTGGGCGGGGGTCTCCTGTCTCGTGGGGAGGCTTGGATGCCCCTCCACACCCTCTTGATGTTCCCTGTGATGTCATCTGGAGCCCTGGTGCTTGCGGTGGCCTATGAAGCTTCCCGGTCTGGCTCCAAGGCCTGGCAGAGTCTTTCCCAGGGAAAGCTACAAGCAGGAAACAGTCCGCATGGGTCATCCCCTTCACTCCCAGCTCTGAGCCCAGGCCAGGGGCCCCCAAGAAAGGCTCTGGTGGAGAACCTGTGCATGAAGGCTGTCAACCAGTCCATAGGCAAGCCTGGCTGCCTCCAGCTGGGTGGACAGACAGGCGCTGGAGAAGGGGAGAAGAGGAAAGGGGGGCTGCCTGCCCTGTCTCCCACCTGAGGCTGAGGAAGGAGAGGGGGATGCACTGTTGGGGAGGCAGCTGTAACTCAAAGCCCTAGCCTCTGTTCCCACGAAGGCAGGGCCATCAGGCACCAAAGGGATTCTGCCAGCATAATGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACAAGCTGTTGGCCTGGATCTGAGCCCTCGTGGAGCTCAAAGCCACCTTTGGTTCTGCCATTGCTGCTGTGTGGAAGTTCAGTCCTGCCTTTTCCTTTCCCGAGAGGCTCCACCACCCCGAGATCGCACTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGGCGCTGCGCCCTTCCTTTGCTCTGCCCGCTGGAGACGGTGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTGTGGAGTCCAGAGTGTTGCCAGGAC CCAGGCACAGGCATTAGTGCCCGTTGGAGAAAACAGGGGAATCCCAAAGAAATGGTGAGTCCTGGCCATCCGTGAGATCTTCCCAGGGCAGCTCCCCTCTGTGGAATCCAATCTGTCTTCCATCCTGCGTGGCAGAGGGCCAGGCTTCTCACTGGGCCTCTGCAGGAGGCTGCCATTTCTGTCCTGCCCACCTTCTAAGAAGCGAGACGGAGGACACCCATCTGCTTCTGCCCTTTCCATAATAACTAAAGTTAGCTGCCCTGGACTATTCACCCCCTAGTCTCTATTTAAAAAGATCCCCATGGCCACAGGGCCCCTGCCTGGGGGCTTGTCACCTCCCCCACCTTCTTCCTGAGTCACTTCTGCAGCCTTGCTCCCTAACCTGCCCCACAGCCTTGCCTGGATTTCTATCTCCCTGGCTTGGTGCCAGTTCCTCCAAGTCGATGGCACCTCCCTCCCTCTCAACTACTTGAGCAAACTTGAAGACATCTTCAACCCCAACACCAGCAATTGTGCCAAGGGCCATTAGGCTCTCAGCATGACTATTTTTAGAGACCCCGTGTCTGTCACTGAAACCTTTTTCGTGGGAGACTATTCCTCCCATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTCTCCTCCCTCTCATCCCAGAGAAACAGGTCAGCTGGGAGCTTCTGCCCCCACTGCCTAGGCACCAACAGGGGCAGGAGGCAGTCACTGACCCCGAGACGTTTGCATCCTGCACAGCTAGAGGTCCTTAATTAAAAGCACACTGTTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCATTTTCTCTGGAAGCCTCTTTAGAGAAGAACACACTGGTGCAGGCTGGCTGGAGCTGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCAG GGAAGCAGGTCTCAGCAGCTTGTCCTGGCTGTGTCCGTGTCAGAGCAACGGCCCAAGTCTGGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCT + +a score=433563 +s hg18.chr1 4560 4714 + 247249719 ACGATTCCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTGAGTGAGGGTGGTTGGTGGGAAACCCTGGTTCCCCCAGCCCCCGGAGACTTAAATACAGGAAGAAAAAGGCAGGACAGAATTACAAGGTGCTGGCCCAGGGCGGGCAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAAAGCCACAGACTGGGGTGAAGAGTTCAGTCACATGCGACCGGTGACTCCCTGTCCCCACCCCCATGACACTCCCCAGCCCTCCAAGGCCACTGTGTTTCCCAGTTAGCTCAGAGCCTCAGTCGATCCCTGACCCAGCACCGGGCACTGATGAGACAGCGGCTGTTTGAGGAGCCACCTCCCAGCCACCTCGGGGCCAGGGCCAGGGTGTGCAGCAccactgtacaatggggaaactggcccagagaggtgaggcagcttgcctggggtcacagagcaaggcaaaagcagcgctgggtacaagctcaAAACCATAGTGCCCAGGGCACTGCCGCTGCAGGCGCAGGCATCGCATCACA-----CCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCATTGCCTTGGACCGCTCTTGGCAGTCGAAGAAGATTCTCCTGTCA--GTTTGAGCTGGGTGAGCTTAGAGAGGAAAGCTCCACTATGGCTCCCAAACCAGGAAGGAGCCATAGCCCAGGCAGGAGGGCTGAGGACCTCTGGT GGCGGCCCAGGGCTTCCAGCATGTGCCCTAGGGGAAGCAGGGGCCAGCTGGCAAGAGCAGGGGGTGGGCAGAAAGCACCCGGTGGACTCAGGGCTGGAGGGGAGGAGGCGATCTTGCCCAAGGCCCTCCGACTGCAAGCTCCAGGGCCCGCTCACCTTGCTCCTGCTCCTTCTGCTGCTGCTTCTCCAGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTTGGCGGATGGACTCTAGCAGAGTGGCC-AGCCACCGGAGGGGTCAACCACTTCCCTGGGAGCTCCCTGGACTGGAGCCGGGAGGTGGGGAACAGGGCAAGGAGGAAAGGCTGCTCAGGCAGGGCTGGGGAAGCTTACTGTGTCCAAGAGCCTGCTGGGAGGGAAGTCACCTCCCCTCAAACGAGGAGCCCTGCGCTGGGGAGGCCGGACCTTTGGAGACTGTGTGTGGGGGCCTGGGCACTGACTTCTGCAACCACCTGAGCGCGGGCATCCTGTGTGCAGATACTCCCTGCTTCCTCTCTAGCCCCCACCCTGCAGAGCTGGACCCCTGAGCTAGCCATGCTCTGACAGTCTCAGTTGCACACACGAGCCAGCAGAGGGGTTTTGTGCCACTTCTGGATGCTAGGGTTACACTGGGAGACACAGCAGTGAAGCTGAAATGAAAAATGTGTTGCTGTAGTTT-----GTTATTAGACCCCTTCTTTCCATTGGTTTAATTAGGAATGGGGAACCCAGAGCCTCACTTGTTCAGGCTCCCTCTGCCCTAGAAGTGAGAAGTCCAGAGCTCTACAGTTTGAAAACCACTATTTTATGAACCAAGTAGAACAAGATATTTGAAATGGAAACTATTCAAAAAATTGAGAATTTCTGACCACTTAACAAACCCACAGAAAATCCACCCGAGTGCACTGAGCACGCCAGAAATCAGGTGGCCTCAAAGAGCTGCTCCCACCTGAAGGAGACGCGCTG CTGCTGCTGTCGTCCTGCCTGGCGCCTTGGCCTACAGGGGCCGCGGTTGAGGGTGGGAGTGGGGGTGCACTGGCCAGCACCTCAGGAGCtgggggtggtggtgggggcggtgggggtggtg---------ttagtACCCCATCTTGTAGGTCTGAAACACAAAGTGTGGGGTGTCTAGGGAAGAAGGTGTGTGACCAGGGAGGTCCCCGGCCCAGCTCCCATCCCAGAACCCAGCTCACCTACCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGGCAGTTCTGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCAATGTACATGAGGTCGTTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTGGCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAAGATTAGGCAGGGACATGTGAGAGGTGACAGGGACCTGCAGGGGCAGCCAACAAGACCTTGTGTGCACCTCCCATGGGTGGAATAAGGGGCCCAACAGCCTTGACTGGAGAGGAGCTCTGGCAAGGCCCTGGGCCACTGCACCTGTCTCCACCTCTGTCCCACCCCTCCCACCTGCTGTTCCAGCTGCTCTCTCTTGCTGATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTGCCCCCAGCATCACATGGGTCTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTCTACCTACAGAGGCGACATGGGGGTCAGGCAAGCTGACACCCGCTGTCCTGAGCCCATGTTCCTCTCCCACATCATCAGGGGCACAGCGTGCACTGTGGGGTCCCAGGCCTCCCGAGCCGAGCCACCCGTCACCCCCTGGCTCCTGGCCTATGTGCTGTACCTGTGTCTGATGCCCTGGGTCCCCACTAAGCCAGGCCGGGCCTCCCGCCCACACCCCTCGGCCCTGCCCTCTGGCCAT ACAGGTTCTCGGTGGTGTTGAAGAGCAGCAAGGAGCTGACAGAGCTGATGTTGCTGGGAAGACCCCCAAGTCCCTCTTCTGCATCGTCCTCGGGCTCCGGCTTGGTGCTCACGCACACAGGAAAGTCCTTCAGCTTCTCCTGAGAGGGCCAGGATGGCCAAGGGATGGTGAATATTTGGTGCTGGGCCTAATCAGCTGCCATCCCATCCCAGTCAGCCTCCTCTGGGGGACAGAACCCTATGGTGGCCCCGGCTCCTCCCCAGTATCCAGTCCTCCTGGTGTGTGACAGGC-----TATATGCGCGGCCAGCAGACCTGCAGGGCCCGCTCGTCCAGGGGGCGGTGCTTGCTCTGGATCCTGTGGCGGGGGCGTCTCTGCAGGCCAGGGTCCTGGGCGCCCGTGAAGATGGAGCCATATTCCTGCAGGCGCCCTGGAGCAGGGTACTTGGCACTGGAGAACACCTGTGGACACAGGGACAAGTCTGAGGGGGCCCCAAGAGGCTCAGAGGGCTAGGATTGCTTGGCAGGAGAGGGTGGAGTTGGAAGCCTGGGCGAGAAGAAAGCTCAAGGTACAGGTGGGCAGCAGGGCAGAGACTGGGCAGCCTCAGAGGCACGGGGAAATGGAGGGACTGCCCAGTAGCCTCAGGACACAGGGGTATGGGGACTACCTTGATGGCCTTCTTGCTGCCCTTGATCTTCTCAATCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGCCTGCACCTGGCTCCGGCTCTGCTCTACCTGCTGGGAGATCCTGCCATGGAGAAGATCACAGAGGCTGGGCTGCTCCCCACCCTCTGCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTACTTGCCAGGGCCGATCTTGGTGCCATCCAGGGGGCCTCTACAAGGATAATCTGACCTGCAGGGTCGAGGAGTTGACGGTGCTGAGTTC CCTGCACTCTCAGTAGGGACAGGCCCTATGCTGCCACCTGTACATGCTATCTGAAGGACAGCCTCCAGGGCACACAGAGGATGGTATTTACACATGCACACATGGCTACTGATGGGGCAAGCACTTCACAACCCCTCATGATCACGTGCAGCAGACAATGTGGCCTCTGCAGAGGGGGAACGGAGACCGGAGGCTGAGACTGGCAAGGCTGGACCTGAGTGTCGTCACCTAAATTCAGACGGGGAACTGCCCCTGCACATACTGAACGGCTCACTGAGCAAACCCCGAGTCCCGACCACCGCCTCAGTGTGGTCTAGCTcctcacctgcttccatcctccctggtgcggggtgggcccagtgatatcagctgcctgctgttccccagatgtgccaagtgcattcttgtgtgcttgcatctcatggaacgccatttccccagacatccctgtggctggctcctGATGCCCGAGGCCCAAGTGTCTGATGCTTTAAGGCACATCACCCCACTCATGCTTTTCCATGTTCTTTGGCCGCAGCAAGGCCGCTCTCACTGCAAAGTTAACTCTGATGCGTGTGTAACACAACATCCTCCTCCCAGTCGCCCCTGTAGCTCCCCTACCTCCAAGAGCCCAGCCCTTGCCCACAGGGCCACACTCCACGTGCAGAGCAGCCTCAGCACTCACCGGGCACGAGCGAGCCTGTGTGGTGCGCAGGGATGAGAAGGCAGAGGCGCGACTGGGGTTCATGAGGAAGGGCAGGAGGAGGGTGTGGGATGGTGGAGGGGTTTGAGAAGGCAGAGGCGCGACTGGGGTTCATGAGGAA +s panTro2.chr15 18045 4735 - 100063422 AGGATTCCCAGTCGTCCTCATCCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTGAGTGAGGGTGGTTGGTGGGAAACCCTGCTTCCCCCAGCCCCCAGAGACTTAAATACAGGAAGAAAAAGGCAGGACACAATTACAATGTGCCGGCCCAGGGCGGGCAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTCCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAAAGCCACAGACTGGGGTGAAGAGTTCAGTCACATGTGACCGGTGGCTCCCTGTCCCCAGCCCCATGACACTCCCCAGCCCTCCAAGGCCACTGTGTTTCCCAGTTAGCTCAGAGCCTCAGTCGATCCCTGACCCAGCACCGGGCGCTGATGAGAAAGCGGCTGTTTGAGGAGCCACCTCCCAGCCACCTTGGGGACAGGGCCAGGGTGTGCAGCACcactgtacaatggggaaactggcccagagaggtgaggcagcttgcctggggtcacagagcaaggcaaaagcagcgctgTGTACAAGCTCAAAACCATAGTGCCCAGGGCATTGCCACTGCAGGCGCAGGCATCGCATCACATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCAAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCATTGCCTTGGACCGCTCTTGGCAGTCGAAGAAGATTCTCCTGTCACAGTTTGAGCTGGGTGAGCTTAGAGAGGAAAGCTCCACTATGGCTCCCAAACCAGGAAGGAGCCATAGCCCAGGCAGGAGGGCTGAGGACCTCTGGT GGCGGCCCAGGGATTCCAGCATGTGCCCTAGGAGAAGCAGGGGCCAGCTGCCAAGAGCAGGGGGTGGGCAGAAAGCACCCAGTGGACTCAGGGCTGGAGGGAAGGAGGCGATCTTGCCCAAGGCCCTCCGACCGCAGGCTCCAGGGCCCGCtcaccttgctcctgctccttctgcttcttcttctccagctttcgctccttcACGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTTGGCGGATGGATTCTAGCAGAGTGGCCCGGCCACCGGAGGGGTCGACCACTTCCCTGGGAGCTCCCTGGACTGGAGCCGGGAGGTGGGGAACAGGGCAAGGAGGAAAGGCTGCTCAGGCAGGGCTGGGGAAGCTTATTGTATCCAAGAGCCTGCTGGGAGGGAAGTCACCTCCCCTCAAACGAGGAGCCCCGCGCTGGGGAGGCCGGACCTTTGGAGACTGTGTG---GGGCCTGGGCACTGACTTCGGCAACCACCTGAGTGCAGGCATCCTGTGTGCAGATACTCCCTGCTTCCTCTCTAGCCCCCACCCTGCAGAGCTGGACCCCTGAGCTAGCCATGCTCTGACAGTCTCAGTGGCACACATGAGCCAGCAGAGGGGTTTTGTGCCACTTCTGGATGCTAGGGTTAGACTGGGAGATACAACAGTGAAGCTGAGAAGAAAAATGTGTTGCTGTAGTTTAGTTGGTTATTAGACCCCTTCTTTCCATTGGTTTAATTAGGAATGGGGAACCCAGAGCCTCACTTGTTCAGGCTCCCTCTGCCCTAGAAGTGAGAAGTCCAGAGCTCTACAGTTTGAAAACCACTATTTTATGAACCAAGTAGAACAAGATATTTGAAATGGGAACTATTCAAAAAATTGAGAATTTCTGACCACTTAACAAACCCACAGAAAATACACCCGAGTGCACTGAGCACGCCAGAAATGAGGTGGCCTCAAAGAGCTGCTCCCACCTGAAGGAGACGCGCTG CTGCTGCTGTCGTCCTGCCTGGCGCCTTGGCCTACAGGGGCCGCGGTTGAGGGTGGGAGTGGGGGTGCACTGGCCAGCACCTCAGGAGCtgggggaggtggtgggggcggtgggggtggtgggggtgctgttagtACCCCATCTTGTAGGTCTGAAACACAAAGTGTGGGGTGTCTAGGGAAGAAGGTGTGTGAGCAGGGAGGTCCCCAGCCCAGCTCCCATCCCAGAGCCCAGCTCACCTGCCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGGCAGTTCTGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCACTGTACATGAGGTCGTTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTGGCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAAGATTAGGCAGGGACATGTGAGAGGTGACAGGGACCTGCAGGGGCAGCCAACAAGACCTTGTGTGCACCTCCCATGGGTGGAATAAGGGGCTCAACAGCCTGGACTGGAGAGGAGCTCTGGCAAGGCCCTGGGCCACTGCACCTGTCTCCACCTCTGTCCCGCCCCTCCCACCTGCTGTTCCAGCTGCTCTCTCTTGCTGATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTGCCCCCAGCATCACATGGGTCTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTGTACCTACAGGGGCGACATGGGGGTCAGGCAAGCTGACACCTGCTGTCCTGAGCCCATGTTCCTCTCCCACATCATCAGGGGCACAGTGTGCACCGTGGGGTCCCAGGCCTCCCGAGCCGAGCCACCCGTCACCCCCTGGCTCCTGGCCTATGTGCTGTACCTGTGTCTGATGCCCTGGGTCCCCACTAAGCCAGGCCGGGCCTCCCGCCCACACCCCTCGGCCCTGCCTTCTGGCCAT ACAGGTTCTCGGTGGTGTTGAAGAGCAGCAAGGAGCTGACAGAGCTGATGTTGCTGGGAAGACCCCCAAGTCCCTCTTCTGCATCGTCCTCGGGCCCCGGCTTGGTGCTCACGCACACAGGAAAGTACTTCAGCTTCTCCTGGGAGGGCCAGAATGGCCAAGGGATGGTGAATATTTAGTGCCGGGCCTAATCAGCTGCCACCCCATCCCGGTCAGCCTCCTCTGGGGGACAGAACCCT-TGGTGGCCCCGGCTCCTCCCCAGTATCCAGTCCTCCTGGTGTGTGACAGGCTAAGTTATGTGCGCGGCCAGCAGACCTGCAGGGCCCGCTCATCCAGGGGGCGGTGCTTGCTCTGGATCCTGTGGCGGGGGCGTCTCTGCAGGCCAGGGTCCTGGGCGCCCGTGAAGATGGAGCCATATTCCTGCAGGCGCTCTGGAGCAGGGTACTTGGCACTGGAGAACACCTGTGGACACAGGGACAAGTCTGAGGGGGCCCCAAGAGGCTCAGAGGGCTAGGATTGCTTGGCAGGAGAGGGTGGAGTTGGGAGCCTGGGCGAGAAGAAAGCCCAAGGTAGAGGTGGGCAGCAGGGCAGAGACTGGGCAGCCTCAGAGGCACGGGGAAATGGAGGGACTGCCCAGTAGCCTCAGGACACAGGGGCATGGGGACTACCTTGATGGCCTTCTTGCTGCCCTTGATCTTCTCAATCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGCCTGCACCTGGCTCCGGCTCTGCTCTACCCGCTGGGAGATCCTGCCATGGAGAAGATCACAGAGGCTGGGCTGCTCCCCACCCCCTGCACACCTCCTGCTCCTAACAGCAGAGCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTTAAGTCAGGGTCACCTGCTTGCCAGGGCTGATCTTGGTGCCATCCAGGGGGCCTCTACAAGGATAATCTGACCTGCAGGGTCGAGGAGTTGATGGTACTGAGTTC CCTGCACTCTCAGTAGGGACAGGCCCTATGCTGCCACCTGTACATGCTATCTGAAGGACAGCCTCCAGGGCACACAGAGGATGGTATTTACACATGCACACATGGCTATTGATGGGGCAAGCATTTCACAACCCCTCATGATCACGTGCAGCAGACAAAGTAGCCTCTGCAGAGGGGGAATGGAGACCGGAGGCTGAGACTGGCAAGGCTGGACCTGAGTGTCATCACCTAAATTCAGACGGGGAACTGCCCCCGCACATAGTGAACGGCTCACTGAGCAAACCCTGAGTCCCAACCACCGCCTCAGTGTGGTCTAGCTcctcacctgcttccatcctccctggtgcggggtgggcccagtgatatcagctgcctgctgttccccagatgtgccaagtgcattcttatgtgcttgcatctcatggaacaccatttccccagacatgcctgtggctggctcctGGTGCCCGAGGCCCAAGTGTCTGATGCTTTAAGGCACATCACCCCACTCATGCTTTTCCATGTTCTTTGGCCGCAGCAAGGCCGCTCTCACTGCAAAGTTAACTCTGATGCGTGTGTA--ACAACATCCTCCTCCCAGTCGCCCCTGTAGCTCCCCTACCTCCAAGAGCCCAGCCCTTGCCCACAGGGCCACACTCCACGTGCAGAGCAGCCTCAGCACTCACCGGGCACGAGCGAGCCTGTGTGGTGCGCAGGGATGAGAAGGCAGAGGCGCGACTGGGGTTCGTGAGGAAAGGCAGGAGGAGGGTGTGGGATGGTGGAGGGGTTTGAGAAGGCAGAGGCGCGACTGGGGTTCATGAGGAA + +a score=94959 +s hg18.chr1 9274 1037 + 247249719 AGGGAGGGGGAGGATGTGGGATGGTGGAGGGGCTGCAGACTCTGGGCTAGGGAAAGCTGGGATGTCTCTAAAGGTTGGAATGAATGGCCTAGAATCCGACCCAATAAGCCAAAGCCACTTCCACCAACGTTAGAAGGCCTTGGCCCCCAGAGAGCCAATTTCACAATCCAGAAGTCCCCGTGCCCTAAAGGGTCTGCCCTGATTACTCCTGGCTCCTTGTGTGCAGGGGGCTCAGGCATGGCAGGGCTGGGAGTACCAGCAGGCACTCAAGCGGCTTAAGTGTTCCATGACAGACTGGTATGAAGGTGGCCACAATTCAGAAAGAAAAAAGAAGAGCACCATCTCCTTCCAGTGAGGAAGCGGGACCACCACCCAGCGTGTGCTCCATCTTTTCTGGCTGGGGAGAGGCCTTCATCTGCTGTAAAGGGTCCTCCAGCACAAGCTGTCTTAATTGACCCTAGTTCCCAGGGCAGCCTCGTTCTGCCTTGGGTGCTGACACGACCTTCGGTAGGTGCATAAGCTCTGCATTCGAGGTCcacaggggcagtgggagggaactgagactggggagggacaaaggctgctctgtcctggtgctcccacaaagg--agaagggctgatcactcaaagttgcgaacaccaagctcaacaatgagccctggaaaatttctggaatggattattaaacagagagtctgtaagcacttagaaaaggccgcggtgagtcccaggggccagcactgctcgaaatgtacagcatttctctttgtaacaggattattagcctgctgtgcccggggaaaacatgcagcacagtgcatctcgagtcagcaggattttgacggcttctaacaaaatcttgtagacaagatggagctatgggggttggaggagagaacatataggaaaaatcagagccaaatgaaccacagccccaaagggcacagtt gaacaatggactgattccagccttgcacggagggatctggcagagtccatccagttcattcaacacctggttagaaaactggggccagc +s panTro2.chr15 22920 1038 - 100063422 AGGCAGGAGGAGGGTGTGGGATGGTGGAGGGGCTGCAGACTCTGGGCTTGGGAAAGCTGGGGTGTCTCTAAAGGTTGGAATGAATGGCCTAGAATCGGACCCAATAAGCCAAAGCCACTTCCACCAACGTTAGAAGGCCTTGGCCCCCAGAGAGCCAATTTCACAATCCAGGAGTCCCCGTGCCCTAATGGGTCTGCCCTGATTACTCCTGGCTCCTTGTGTGCAGGGGGCTCAGGCATGGCAGGGCTGGGAGTACCAGCAGGCACTCAAGCGGCTTAAGTGTTCCATGACAGACTGGTATGAAGGTGGCCACAATTCAGAAAGAAAAAAGAAGAGCACCATCTCCTTCCAGTGAGGAAGCGGGGCCACCACCCAGCGTGTGCTCCATCTTTTCTGGCTGGGGAGAGGCCTTCATCTGCTGTAAAGGGTCCTCCAGCACAAGCTGTTTTAATTTACCCTAGTTCCCAAGGCAGCCTCATTCTGCCTTGGGTGCTGACACGACCTTCGGTAGGTGCATAAGCTCTGCATTCGAGGTCcacaggggcagtgggagggaactgagactggggagggacaaaggctgctctgtcctggtgctcccacaaaggacagaagggctgatcactcaaagttgcgaacaccaagctcaacaatgagccctggaaaatttctggaatggattattacacagagagtctgtaagcacttagaaaaggccgcggtgagtcccaggggccagcactgctcgaagtgtacagcatttctctttgtaacaggattagtagcttgctgtgcccggggagaacatgcagcacagcgcatctcgagtcagcaggatttcgacggcttctaacaaaatcctgtagacaagatggagctatgggggttggaggagagaacatatagg-aaaatcagagccaaatgaaccacagccccaaagggcacagtt gaacaatggactgattccagccttgcacggagggatctggcagagtccatccggttcATTCAACACCTGGTTAGAAAACTGGGGCCAGC + +a score=34201 +s hg18.chr1 10311 370 + 247249719 acacaggggaagggtaagctggtttcatgatcgaatcaaggctcagacaatttttaaaggccagagggtagactgcaatcaccaagatgaaatttacaaggaacaaatgtgaagcccaacatttaggttttaaaaatcaagcgtataaatacagaaggtggagggaacttgctttagacacagttcaggtgaagaaagacctggaaacttctgttaactataagctcagtaggggctaaaagcatgttaatcggcataaaaaggcaatgagatcttaggGCACACAGCTCCCCGCCCCTCTTCTGCCCTTCATCCTTCTTTCAATCAGCAGGGACCGTGCACTCTCTTGGAGCCACCACAGAAAACAGAG +s panTro2.chr9_random 4675777 370 + 7733331 acacaggggaagggtaagttggtttcatgatcgaatcaaggctcagacaattttcaaaggccagagggtagactgcaatcacccagatgaaatttacaaggaacaaatgtgaagcccaacatttaggttttaaaaatcaagcgtataaatatagaaggtggagggaacttgttttagacacagttcaggtgaagaaagacctggaaacttctgttaactataagctcagtaggggctaaaagcatgttaatcggcataaaaaggcaatgagatcttaggGCACACAGCTCCCCGCCCCTCTTCTGCCCTTCATCCTTCTTTCAATCAGCAGGGACGGTGCACTCTCTTGGAGCCACCACAGAAAACAGAG + +a score=11150 +s hg18.chr1 10770 199 + 247249719 CAGAGCAGGAGGAGAGAGCACAGCCTGCAATGCTAATTTGCCAGGAGCTCACCTGCCTGCGTCACTGGGCACAGACGCCAGTGAGGCCAGAGGCCGGGCTGTGCTGGGGCCTGAG-CCGGGTGGTGGGGAG-------AGAGTCTCTCCCCTGCCC--CTGTCTCTTCCGTGCAGGAGG---------------AGCATGTTTAAGGGGACGGGTTCAAAGCTG +s panTro2.chr12 77693524 219 - 135371336 CAGAGCAGGAGGAGAGAGCATGGCCAGGAATGCTAATTTGCCAGGAGCTCACCTGCCTGCGTCACAAGGCACAGGTGCCAATGAGGCCAGGGTCCAGTCTG-----GGGCATGAGATGGGGTGGTGGGGAGGAGAGAGACAGTCTCTCCTCTACCCACCTGTCTCTTCTGTGCAGGTGGTTTCCGAGCAGGTGAAGCACATTTAAAGGGGGAGGTTCTAAACTG + +a score=30487 +s hg18.chr1 10997 330 + 247249719 ACAACGAAAAGCCCACTAGCTTGTCCAGTGCCACAGGAGGGGCAAGTGGAGGAGGAGAGGTGGCGGTGCTCCCCACTCCACTGCCAGTCGTCACTGGCTCTCCCTTCCCTTCATCCTCGTTCCCTATCTGTCACCATTTCCTGTCGTCGTTTCCTCTGAATGTCTCACCCTGCCCTCCCTGCTTGCAAGTCCCCTGTCTGTAGCCTCACCCCTGTCGTATCCTGACTACAATAACAGCTTCTGGGTGTCCCTGGCATCCACTCTCTCTCCCTTCTTGTCCCTTCCGTGACGGATGCCTGAGGAACCTTCCCCAAACTCTTCTGTCCCATC +s panTro2.chr9_random 4677170 330 + 7733331 ACAACGAAAAGCCCACTTGCTTGTCCAGTGCCACAGGAGGGGCAAGTGGAGGAGGAGAGGTGGCGGTGCTCCCCACTCCACTGCCAGTCATCACTGGCTCTCCCTTCCCTTCATCCTCGTTCCCTATCTGTCACCATTTCCTGTCGTCGTTTCCTCTGAATGTCTCACCCTGCCCTCCCTGCTTGCAAGTCCCCTGTCTGTAGCCTCACCCCTGTCACATCCTGACTACAATAACAGCTTCTGGGTGTCCCCAGCATCCACTCTCTCTCCCTTCTTGTCCCTTCCGTGATGGATGCTTGAGGAACCTTCCCCAAACTCTTCCGTCCCATC + +a score=780471 +s hg18.chr1 11327 8563 + 247249719 CCTGCCCTGCTCAAAATCCAATCACAGCTCCCTAACACGCCTGAATCAACTTGAAGTCCTGTCTTGAGTAATCCGTGGGCCCTAACTCACTCATCCCAACTCTTCACTCACTGCCCTGCCCCACACCCTGCCAGGGAGCCTCCCGTGGCACCGTGGGGACACAAAGGAACCAGGGCAAAGCTCCCTCAGCCCCATTCAAAGAGGCCTGGCCCACAGGCTCACGGAAAGTCAGCCTCTCATGCCCCGAGAGCTGAGTGCAAGGGAGAGGCAGCGCTGTCTGTGCTTCCCATGCAGAAGCACCCCCCTCCCACCCCTGTGCAGGCCGGCCTTCGCGGCAGACCACCATACACCACGTTCCAAGCCACACTGAGGCCTCCCTCCAAGCCTGCAGCCCCCATTTCCAGACCCTGCCAGGGCAACCTGCATATCCACCTCCCTACCCTGCCCCCCTCTTCCAGGAGTCTGCCCTATGTGGAGTAAGCACgtggttttcctcttcagcaactatttcctttttactcaagcaatggccccatttcccttggggaatccatctctctcgcaggcttagtcccagagcttcaggtggggctgcccacagagctcctcagtctaagccaagtggtgtgtcatagtcccctggccccattaatggattctgggatagacatgaggaccaagccaggTGGGATGAGTGAGTGTGGCTTCTGGAGGAAGTGGGGACACAGGACAGCATTCTTTCCTGCTGGACCTGACCCTGTGTCATGTCACCTTGCTACCACGAGAGCATGGCCTGTCTGGGAATGCAGCCAGACCCAAAGAAGCAAACTGACATGGAAGGAAAGCAAAACCAGGCCCTGAGGACATCATTTTAGCCCTTACTCCGAAGGCTGCTCTACTGATTGGTTAATTTTTGCTTAGCTTGGTCTGGGGAGTTCTGACAGGCGTGC CACCAATTCTTACCGATTTCTCTCCACTCTAGACCCTGAGAAGCCCACGCGGTTCATGCTAGCAATTAACAATCAATCTCGCCCTATGTGTTCCCATTCCAGCCTCTAGGACACAGTGGCAGCCACATAATTGGTATCTCTTAAGGTCCAGCACGAGGTGGAGCACATGGTGGAGAGACAGATGCAGTGACCTGGAACCCAGGAGTGAGGGAGCCAGGACTCAGGCCCAAGGCTCCTGAGAGGCATCTGGCCCTCCCTGCGCTGTGCCAGCAGCTTGGAGAACCCACACTCAATGAACGCAGCACTCCACTACCCAGGAAATGCCTTCCTGCCCTCTCCTCATCCCATCCCTGGGCAGGGGACATGCAACTGTCTACAAGGTGCCAAGTACCAGGACAGGAAAGGAAAGACGCCAAAAATCCAGCGCTGCCCTCAGAGAAGGGCAACCACGCAGTCCCCATCTTGGCAAGGAAACACAATTTCCGAGGGAATGGTTTTGGCCTCCATTCTAAGTGCTGGACATGGGGTGGCCATAATCTGGAGCTGATGGCTCTTAAAGACCTGCATCCTCTTCCCTAGGTGTCCCTCGGGCACATTTAGCACAAAGATAAGCACAAAAGGTGCATCCAGCACTTT--GTTACTATTGGTGGCAGGTTTATGAATGGCAACCAAAGGCAGTGTACGGGTCAAGATTATCAACAGGGAAGAGATagcatttcctgaaggcttcctaggtgccaggcactgttccattcctttgcatgttttgattaatttaatatttaaaataattctaccaggaag--------------ctaccattattaccacaacttcacaaatgagaacaccgaggcttagaggggttgggttgcccaaggttacagaggaagaaaacaggggagctggatctgagccaaggcatcaactccaaggtAACCCCTCAGTCACTTCACTGTGTGTCCCCTGGTTACTGGGACATTC TTGACAAACTCGGGGCAAGCCGGTGAGTCAGTGGGGGAGGACTTTCAGGAAGAGGTGGGTTCCCAGTTGGTGACAGAAGAGGAGGCTGCAAAGTGAAGGAGCAGGGGCTCCAGGTCTGGCGACAACCAGGGAAGGGACAGGGCAGGGATGGCTTGGACCACGAGAGGCACCTGAGTCAGGCAGTCACATACTTCCCACTGGGGTCTACCATGTGAGGCATGGTGTGGGATCCTGGGAAGGAGACCAAGCCTCATTTCAGTTTGCTTATGGCCAAAGACAGGACCTGTGTACCCGACAACCCCTGGGACCTTTACCAAAAAAAGAGCAAACACCATTCACTCACTCATGTTAGATAAACACTGAGTGAAGTCACTGGAGCCCAAGGACTGTGCGAGGTCAGCACTGCCAATACAAGAAGCTGCAGCCCTCCAGCTCGCctccctcaatggccactccgtgctccagccatgctggcttccttttaggtcctccacctccaggctgtagttcatgtgcttctttctggaatgttcttcccaacctacccactcaaccctcagactttaccataaatgtcatttcctcacgtctgccttccctgacctgagaccaagccaggCTTCCCATGACGAGCCTCACAGTACCCCATCTCCCCTGAACAGATGCAGTAATAACCTACATAACccggggccatgatctatggctttgaatcctggctctgtcactaggccaggtctctcagcccttctgtgcctcagtttcctcatctataaaatgagatgacggcagtgcctgctcatgaagtgtgagttaatgcactcaaatcaatggttgtgcacggtttatatgaatattagtgattaCAAAATATTATCAatagaccttgtcacaactgttattgaagaactaatcatctattgcttatttaggtctttctctcctgccagaatgtgcgctccaggtggagaggtatgttgccttatccgtgg ctggatatatagagattcccacactgccttgcacacgagcactgctgggtaaatatttgttggctgcaggaaAACGTGAAGGAATAGGCCCTCCAATGGGAGGAAAAGCATGAGTTGTGAGAGCAGAGCCACCACAGGAAACCAGGAGGCTAAGTGGGGTGGAAGGGAGTGAGCTCTCGGACTCCCAGGAGTAAAAGCTTCCAAGTTGGGCTCTCACTTCAGCCCCTCCCACACAGGGAAGCCAGATGGGTTCCCCAGGACCGGGATTCCCCAAGGGGGCTGCTCCCAGAGGGTGTGTTGCTGGGATTGCCCAGGACAGGGATGGCCCTCTCATCAGGTGGGGGTGAGTGGCAGCACCCACCTGCTGAAGATGTCTCCAGAGACCTTCTGCAGGTACTGCAGGGCATCCGCCATCTGCTGGACGGCCTCCTCTCGCCGCAGGTCTGGCTGGATGAAGGGCACGGCATAGGTCTGACCTGCCAGGGAGTGCTGCATCCTCACAGGAGTCATGGTGCCTGTGGGTCGGAGCCGGAGCGTCAGAGCCACCCACGACCACCGGCACGCCCCCACCACAGGGCAGCGTGGTGTTGAGACAACACAGCCCTCATCCCAACTATGCACATAGCTTCAGCCTGCACAGATAGGGGAGTAGGGGACAGAGCATTTGCTGAGAGGCCAGGAGCGCATAGATGGGACTCTGCTGATGCCTGCTGAGTGAATGAGGGAAAGGGCAGGGCCCGGGACTGGGGAATCTGTAGGGTCAATGGAGGAGTTCAGAGAAGGTGCAACATTTCTGACCCCCTACAAGGTGCTTGCTACCTGCCAGGCACCCTTTCCATACCTTGTCTCAGTTCAGCTCCCCACCTTGGATAAACAAGAAACCTTGGTTGCAGAGGAAAAAAGAGGCTGGAAACAAAGGGGTAGAAATGGGGTAGCAGGGGAGATTGCCTGATCAACTGCCAAATGGTACACAGTTCTGGAAAAGCACA AAAAATGTGCACACACGGGTTCTTCCCACTTTAACCCCTGAGGAATCTGAGGCCTGCTCCTGAAACAGACTGGGCAGTGGCTAGTGACTCTAGGTATAGGAGTATCCAGCCCTGCTCACCCAGGCTAGAGCTTAGGGGGACAAGAGGAAAGAGGTGCCTGTGGGGGTGGAGGACAGGAAGGAAAAACACTCCTGGAATTGCAAAGTGAGGGCAGAGTCTATTTATATTGGGTTTAATTAACTCCTCTCCCTGGTGCCACTAAAGCAGCAATCACACTGCAGACAGCACTGATTTGATTGGCAAGAGATGCACCAGGCAGAATATTAAGGGACCAGGCCCCTATAAATAGGCCTAATCACAGCCCCTCACTGGAAAATGGTAAGGAAGACATTAATCAGGCCTGGCACTGTGCCCTAGACCTGCTCCCCTAGGCACTACAGTGGGGCCCTTGGTTGCAACACAAGTAGGTAGGGATGGATGAGTGTGGCATGAAGGGCCTAGGAGATTTCACTTGGGTTTAAAATGCTGTGACCTTGAGTAAGTTGCCGTCTCTGAATCTGATCCTTTCGATTTCCCATTCTCCAAACTGAGAACTAGCACTGCTGAGACGTGGTTATTTCCAATAATAATTTGTATATTTTACATAACGCACCACACCAACATCTTCACCCAGTTGGAGCCTACTCCTTTGCTCCCGCTGCTGGCTTCCCCAGCCCTCCCTTCTGCCCTCCTCAGGCCAGCACTTTTCAGTGAGTTCCTCCTTTGCATACAGGCTTTCCAGATCTGTACTTGCCTTGAATACTCATCAGAGCCCAGGAGTTACTCCTCACCTCCCACTTATTTTTCCTCCCATCAAATAACTAAAGCATGGCCAGCTGATGCCCAGCCAACTGAGAAACCCAACCCTCTGAGACCAGCACACCCCTTTCAAGCATGTTCCTCCCTCCCCTTCTTTGTATTTATACTGATGCAAGTTTGCTGGCTGTcct aacttatttctgtgcctcagttctcccatatgtaagatcacaaagggggtaaagaTGCAAGATATTTCCTGTGCACATCTTCAGATGAATTTCTTGTTAGTGTGTGTGTGTTTGCTCACACATATGCGTGAAAGAAGAGTACATACACAGATCTCCTCAAAAAGGAGGCAGCAAGCCCGTTCAAGAATGGGACTGAATACACCTGATGAGTGGTTTACTTTCTGTCTGCAAACATCTACTGATCATCTGTTAGGTGCAGGCCATGATCACAACAAAGACGAATAAGACACTACACTAGCCAGGGAGAGTCTCAAAAACAACTAAACTCAAATTAAATTCATTCTACTCCAGTCATGGGTACAAAGCTAAGGAGTGACAAATCCCTCTTGGAGTTAGGGGAGTCAGGAAAAAGCTCTTAGCAGAATGTGTGCCTCTCggccgggcgcagcggctcacgcctgtaatcccagcactttgggaggcgaaggcaggcagatcacctgaggtcgggagttcgagaccagtctgaccaacatggtgaaactccatctctactaaaaatacaaaattagccaggcgtggtggtgcatgcctgtaatccccgctactcgggaggctgaggaaggagaatcacttgaaccaggaaggtggaggttgcagtgtgccaagatcgcgccatggcactccagcctaggcaacgagggtgaaCCAGGTCCAGGAAGAAGGTGCAAAGACAGCATTCCAGGTAAAAGAAACAGCTTGAACAAAAAGTGTGTAGGGGAACCGCAAGCGGTCTTGAGTGCTGAGGGTACAATCATCCTTGGGGAAGTACTAGAAGAAAGAATGATAAACAGAGGCCAGTTTGTTAAAAACACTCAAAATTAAAGCTAGGAGTTTGGACTTGTGGCAGGAATgaaatccttagacctgtgctgtccaatatggtagccaccaggcacatgcagccactgagcacttgaaatgtggat agtctgaattgagatgtgccataagtgtaaaatatgcaccaaatttcaaaggctagaaaaaaagaatgtaaaatatcttattattttatattgattacgtgctaaaataaccatatttgggatatactggattttaaaaatatatcactaatttcatctgtttctttttacttttAGAAATCACATATGTGACTTAAATATTTCTTTTCTTTTTCTTTCCTCTCACTCAGCGTCCTGTGATTCCAAAGAAATGAGTCTCTGCTGTTTTTGGGCAGCAGATATCCTAGAATGGACTCTGACCTAAGCATCAAAATTAATCATCATAACGTTATCATTTTATGGCCCCTTCTTCCTATATCTGGTAGCTTTTAAATGATGACCATGTAGATAATCTTTATTGTCCCTCTTTCAGCAGACGGTATTTTCTTATGCTACAGTATGACTGCTAATAATACCTACACATGTTAGAACCATTCTGACTCCTCAAGAatctcatttaactcttattatcagtgaatttatcatcatcccctattttacataaggaaatggggttagaaagaccaaataacattttttcaacatcaaaacactagcttgagatcaagcccagacttggatctgtcgtctgaattccaagctttttgttatttattgatatgttttgttgtTTTCATGCAATAATGCAAATCTTAGCCCAAACATTTTGTTAGTAGTACCAACTGTAAGTCACCTTATCTTCATACTTTGTCTTTATGTAAACCTAAATTAGATCTGTTTTTGATACTGAGGGAAAAACAAGGGAATctaacactaaccagcccgtagtgtgtggtcaacactttcgttactttagtatacatcaccccaattgtttgtcttcaccacacactttggagttaggtagtagtatctatttttacaaataagaaaacccaggcacaaaggggttgattagcAATTATCTTTTGAAAAGCCTGTAGTTGCTC ATCTGAAGAAGTGACGGACCACCTCTTATTTAGTGGACAGACAGTAACTAGTTGAGAAGACAGGGGATTTTGTTGGCGGAAAAAAAAATTTATCAAAAGTCGTCTTCTATCAGGGAGTTTTATGAGAAACCCTAGCTCCTCAGTTCCACAGTGGGTAACTGTAATTCATTCTAGGTCTGCGATATTTCCTGCCTATCCATTTTGTTAACTCTTCAATGCATTCCACAAATACCTAAGTATTCTTTAATAATGGTGGTTTTTTTTTTTTTTTGCATCTATGAAGTTTTTTCAAATTCTTTTTAAGTGACAAAACTTGTACATGTGTATCGCTCAATATTTCTAGTCGACAGCACTGCTTTCGAGAATGTAAACCGTGCACTCCCAGGAAAATGCAGACACAGCACGCCTCTTTGGGACCGCGGTTTATACTTTCGAAGTGCTCGGAGCCCTTCCTCCAGACCGTTCTCCCACACCCCGCTCCAGGGTCTCTCCCGGAGTTACAAGCCTCGCTGTAGGCCCCGGGAACCCAACGCGGTGTCAGAGAAGTGGGGTCCCCTACGAGGGACCAGGAGCTCCGGGCGGGCAGCAGCTGCGGAAGAGCCGCGCGAGGCTTCCCAGAACCCGGCAGGGGCGGGAAGACGCAGGAGTGGGGAGGCGGAACCGGGACCCCGCAGAGCCCGGGTCCCTGCGCCCCACAAGCCTTGGCTTCCCTGCTAGGGCCGGGCAAGGCCGGGTGCAGGGCGCGGCTCCAGGGAGGAAGCTCCGGGGCGAGCCCAAGACGCCTCCCGGGCGGTCGGGGCCCAGCGGCGGCGTTCGCAGTGGAGCCGGGCACCGGGCAGCGGCCGCGGAACACCAGCTTGGCGCAGGCTTCTCGGTCAGGAACGGTCCCGGGCCTCCCGCCCGCCTCCCTCCAGCCCCTCCGGGTCCCCTACTTCGCCCCGCCAGGCCCCCACGACCCTACTTCCCGCGGCCCCGGACGCCTCCTCACC TGCGAGCCGCCCTCCCGGAAGCTCCCGCCGCCGCTTCCGCTCTGCCGGAGCCGCTGGGTCCTAGCCCCGCCGCCCCCAGTCCGCCCGCGCCTCCGGGTCCTAACGCCGCCGCTCGCCCTCCACTGCGCCCTCCCCGAGCGCGGCTCCAGGACCCCGTCGACCCGGAGCGCTGTCCTGTCGGGCCGAGTCGCGGGCCTGGGCACGGAACTCACGCTCACTCCGAGCTCCCGACGTGCACACGGCTCCCATGCGTTGTCTTCCGAGCGTCAGGCCGCCCCTACCCGTGCTTTCTGCTCTGCAGACCCTCTTCCTAGACCTCCGTCCTTTGTCCCATCGCTGCCTTCCCCTCAAGCTCAGGGCCAAGCTGTCCGCCAACCTCGGCTCCTCCGGGCAGCCCTCGCCCGGGGTGCGCCCCGGGGCAGGACCCCCAGCCCACGCCCAGGGCCCGCCCCTGCCCTCCAGCCCTACGCCTTGACCCGCTTTCCTGCGTCTCTCAGCCTACCTGACCTTGTCTTTACCTCTGTGGGCAGCTCCCTTGTGATCTGCTTAGTTCCCACCCCCCTTTAAGAATTCAATAGAGaagccagacgcaaaactacagatatcgtatgagtccagttttgtgaagtgcctagaatagtcaaaattcacagagacagaagcagtggtcgccaggaatggggaagcaaggcggagttgggcagct +s panTro2.chr15 23958 8553 - 100063422 CCTGCCCTGCTTAAAATCCAATCACAGCTCCCTAACACTCCTGAATCAACTTGAAGTCCTGTCTTGAGTAATCCGTGGGCCCTAACTCACTCACCCCAACTCTTCACTCACTGCCTTGCCCCACACCCTGCCAGGGAGCCTCCCGTGGCACCGTGGGGACACAAAGGAACCAGGGCAAAGCTCCCTCAGCCCCATTCAAAGAGGCCTGGCCCACAGGCTCACGGAAAGTCAGCCTCTCATGCCCCGAGAGATGAGTGCAAGGGAGAGGCAGCGCTGTCTGTGCTTCCCATGCAGAAGCACCCTCCTCCCACCCCTGTGCAGGCCGGCCTTCATGGCAGACCACCATACACCACGTTCCAAGCCACACTGAGGCCTCTCTCCAAGCCCGCGGCCCCCATTTCCAGACCCCACCAGGGCAACCTGCATATCCACCTCCCTACCCTGCCCCCCTCTTCCAGGAGTCTGCCCTATGTGGAGTAAGCACgtggttttcctcttcagcaactatttcctttttactcaagcaatggccccatttcccttggggaatccatctctctcgcaggcttagtcccagagcttcaggtggggctgcccacagagttcctcagtctaagccaagtggtgtgtcatagtcccctggccccagtaatggattctgggatagacatgaggaccaagccaggtgggatgggtaagtgtggcttctggaggaagtggggacacaggagagcattctttcctgctggACCTGACCCTGTGTCATGTCACCTTGCTACCACGACAGCATGGCCTGTCTGGGAATGCAGCCAGACCCAAAGAAGCAAACTGACATGGAAGGAAAGCAAAACCAGGCCCTGAGGACATCATTTTAGCCCTTACTCCGAAGGCTGCTCTACTGATTGTTTAATTTTTGCTTAGCTTGGTTTGGGGAGTTCTGACAGGCGTGC CACCAATTCTTACCGATTTCTCTCCACTCTAGACCCTGAGAAGCCCACGCGGTTCATGCTAGCAATTAACAATCAATCTCGCCCTATGTGTTCCCATTCCAGCCTCTAGGACACAGTGTCAGCCACATAATTGGTATCTCTTAAGGTCCAGCACGAGGTGGAGCACATGGTGGAGAGACAGATGCAGTGACCTGGAACCCAGGAGTGAGGGAGCCAGGACTCAGGCCCAAGGCTCCTGAGAGGCATCCGGCCCTCCCTGGGCTGTGCCAGCAGCTTGGAGAACCCACACTCAATGAACGCAGCACTCCACTACCCAGGAAATGCCTTCCTGCCCTCTCCTCATCCCATCCCTGGGCAGGGGACATGCAACTGTCTACAAGGTGCCAAGTACCAGGACAGGAAAGGAAAGATGCCAAAAATCCAGGGCTGCCCTCAGAGAAGGGCAACCATGCAGTCCCCATCTTGGCAAGGAAACACAATTTCCGAGGGAATGGTTTTGGCCTCCATTCTAAGTGCTGGACATGGGGTGGCCACAATCTGGAGCTGATGGCTCTTAAAGACCTGCGTCCTCTTCCCTAGGCGTCCCTTGGGCACATCTAGCACAACGATAAGCACAAAAGGTGCATCCAGCACTTTCTGTTACTATTGGTGGCAGGTTCATGAATGGCAACCAAAGGCAGTGTACGGGTCAAGATCATCAACGGGGAAGAGATagcatttcctgaaggcttcctaggtgccaggcactgttccattcctttgcatgttttgattaatttaatatttacaataattctaccaggaagaattattaccattattaccattattaccacaacttcacaaatgagaacactgaggcttagaggggttgggttgtccaaggttacagaggaagaaaacaggggagctggatctgagccaaggcatcaactccaaggtAACCCCTCAGTCACTTCAGTGCGTGTGCCCTGGTTACTGGGACATTC TTGACAAGCTTGGGGCAAGCCGGTGAGTCAGTGGGGGAGGACTTTCAGGAAGAGGTGGGTTCCCAGTTGGTGACAGAAGAGGAGGCTGCAAAGTGAAGGAGCAGGGGCTCCAGGTCTGGCGACAACCAGGGAAGGGACAGGGCAGGGATGGCTTGGACCACGAGAGGCACCCGAGTCAGGCAGTCACATACTTCCCGCTGGGGTCTACCATGTGAGGCATGGTGTGGGATCCTGGGAAGGAGACCAAGCCTCATTTCAGTTTGCTTATGGCCAAAGACAGGACCTGTGTACCCGACAACCCCTGGGACCTTTGCCAAAAAAACAGCAAACACCATTCACTCACTCATGTTAGATAAACACTGAGTGAAGACACTGGAGCCCAAGGACTGTGCGAGGTCAGCGCTGCCAATACAAGAAGCTGCACCCCTCCAGCTCGCctccctcaatggccactctgtgctccagccatgctggcttccttttaggtcctccacctccaggctgtagttcatgtgcttctttctggaatgttcttcccaacctacccactcaaccctcagactttaccataaatgtcatttcctcacatctgccttccctgacctgagaccaagccaggcttcccatgacgagcctcacagtacccCATCTCCGCTGAACAGATGCAGTAATAACCTACATAACccggggccatgatctatggctttgaatcctggctctgtcacttggccaggtctctcagcctttctgtgcctcagtttcctcatctataaaatgagatgacggcagtgcctgctcatgaagtgtgagTTAATGCACTCAAATCAATGGTGGTGCACGGTTTATATGAATATTAGTGATTACAAAATATTATCAATAGACCTTGTCACAACTGTTATTGAAGAATTAATCATGTAttggttatttaggtctctctctcctgccagaatgtgcgctcca--tggagaggtatgttgccttatccgtgg ctggatatatagagattcccacactgccttgcacaccagcactgctgggtaaatatttgctggctgcaggaaAACGTGAAGGAATAGGCCCTCCAGTGGGAGGAAAAGCACGAGTTGTGAGAGCAGAGCCACCACAGGAAACCAGGAGGCTAAGTGGGGTGGAAGGGACTGAGCTCTCGGACTCCCAGGAGTAAAAGCTTCCAAGTTGGGCTCTCACTTCAGCCCCTCCCACACAGGGAAGCCAGATGGGTTCCCCAGGACCAGGATTCCCCAAGGGGGCTGCTCCCAGAGGGTGTGTTGCTGGGATATCCCAGGACAGGGATGGCCCTCTCATCAGGTGGGGGTGGGTGGCAGCACCCACCTGCCGAAGATGTCTCCAGAGACCTTCTGCAGGTACTGCAGGGCATCCGCCATCTGCTGGACGGCCTCCTCTCGCCGCAGGTCTGGCTGGATGAGGGGCACGGCATAGGTCTGACCTGCCAGGGAGTGCTGCATCCTCACAGGAGTCATGGTGCCTGTGGGTGGGAGCCGGAGCATCAGAGCCACCCACGACCACCTGCACCCACCCACCACAGGGCAGCGTGGTGTTGAGACAACACAGCCCTCATCCCAACTATGCACATAGCTTCAGCCTGCACAGATAGGGGAGTAGGGGACAGAGCATTTGGTGAGAGGCCAGGAGCGCATAGATGGGACTCTGCTGATGCCTGCTGAGTGAATGAGGTAAAGGGCAGGACCAGGGACTGGGGAATCTGTAGGGTCAATGGAGGAGTTCAGAGAAGGTGCAACATTTCTGACCCCCTACAAGTTGCTTGCTACCTGCCAGGTACCCTTTCCATACATTGTCTCAGTTCAGCTCCCTACCTTGGATAAACAAGAAACCTTGGTTGCGGAGGAAAAAAGAGGCTGGAAACAAAGGGGTAGAAATGGGGTAGTGGGGGAGATTGCCTGATCAACTGCCAAATGGTACCCAGTTCTGGAAAAGCACA AAAAATGTGCACACACGGGTTCTTCCCACTTTAACCCCTGAGGAATTTGAGGCCTGCTCCTGAAACAGACTGGGCAGTGGCTAGTGACTCTAGGTATAGGAGTATCCAGCCCTGCTCACCCAGGCTAGAGCTTAGGGGGCCAAGAGGAAAGAGGTGCCTGTGGGGGTGGAGGACAGGAAGGAAAAACACTCCTGGAATTGCAAAGTGAGGGCAGAGTCTATTTATATTGGGTTTAATTAACTCCTCTCCCTGGTGCCACTAAAGCAGCAATCACACTGCAGACAGCACTGATTTGATTGGCAAGAGATGCACCAGGCAGAATATTAAGGGACCAGGCCCCTATAAATAGGCCTAATCACAGCCCCTCGCTGGAAAATGCTAAGGAAGACATTAATCAGGCCTGGCACTGTGCCCTAGACCTGCTCCCCTAGGCACTACAGTGGGGCCCTTGGTTGCAACACAAGTAGGTAAGGATGGATGAGTCTGGTATGAAGGGCCTAGGAGATTTCATTTGGGTTTAAAATGCTGTGACCCTGAGTAAGTTGCTGTCTCTGAATCTGATCCTTTCCATTTCCCATTCTCCAAACTGAGAACTAGCACTGCTGAGACGTGGTTATTCCCAATAATAATTTGTATATTTTACATAACGTACCACACCAACATCTTCACCCAGCTGGAGCCTACTCCTTTGCTCCCCCTGCTGGCTTCCCCAGCCCTCCCTTCTGCCCTCCTCAGGCCAGCACTTTTCAGTGAGTTCCTCCTTTGCATACAGGCTTTCCAGATCTGTACTTGCCTTGAATACTCATCAGAGCCCAGGAGTTACTCCTCACCTCCCACTTATTTTTCCTCCCATCAAATAACTAAAGCATGGCCAGCTGATGCCCAGCCAACTGAGAAACCTAACCCTCTGAGACCACCACACCCCTTTCAAGCATGTTCCTCCCTCCCCTTCTTTGTATTTATACTGACGCAAGTTTGCTGGCTGTcct aacttatttctgtgcctcagttctcccatatgtaagatcacaaagggggtaaagatgcaagATATTTCCTGTGCACATCTTCAGATGAATTTCT------TGTGTGTGTGTTTGCTCACACATATGCGTGAAAGAAGAGTACATACACAAAT---CTCAAAAAGGAGGCAGCAAGCCCGTTCAAGAATGGGACTGAATACACCTGATGAGTGGTTTACTTTCTGTCTGCAAACATCTACTGATCATCTGTTAGGTGCAGGCCATGATCACAACAAAGACGAATAAGACACTACACTAGCCAGGGAGAGTCTCAAAAACAACTAAACTCAAATTAAATTCATTCTAATCCAGTCATGAGTACAAAGCTAAGGAGTGACAAATCCCTTTTGGAGTTAGGGGAGTCAGGAAAAAGCTCTTAGCAGAATGTGTGCCTCTCggctgggcacagcggctcacgcctgtaatcccagcactttgggaggcgaaggcaggcagatcacctgaggtcaggagttcgagaccagtctgaccaacatggtgaaactccatctctactaaaaatacaaaattagccaggcgtggtggtgcatgcctgtaatcccagctactcgggaggctgaggaaggagaatcacttgaaccggggaggtcgaggttgcagtgtgccgagatcgcgccattgcactccagcctgggcaacaaaagtgaaCCAGGTCCAGGAAGAAGGTGCAAAGACAGCATTCCAGGTAAAAGAAACAGCTTGAACAAAAAGTGTGTAGGGGAACAGCAAGCGGTCTTGAGTGCTGAGGGTACAATCATCCTTGGGGAAGTACTAGAAGAAAGAATGATAAACAGAGGCCAGTTTGTTAAAAACACTCAAAATTAAAGCTAGGAGTTTGGACTTGTGGCAGGAATgaaatccttagacctgtgctgtccaatatggtagccaccaggcacatgcagccactgagcacttgatatgtggat agtctgaattgagatgtgccataagtgtaaactatgcaccaaatttcaaagactagaaaaaaagaatgtaaaatata-----attttatattgattacatgctaaaataaccatatttgggatatactggattttaaaaatatattgctaatttcatctgtttctttttacttttAGAAATCACATATGTGACTTAAATATTTCTTTTCTTTTTCTTTCCTCTCACTCAGCGTCCTGTGATTCCAAAGAAATGAGTCTCTGCTCTTTTTGGGCAGGAGATATCCTAGAATGGACTCTGACCTAAGAATCAAAATTAATAATCATAACGTTATCATTTTATGGCCCCTTCTTCCTATATCTGGTAGCTTTTAAATGATGACCATGTAGATAATCTTTATTATCCCTCTTTCAGCAGACGGTATTTTCTTATGCTACAGTATGACTGCTAATAATACCTACATACGTTAGAACCATTCTGACTCCTCAAGAatctcatttaactcttattatcagtgaatttatcatcatccccaattttagataaggaaatggggttagaaagaccaaataacattttttcaacatcaaaacactagcttgagatcaagcccaaacttggatctgttgtctgaattccaagctttttg----ttattgatatgttttgttgtTTTCATGCAATAATGCAAATCTTAGCCCAAACATTTTGTTAGTAGTACCAACTGTAAGTCACCTTATCTTGATACTTTGTCTTTATGTAAACCTAAATTAGATCTGTTTTTGATACTGAGGGAAAAACAAGGGAATCTAACACTAACCagcccgtagtgtgtggtcaacactttcgttactttagtatacatcaccccaattgtttgtcttcaccacacactttggagttaggtagtactatctatttttacaaataagaaaacccaggcacaaaggggttgattagcAATTATCTTTTGAAAAGCCTGTAG-TGCTC ATCTGAAGAAGTGACGGACCATCTCTTATTTAGTGGACAGACAATAACTAGTTGAGAAGACAGGGGATTTTGTTGGCGGAAAAAAAAATTTATCAAAAGTCGTCTTCTATC--GGAGTTTTATGAGAAACCCTAGCTCCTCAGTTCCACAGTGGGTAACTGCAATTCATTCTAGGTCTGCGATATTTCCAGCCTATCCATTTCGTTAACTCTTCAATGCATTCCATAAATGCCTAAGTATTCTTTAATAATGGTGG--TTTTTTTTTTTTTGCATCTATGAAGTTTTTTCAAATTCTTTTTAAGTGACAAAACTTGTACATGTGTATCGCACAATATTTCTAGTCGACAGCACTGCTTTCGAGAATGTAAACCGTGCACTCCCAGGAACATGCAGACACAGCGCGCCTCTTTGGGACCACGGTTCATAATTTGGGAGTGCTCGGAGCCCTTCCTCCAGACCGTTCTCCCACACCCCGCTCCAGGGTCTCTCCCGGAGTTACAGGCCTCGCTGTAGGTCCCGGGAACCCAACGCGGTGTCAGAGAAGTGGGGTCCCCTACGAGGGACCAGGAGCTCCGGGCGGGCAGCAGCTGCGGAAGAGCCGCGCGAGGCTTCCCAGAACCCGGCCGGGGCGGGAAGACGCAGGAGTGGGGAGGCGGAACCGGGACCCCGCAGAGCCCGGGTCCCTGCGCCCCACAAGCCTTGGCTTCCCTGCTAGGGCCGGGCAAGGCCGGGTGCAGGGCGCGGCTCCAGGGAGGAAGCTCCGGGGCGAGCCCAAGACGCCTCCCGGGCGATCGGGGCCCAGCGGCGGCGTTCGCAGTGGAGCCGGGCACCGGGCAGCGGCCGCGGAACACCAGCTTGGCGCAGGCTTCTCGGTCAGGAACGGTCCCGGGCCTCCCGCCCGCCTCCCTCCAGCCCCTCCGGGTCCCCTACTTCGCCCCGCCAGGCCCCCACGACCCTACTTCCCGCGGCCCCGGACGCCTCCTCACC TGCGAGCCGCCCTCCCGGAAGCTCCCGCCGCCGCTTCCGCTCTGCCGGAGCCGCTGGGTCCTAGCCCCGCCGCTCACAGTCCGCCCGCGCCTCCGGGTCCTAACGCCGCCGTTCACCCTCCGCTGCGCCCTCCCCGAGCGCGGCTCCAGGACCCCGTCGACCCGGAGCGCTGTCCTGGCGGGCCGAGTCGCGGGCCTGGGCACGGAACTCACGCTCACTCCGAGCTCCCGACGTGCACACGGCTCCCATCCGTTGTCTTCCGAGCGCAGGGCCTCCCCTACCCGTGCTTTCTGCTCTGCAGACCCTCTTCCCAGACCTCCGTCCTTTGTCCCATCGCTGCCTTCCCCTCAAGCTCAGGGCCAAGCTGTCCGCCAGCCTCGGCTCCTCCGGGCAGTCCTCGCCCTGGGTGCGCCCCGGGGCAGGACCCCCAGCCCAGGCCCAGGGCCCGCCCCTGCCCTCCAGCCCTACACCTTGACCCGCTTTCCTGCCTCTCTCAGCCTACCTGACCTTGTCTTTACCTCTGTGGGCAGCTCCCTTGTGATCTGCTTAGTTCCCA-CACCCTTTAAGAATTAAATAGAGaagccagacgcaaaactacagatatcgtatgagtccacttttgtgaagtgcctagaatagtcaaaattcacagagacagaagcagtggtcgccaggaatggggaagcaaggcggagatgggcagct + +a score=78125 +s hg18.chr1 19890 845 + 247249719 cgtgttcaatgggtagagtttcaggctggggtgatggaagggtgctggaaatgagtggtagtgatggcggcacaacagtgtgaatctacttaatcccactgaactgtatgctgaaaaatggtttagacggtgaattttaggttatgtatgttttaccacaatttttaaaaaGCTAGTGAAAAGCTGGTAAAAAGAAAGAAAAGAGGCTTTTTTAAAAAGTTAAATATATAAAAAGAGCATCATCAGTCCAAAGTCCAGCAGTTGTCCCTCCTGGAATCCGTTGGCTTGCCTCCGGCATTTTTGGCCCTTGCCTTTtagggttgccagattaaaagacaggatgcccagctagtttgaattttagataaacaacgaataatttcgtagcataaatatgtcccaagcttagtttgggacatacttatgctaaaaaacattattggttgtttatctgagattcagaattaagcattttatattttatttgctgcctctggccaccctaCTCTCTTCCTAACACTCTCTCCCTCTCCCAGTTTTGTCCGCCTTCCCTGCCTCCTCTTCTGGGGGAGTTAGATCGAGTTGTAACAAGAACATGCCACTGTCTCGCTGGCTGCAGCGTGTGGTCCCCTTACCAGAGGTAAAGAAGAGATGGATCTCCACTCAtgttgtagacagaatgtttatgtcctctccaaatgcttatgttgaaaccctaacccctaatgtgatggtatgtggagatgggcctttggtaggtaattacggttagatgaggtcatggggtggggccctcattatagatctggtaagaaaagagaGCATTGtctctgtgtctccctctc +s panTro2.chrUn 57103829 845 - 58616431 tgtgttcaatgggtagagtttcaggctggggtgatggaagggtgctggaaatgagtggtagcgatggcggcgcaacagtgtgaatctacttaatcccactgaactgtatgcttaaaaatggtttagacggtgaattttaggttatgtatgttttaccacaatttttaaaaaGCTAGTGAAAAGCTGGTAAAAAGAAAGAAAAGAGGCTTTTTTAAAAAGTTAAATATATAAAAAGAGCATCATCAGTCCAAAGTCCAGCAGTTGTCCCTCCTGGAATCCGTTGGCTTGCCTCCGGCATTTTTGGCCCTTGCCTTTtagggttgccagattaaaatacaggatgcccagttagtttgaattttagataaacaacgaataatttcgtagcataaatatgtcccaagcttagtttgggacatacttatgctaaaaaacattattggttgtttatctgagattcaaaattaagcattttatattttatttgctgcctctggccaccctaCTCTCTTCCTGACACTCTCTCCCTCTCCCAGTTTTGTCCGCCTTCCTTGCCTCCTCTTCTGGGGGAGTTAGATCGAGTTGTAACAAGAACATGCCACTGTCTCACTGGCTGCAGCGTGTGGTCCCCTTACCAGAGGTAAGGAAGAGATGGATCTCCACTCAtgttgtagacagaatgtttatgtcctctccaaattcttatgttgaaaccctaacccctaatgtgatggtatgtggagatgggcctttggtaggtaattacggttagatgaggtcatggggtggggccctcattatagatctggtaagaaaagagagcattgtctctctgtctccctctc + +a score=1847 +s hg18.chr1 20735 23 + 247249719 tctctctctctctctctctcatt +s panTro2.chr15_random 1995870 23 - 3087076 tctctctctctctccctctcttt + +a score=89580 +s hg18.chr1 20758 992 + 247249719 tctctctatctcatttctctctctctcgctatctcatttttctctctctctctttctctcctctgtcttttcccaccaagtgaggatgcgaagagaaggtggctgtctgcaaaccaggaagagagccctcaccgggaacccgtccagctgccaccttgaacttggacttccaagcctccagaactgtgagggataaatgtatgattttaaagtcgcccagtgtgtggtattttgttttgactaatacaaCCTGAAAACATTTTCCCCTCACTCCACCTGAGCAATATCTGAGTGGCTTAAGGTACTCAGGACACAACAAAGGAGAAATGTCCCATGCACAAGGTGCACCCATGCCTGGGTAAAGCAGCCTGGCACAGAGGGAAGCACACAGGCTCAGggatctgctattcattctttgtgtgaccctgggcaagccatgaatggagcttcagtcaccccatttgtaatgggatttaattgtgcttgccctgcctccttttgagggctgtagagaaaagatgtcaaagtattttgtaATCTggctgggcgtggtggctcatgcctgtaatcctagcactttggtaggctgacgcgagaggactgcttgagcccaagagtttgagatcagcctgggcaatattgtgagattccatctctacaaaaataaaataaaatagccagtcatggtgtcacacacctgtagtcccagctacatgggaggctgaggcgggaggatcacttgagcttgggagatcgaggctgcagtgagctatgattgtaccactgcactccaggctgggcgacagagagagaccctgtctcagaaaaaaaaaaaaaaGTACTTTGTAATCTGTAAGGTTTATTTCAACACACACAAAAAAAGTGTATATGCTCCACGATGCCTGTGAATATACACACACACCACATCATATACCAAGCCTGGCTGTG TCTTCTCACAAATGCACTGCTAGGCACCACCCCCAGTTCTAGAA +s panTro2.chrUn 57104674 981 - 58616431 tctctctatgtcatttctctctct----ctatctca--tttctctctctctctctctctcctctgtcttttcccaccaagtgaggatgcgaagagaaggtggctgtctgcaaaccaggaagagagccctcaccaggaacccgtccagctgccaccttgaacttggacttccaagcctccagaactgtgagggataaatgtatgattttaaagtcgcccagtgtgtggtattttgttttgactaatacaaCCTGAAAACATTTTCCCCTCACTCCACCTGAGGAATATCTGAGTGGCTTAATGTACTCAGGACACAACAA---AGAAATGTCCCATGCACAAGGTGCACCCATGCCtgggtaaagcagcctggcacagagggaagcacacaggctcagggctctgctattcattctttgtgtgaccctgggcaagccatgaatggagcttcagtcaccccatttgtaatgggatttaattgagcttgccctgcctccttctgagggctgtagagaaaagatgtcaaagtattttgtaatctggctgggcgtggtggctcatgcctgtaatcccagcactttggtaggctgacgcgagaggactgcttgagcccaagagtttgagatcagcctgggcaatattgtgagattccatctctacaaaaataaaataaaatagccagtcatggtgtcacacacctgtagtcccagctacatgggaggctgaggcgggaggatcacttgagcttgggagatcgaggctgcagtgagctatgattgtaccactgcactccaggctgggcgacagagagagaccctgtctcag--aaaaaagaaaaagtactttgtaatctgtaaggtttatttcaacacACACAAAAAAAGTGTATATGCTCCACGATGCCTGTGAATATACACACACACCACATCATATACCAAGCCTGGCTGTG TCTTCTCACAAATGCGCTGCTGGGCACCACCCCCAGTTCTAGAA + +a score=178881 +s hg18.chr1 21750 2038 + 247249719 TCACACCAGCCAGTTCACCCTCCAGATGGTTCACCCTCAACTTCATAAAAGTTCCCTACCTAATCTACT---GACAGGCTCATCCCCGACCTAATTTTAAAGATTTCCTAGGA----------------------------------GCTGCAGTGGGAATCCTGGACCTCAGCCTGGACAAAGAACAGCTGCAGGTCATTCTCATGTGTGGACACAGAAGCTCTGCCTGCCTTTGCTGGCCAGCTGGGCTGAGCGGGCCTGGGAA-TTAAGGCTGCAGGGTTGGTCCCAGGCAGTCTTGCTGAAGCTTGCCACATCCCCCAGCCTCCTGGATTTGCCAGGATCCAAGAGCATGGACTTTAGGAATTCCTGGTGGAGGAGTGAAGAAAATGTGACAGGGTGTCCTAAGCCCCGATCTACAGGAAGAAAACTGGAAATAAGACTGAGGACTTAGTTTAAGATGTTCCTACTCAGCCTCTAGCTTTTGTGCTACAGTTCTGGGAACAGACTCCTCTCTCCTGAAAACCACTTCCCTCCGCAGCATTAGATTTCACCAAGATGTCTTGCTTGTGGGAAAGACTTCCAAGGATGCCTGGAGAGAGGAGGATGGAAATGTCCTGCTCTCTAAACAGATAGACAGATGCAGCCAGACAGAAAATAGTTTATCTTGCTGAGGTTTCTAATGTATTTGAAAGAGGCCTGGGTCTAGAAGTCTACCCAGAGGGCTCTGTGTTGTGCACGCAAAGATAAGAACCTTCCCTGTGGGAGTTCCAGAGCCAGTTTTCATAAACACCCATCGGTGACTGTGTTCAGAGTGAGTTCACACCATCCTGACCTGCCCTGAGTTAGACCTTACATGGTCTTCCTCCTCTAGGAAGCCTCTGCAGCCCAGGAACCTCCCCTTATCGGAAATGAACAGCATTTGAAGCTTCACCAGACAGACCAGAC AGCTTAGCCCTCGTGTTGTGCCATGTGGGTTGTTCTCTGAGAGGcaggagagcatagtggttactaggaagggaaggactttgggactagactgcctcggctggagtcctctttctgcttcatagccacgtgatcctaggcatgttacctgtgcctcagttttcactctgtcaatatgtaataactgaatctgtctttgtggtgaggattcagtgagttaacatatttgaagtgcttaaaaATGAGGCTTGtgtccatagattaatgagtgaatacacaaatggtgatatggacatacagtggagtattagtcataaaaaggaaggcagagctgatccatggcaccatgtgacagaacctcaaaagcattaggttaagtggaagaagccagacacaggtcacctattgtgtaattccatttataggaaatatacagaatatgtaaatccgtggagaaagaaagccgatttccaggggctaaggggaggggagaatgggaagtggctgcttcatgggtacaaggtttcattttgagctgatgaaaatgttttggaactacatagagatagtgttggcacaacatggtgaatgtactgaatgccactgattgttcaatttaaaatggtcaaacttatatgaatttcacctccatt-aaaaaaaAAAAAAAAGgaccagatgtggttgctcacacccataatcccaacactttggaaAAAGGTGAAAGTTTTTTTTtctt------tttttttttatatacttaagttctagggtacatgtgcataatgtgcaggttggatacatagatatgcgtgtgccatgttggtttgctgcacccatcaacttgtcatttacattaggtatttcttctaatgctatccctcccccagccccccacccactgacaggccccagtgtatgatgttctctgccccatgtccaagcgttctcattgttcaattcccacctgtgagtgagaacatgcagtgtt tggttttctgtctttgtgatagtttgctcagaatgatggtttccagcttcatccatgtccctgcaaaggacatgaactcatcctttttaatgg-ctgcatagtat-cccatggt-atatatgtgcc-acattctcttaatcc-agtctgtca +s panTro2.chrUn 57107018 2082 - 58616431 CCAGACCAGACAGTTCACCCTCCAGACGGTTCACCCTCAACTGTATAAAAGTTCTCTACCTAATCTACTACTGACAGACTCATCTCAGACCTAATTTTAAAGATTTCCTAGGAACTGAATTGCAAAAACTTTTACCCTCACCCTAGAGCTGCAATGGGAATCCTG-ACCTCAGCGTAGACAAAGAAAAGCTGCAGGTCATTCTCATGTGTGGACACGGAAGCCCTGCCTGCCTTTGCTGGCCAGCTGGGCTGAGTGGGCCTGGGAAATTAAGGCTGCAGGGTTGGTCCCAGGCAGTCTTGCTGAAGCTTGCCACATCCCCCAGCCTCCTGGATTTGCCAGGATCCAAGAGCATGGACTTTAGGAATTCCTGGTGGAGGAGTGAAGAAAATGTGACAGGGTGTCCTAGGCCCCAATCTACAGGAAGAAAACTGGAAATAAGACTGAGGACTTAGTTTAAGATGTTCCTACTCAGCCTCTAGCTTTTGTGCTACAGTTCTGGGAACAGACTCCTCTCTCCTGAAAACCACTTCCCTCTGCAGCATTAAATTTCACCAAGATGTCTTGCTTGTGG-AAAGACTTCCAAGGATGCCTGGAGAGAGGAGGATGGAAATGTCCCGCTCTCTAAACAGATAGACAGATGCAGCCAGACAGAAAATAGTTTATCTTGCTGAGGTTTCTAAT----TTGAAAGAGGCCTGGGTCTAGAAGTCTACCCAGAGGGCTCTGTGTTGTGCAGGCAAAGATAAGAACCTTCCCTGTGGGAGTTCCAGAGCCAGTTTTCATAAACACCCATCGGTGACTGTGTTCAGAGTGAGTTCACACCATCCTGACCTGCCCTGAGTTAGACCTTACATGGTCTTCCTCCTCTAGGAAGCCTCTGCAGCCCAGGAACCTCCCCTTATCTGAAATGAACAGCATTTGAAGCTTCACCAGACAGACCAGAC AGCTTAGCCCTCGTGTTGTGCCATGTGGGTTGTTCTCTGAGAGGcaggagagcatagtggttactaggaaggggaggactttgggactagactgcctcggctggagtcctctttctgcttcatagccacgtgatcctaggcatgttacctgtgcctcagttttcactctatcaatatgtaataactgaatctgtccttgtggtgaggattcagtgagttaacatatttgaagtgcttaaaaATGAGGCTTGtgtccatagattaatgagtgaatacacacatggtgatatggacatacagtggagtattagtcataaaaaggaaggcagagctgatccatggcaccatgtgactgaacctcaaaagcattaggttaagtggaagaagccagacacaggtcacctattgtgtaattccatttataggaaatatacagaatatgtaaatccgtggagaaagaaagccgatttccaggggctaaggggaggggagaatgggaagtggctgcttcatgggtacaaggtttcattttgaggtgatgaaaatgttttggaactacacagagatagtgttggcacaacatggtgaatgtactgaatgccactgattgttcactttaaaatggtcaaacttatgtgaatttcacctccattaaaaaaaAAAAAAAAAGgaccagatgtggttgctcacacccataatctcaacactttggaaAAAGGTGAAAGATTTTTTTTCTTTTtttctttttttttatatacttaagttctagggtacatgtgcataatgtgcaggttggatacatagatatgcgcgtgccatgttggtttgctgcacccatcaacttgccatttacattaggtatttctcctaatgctatccctcccccagccccccacccactgacaggccccagtgtgtgatgttctctgccccatgtccaagcgttctcactgttcaattcccacctgtgagtgaaaacatgcagtgtt tggttttctgtctttgtgatagtttgctcagaaggatggtttccagcttcatccacgtccctgcaaaggacataaactcatcctttttaatgntcttcatagaatccccatggtaatatatgtgccaacattttcttaatccaagtctgtca + +a score=157011 +s hg18.chr1 23788 1709 + 247249719 ttgatggacatttgggttggttcaaagtctttgctattgtgaatactgccacaataaacatacatgtgcatgtgtctttatagtagcacgatttataatcctttgggtatatacccTAAGACctgggacgcatttaaagcagtgtgtaaagagacatttatagcactaaatgcccacaagagaCCTCTGCCTGAGAACGTGGGTTTCAGCCTAAGAGTTGTAATATGTGTGCCCATTCACAGGTGCTGCATCAGAGTCCCAGGTGGGAAGAAGGCAAGCATACACAAAAATGGTAAaaggcagaaaggagcccagtctcgttctttttaagaagttttcctaagaatctccacccagcgacttgctctcacatcttcttggccagcactggaccacacaactccttctagatacagaggagTCCTAGGATTCTATGAGAAAGAAGGGGAGGGTGGGCAAAGGGCAGCCAGCTGTGCAGCATCTGCTGGAGACACCTAACCCTTGGTGGAGGGGTTGTGGTGCTGGgagaaggctttctggacggtgtgacagcagagataaacttaaaggccaagtaggagttaccctggtgaagcagggcagggttacaagcattccagcaacatgaagcagcaGGAGtgttttaattaaaagaaggcagttgctgtaaccaactataaacaaataaaggcttaaacacaatggaagtttatttctcactaagggaacatccaaatccatgatactttaagtcagggacccaggttcctcccatctatggttctgccatcactaatctgggtcttccacaattgccgtgctccttggaggtgggaagagcaggcggaggacacgtgggaggttttagggacaagcctggaggcagcatgcgtcactcccatgcagagtccattggccaatgctggctccgatggccacat ctcactgcaggggcagctgggaaatacagtctggctgtctacccaggaggaagagcagccagtttctgctgCTGATGATCAGGAGGTGGAGAAAATGTTCAGTCAGGCAGGGAGTGGGAATAGACAAGACCACAAGCAGCTTGGTGCCTCTGAAAGGGAGAGGGGTGGAGGGGAGACTAGAGAGGTGGGTAGGAATACTGGATTCCACTGACCACGTGCTGGATGTCACGCTTAGCCCTCCTGCTCTGTGCCGGGTTAGGCACCTGGTGTTTTACGTACATAATCTCAATTCTGTGAGGGCATCCGACCTGTGGGAAAAGAGCTGTTTGTTTCAAATGCCAGTCCTGCTTCCTAACAAGTGTTTAGAGCTTAATCGTGTTCAAAAtacatatacaatgtttaatacttacaagaatttggtggggaaaatattaccatctttcccttttgtgattggagaaaaatgaggctttgaagggtttaagaacttgcccaaggtcggccaggtgcagtggctcatgtctataatcccaacactttgggaggctgaggtgggaggatcgcttgaggccaggagttcaagaccagcctgagcaacatagtgagactttgtctctataaaaaataaataaataaataaaaaCAACTTGTCCAAGGTCAGACAGGCAGCCTCTTAGTAAGCACACATATCCTCTATATTATACTACCTCTCATGGAGGATCT-CCTGTGTTCTACAAATAGTCTGGACTTGAGCCAGAATGTGTTATA +s panTro2.chr15_random 1999027 1707 - 3087076 ttgatggacatttgggttggttcaaagtctttgctattgtgaatagtaccacaataaacatacatgtgcatgtgtctttatagtagcacgatttataatcctttgggtatatacccTAAGACctgggacgcatttaaagcagtgtgtaaagagaaatttatagcactaaatgcccacaagagaCCTCTGCCTGAGAACGTGGGTTTCAGCCTAAGAGTTGTAATATGTGTGCCCATTCACAGGTGCTGCATCAGAGTCCCAGGTGGGAAGAAGGCAAGCATACACAAAAATGGTAAAAGGCAGAAAGGAGCCCAGTCTCATTCTTTCTAAGAAGTTTTCCTAAGAATCTCCACCCAGCGACTTGCTCTCACATCTTCTTGGCCAGCACTGGACCACACAACTCCTTCTAGATACACAGGAGTCCTAGGATTCTATGAGAAAGAAGGGGAGGGTGGGCAAAGGGCAGCCAGCTGTGCAGCATCTGCTGGAGACACCTAACCCTTGGTGGAGGGGTTGT-GTGCTGGgagaaggctttctggacggtgtgacagcagagataaacttaaaggccaagtaggagttaccctggtgaagcagggcagggttacaagcattccagcaacatgaagcagcaGGAGtgttttaattaaaagaaggcagttgctgtaaccaactataaacaaataaaggcttaaacacaatggaagtttatttctcactaagggaacatccaaatccatgatactttaagtcagggacccaggttcctcccatctatggttctgccatcactaatctgagtcttccacaattgccgtgctccttggaagtgggaagagcaggcggaggacacgtgggaggttttagggacaagcctggaggcagcatgcgtcactcccatgcagagtccattggccaatgctggctccaatggccacat ctcactgcaggggcagctgggaaatacagtctggctgtctacccaggaggaagagcagccagtttctgctgCTGATGATCAGGAGGTGGAGAAAATGTTCAGTCAGGCAGGGAGTGGGAATAGACAAGACCACAAGCAGCTTGGTGCCTCTGAAAGGGAGAGGGGTGGAGGGGAGACTAGAGAGGTGGGTAGGAATACTGGATTCCACTGACCACGTGCTGGATGTCACACTTAGCCCTCCTGCTCTGTGCCGGGTTAGGCACCTGGTGTTTTGCGTACATAATCTCAATTCTGTGAGGGCATCCGACCTGTGGGAAAAGAGCTGTTTGTTTCAAATGCTACTCCTGCTTCCTAACAAGTGTTTAGAGCTTAATCATGTTCAacatacatatacaatatttaatacttacaagaatttggcggggaaaatattaccatctttcccttttatgattggagaaaaatgaggctttgaagggtttaagaacttgcccaaggtcggccaggtgcagtggctcatgtctataatcccaacactttgggaggctaaggtgggaggatcgcttgaggccaggagttcaagaccagcctgagcaacatagtgagactttgtctctataaaaaataaataaatAAATAAAAAGAACTTGTCCAAGGTCAGACAGGCAGCCTCTTAATAAGCGCACATATCCTCTATA-TATACTACCTCTCGTGGAGGATCTCCCTGTG-TCTACAAATAGTCTGTACTTGAGCCAGAATGTGTTATA + +a score=465064 +s hg18.chr1 25497 5098 + 247249719 ATCCTGGGATCACGGCCAGTGGGCTTAGAAGAAGCCATCTCTTTCTCATGCCAAGATGAGGCTCCCCCAGATTTGCTCAGACTTACCTATAGTCAGCAGCATCGGGGGTCAGGAAAGACTTCACGAAGCCATAAATGCATCCTTCTCGGGGCAGCACCTGGCTCTCCCAGGTGAGAGAGGACTCCATTTTCACAGGCAGGCGTGGGAGCTTCAGCACCCATCTCTGGGCCCAGAATGACCCACTGGAGACCTTACAGCTCTCCTGTCACCCCCAATTCCTGCCCCCTCTGCAGCCTTGGAGGAGAATGGAGCTGAAGGGCCTGCCCTCTGTAGGGTGAGAAAGGGAGGCTAAAGCCTGGTGCCCACTGCCCTGGCTGCTCCGCATTGCAGGAGCTGCGCCCTTCCTTTCCTGGCACAGGGTCCACAGCCCCGAAACCCCGTTGTGTGGGAGCTGGGCACAGGGCAGCAGGACTAATCCTTGGAACAGCTCAGGGAGGATTATCCCAGCCACTGTCAGCAGCGGTGCAGCTGGCTCATTCCCATATAGGGGGAGGCCAGAGCCAGGGGCCTGCCACAAGTTGGA--AGGCTGGGGAAGGGGAGGCCAGCAGAGGTGTCCTGGCTGTGGGTGGCTCTGAGGGGGCTCTCAGGGGTGGGGCTAAATCTCAGGGGCAGGATTATGTAAATCAAACCAATTCTAGCCACAGATTTAAAGTTTGG---AAAAAAAAAAAAACCCAGCCTGGCGGAAAGAATTTAAATTATAAAAACTTAGAAGTATGGAATGTGAAATCATCCTGTAGGTGCTTATTTAACAACGAAATCATCCCGACACAATGAGCCATATGTGAAAAGTCATCCTTCCCCAACACATCCCCCAACAGGCACTCCTCAAGCCTCTCCCACCCAAGTGCTGGCATCCTCCCTGTCCTGCTTCACCTGAGACACCC CTTGTCTCATTAGACATGCAACTACGGGAGGGGTGACAGGAAGACAAGACACTATTTCCTCAGGCCCAGTTTGGTGTGGGGAGAAAGCCTCCTGATCCTGAAAGCAAGAATTTGACCAGAGCAGAAGTAATCAGTATGCAGATTGATTCTGTGGTATGTTAATGTTTATGCATAGATTATGAGGACCAGGTGAAAAGTGGGCCAGGGGAGCCAGATGTGTGTGTGAGTCATGGGTGGCTGAGATGAGGACAGGAGGGAAACTGGTTTGGAGGGTGCTGGCGATGGGGTGGGGGTGCCAGGAGGAAGGGAGGCTAGTTGTTTGAATGTCTGCATGAAAAAGCGGACGACAGCGGGGTCTGGGTGAATTCGGGCAACCATTTGGACCGTGGAGAAAACTGCCTGCGTGCGGCTGAGGACCTGCACTATTAATTTGTTTTTTAGCTAAGGCAAAGATAAATATAAAAACtgatactccacccagttaccagaaaacatttaggtatgtgtgagacaacttgggtatgtgaacctaccttttcaatgtaaattcagtgaaatctaagtgcagatcccatatttccaataaaaaggtaacatccaaactcagatgtcctatgagtataaaatacacaaagatcttctggacttagtatgaaaagggattttttttttgtcaggtacctcactagttatttttaaaataggattgcatgttgaaatgataatcttttggatatattgggttaaataaatttattattaaagttaatttcacttaaaaatgtttaatgtagctactagaaattttaaaattaagcatgttgctcaccttatgtttctattggacggctctCTCTAGATACAAAGGCTGCCAAGAGGGACCTCACTCTAGCTTCAGGGAGAAGAGAGGAATTAGCAAGGCCAAGCAGAGGCTCCTGAGGGCAGGGCCAAGGGCGGCTTGGTGGGGTGGGGATGGGATGCACAGAGAT AACTCCAACCCTTAAGAAGGTGTTTCCTAGAGCAGGCTGTGACCTGTCAGTTTATATACTGAGGCTTAGGAGCCTCTTGGATGCCCCCAGATCTGCACCCCTGAATTGCCCTGTGCCCCTGCCGTCTTTGTTCCTGTGCTGGCATAGTGGTCTCACCTCCGGCAGtatcaccaccactgggcacaagcttctccagcacagcaactgtgtcttatttctccttgtactcccagtgttcacaccatgctgcactcacagaagactcttcgttgatattttgtggacagagagaatGCCTGTGAGAGTGGGCTGAAGTGTGCGTTGGGCTCCAGAGACCTTAAGGAGGGGAGACCAGGTCCTGAGTAAAGTTGAAGGGGAGGGGCTGAGTCCTGCTAGCCAGGAGTCTCATCCCCTGGGGAAGTTCCAGGGACCCCTCAGAAGTGCAAGGGGACGGTGTTAGTGTTAGTCCAGTAACACAGCCCAGAGCCTGCcttccacgtgggtttgacaggagcctcctaactgctcttctgcttccatttttgccccttcagtctattctcaacagggaagccagaggcatccttaaccatgtcagatcatgtggctcctcagctcaaagccTCATCTCAGAGGAAAGCTCTGGTCCCTTAGAAATGGCCCAAGTGGTGACAGACAGACTCTAAGGtgagcagactgttgctagatatctgggctcggaggactcgccactgctcaaaggcagtgaggattttcgcactagaagctggaggacagggatccttgttaggtaggagcagaaagcttagaaaagtggtctcctgcagttacgtggcaaacacatcatgtaagtgataaattgggtatgcagttgaggagatttccaagtaaaatgttgaggatgctgcctggtttcttcttactgcttataatatagtgtgagagaagagagataaattgagaaagagactggtttttaaactgttaaa attgaatcaggacttgatgattttgaaaattgtcagtctccccacatggaaaaagatgctgaaattaacaaatggcttctgagcatgtggcatagggtgtaactgtacagtcttttgtgattatgcataaagatcaaaggatgggagtagcaatgagtcacacagaggtctgttgcaagagattacaagggtgtaccatgcagaacctctccaccaaaccttagggcccttgggaagcttcagtgagttaccctgggggccatcttggcaggagctgaaggtagaaaggtagagtttatctctaaaagattcatgggtatggctcttgacaaatcgactatgagccccaccgaaacccacagaggacaggcaaagggtttgggaaagctgtttcacccacagtgctggcagattggtctgtaggggacagagtgcaaaatgaaagaagactgtcagagaccccaaactctgctgtcaagaagaaggctgataaaactacttggctgcaaacacgtggatctttcgtgagaaaagaaggatgacccagaggcagaagcccagaaggcagagccaagagacatggaatcttcccacatcttaaaacctgtttagggaacaccagcatctgtccagctggatttcagaaccaccattccttcatccttcccctgctgcctctttctgaacagcaatgtctcaagctttacccaccattgtgtgttgcatatgtagggggcagatagcttgtatctttagttttccagatcagaggaacatccaaagaaatctgttctacacctaaacccgatttagatgagattcgggactgtgagcatgaagggatctcaagaggggtgaatgtgttttgcatgcacaagggacaggagtcttggggacagaggacaggctgtggtggcagatactaaggtgacccccacaacccccacctctgccattcacacccttgaataatccccttctctggttgt aagcagaacctgtggcttgcttatgaaggaggcggtatatatgtgattcatgtactgatcatattgtataagatcactggctggatgcagtggctcgtgcctgtaatcccaacactttgggaggctgaggcgggtggatcacctgaggtcaggagttcgagaccaggctggccaacatggcaaaaccccgcctctactaaaaatacaaaaattagccaggcatagtggtgcacgcctgtaatcacagctactcaagaggctgaagcaggagaattgcttgaactcaggaggtggaggtggcagtgagccaagatcgtgccactgcactccagcctcagtgacagagcgagactctgtctcaaaaaataaataaataaaatgttaagatcataacctgtctttctggggactctctcttgacgcctttgaagaagcaggctgccatgttgcaagctgcctcatggaggggatcagctgcgaggagctaagagccccctccagtcgatgctcaccaggaagctgaggtcttgtgtccagcaccctgcatagaactgaatgctgccatgtgagcttggaagcagagccatccacacagctgagccctagatgagaacccagtgctggctgacaccctgatggcaccttacagaggaccagttaggctgtgccaactcctgacctgcagaagctggggaacactgggtcgtatttgcagctgctggatttgtgggaatttgtcacacagcaatTGGGAGTCACACAGCCTGTGACGCCCCAACAATCCACAcctcctgcatctccctgccttcacttcctagcacactgccctgactccctctgccgcagccacgctggccctctgctgttcttcgaagccaccagggctgcattggctcccagcctttgctctcactgctttctcctcctagagagcccttcctgcatgtatatgtttgactcactcccttgcctccttcagacttgtactt aaaaatctcagtaagcatttccctggctacccttttaaaaattgcaacccacttccatccccatccccaacatgccatatttcctttcttcttcttccttcttcc--------tttttttttttttttttttgacacaggt----tctctgtcacccagcctggagtgcagtgacatgatctcggctcactgcaacctctgcctcccCAG +s panTro2.chrUn 134455 5104 + 58616431 ATCCTGGGATCACGGCCAGTGGGCTTAGAAGAAGCCATCTCTTTCTCATGCCAAGATGAGGCTCCCCCAGATTTGCTCAGACTTACCTATAGTCAGCAGCATCGGGGGTCAGGAAAGACTTCATGAAGCCATAAATGCATCCTTCTCGGGGCAGCACCTGGCTCTCCCAGGTGAGAGAGGACTCCATTTTCACAGGCAGGTGTGGGAGCTTCAGCACCCATCTCTGGGCCCAGAATGACCCACTGGAGACCTTACAGCTCTCCTGTCACCCCCAGTTCCTGCCCCGTCTGCAGCCTTGGAGGAGAATGGAGCTGAAGGGCCTGCCCTCTGTAGGGTGAGAAAGGGAGGCTAAAGCCTGGTGCCCACTGCCCTGGCCGCTCTGCATTGCAGGAGCTGCGCCCTTCCTTTCCTGGCACAGGGTCCACAGCCCCGAAACCCCGCTGTGTGGGAGCTGGGCACAGGGCAGCAGGACTAATCCCTGGAACAGCTCGGGGAGGATTAT-CCAGCCACTGTCAGCAGCGGTGCAGCCGGCTCATTCCCAGATA-GGGGAGGCCAGAGCCAGGGGCCTGCCACAAGTTGGAAGAGGCTGGGGAAGGGGAGGCCAGCAGAGGTGTCCTGGCTGTGGGTGGCTCTGAGGGGGCTCTCAAGGGTGGGGCTAAATCTCAGGGGCAGGATTATGTAAATCAAACCAATTCTAGCCACAGATTTAAAGCTTGGAGAAAAAAAAAAAAAACCCAGGCTGGTGGAAAGAATTTAAATTATAAAAACTTAGAAGTATGAAATGTGAAATCATCCCGCAGGTGCTTATTTAACAACGAAATCATCCCGACACAACGAGCCATATGTGAAAAGTCCTCCTCCCCCGACACATCCCCCAACAGGCACTCCTCACACCTCTACCACCCAAGTGCTGGCATCCTCCCTGTCCTGCTTCACCTGAGACACCC CTTGTCTCATTAGACATGCAACTATGGGAGGGGTGACAGGAAGACAAGACACGATTTCCTCAGGCCCAGTTTGGTGTGGGGAGAAAGCCTCCTGATCCTGAAAGCAAGAATTTGACCAGAGCAGAAGTAATCAGTATGCAGATTGACTCTGTGGTATGTTAATGTTTATGCATAGATTATGAGGACCAGGTGAAAAGTGGGCCAGGGGAGCCAGATGTGTGTGTGAGTCATGGGTGGCTGAGATGAGGACAGGAGGGAAACTGGTTCGGAGGCTGCTGGCGATGGGGTGGGGGTGCCAGGAGGAAGGGAGGC-AGTGGTTTGAATGTGTGCATGAAAAAGCGGAGGACAGCGGGGTCTGGGTGAATTCGGGCAACCATTTGGACCGTGGAGAAAACTGCCTGCGTGCGGCTGAGGACCTGAACTGTTAATTTGTTTTTTAGCTAATGCAAAGATAAATATAAAAACtgatactccatccagttaccagaaaacatttaggtatgtgtgagacaacttgggtatgtgaacctaccttttcaatgtaaattcagtgaaacctaagtacagatcccatatttccaataaaaaggtaacatccaaactcagatgtcctatgagtataaaatacacaaagatcttctggacttagtatgaaaagggatttttttttggtcaggtacctcactagttatttttaaaataggattgcatgttgaaatgataatcttttggatatattgggttaagtaaatgtattattaaagttaatttcacttaaaaatgtttaatgtagctactagaaattttaaaattaagcatgttgctcaccttatgtttctattggacagctctCTCTAGACACAAAGGCTGCCAAGAGGGACCTCACTCTAGCTTCAGGGAGAAGAGAGGAATTAGCAAGGCCAAGCAGAGGCTCCTGAGGGCAGGGCCAAGGGTGGCTTGGTGGGGTGGGGATGGGATGCACAGAAAT AACTCCAACCCTTAAGAAGGTGTTTCCTAGAGAAGGCTGTGACCTGTCAGTTTGTATACTGAGGCTTAGGAGCCTCTTGGATGCCCCCAGATCTGCACCCCTGAATTGCCCTGTGCCCCTGCCATCTTTGTTCCTGTGCTGGCATAGTGGTCTCACCTCCAGCAGtatcaccaccactgggcacaagcttctccagcacagcaactgtgtcttatttctccttgtactcccagtgttcacaccatgctgcactcacagaagactcttcggtgatattttgtggacagagagaatGCCTGTGAGAGTGGGCTGAA------GTTGGGCTCCAGAGACCTTAAGGAGGGGAGACCAGGTCCTGAGTAAAGTTGAAGGGGAGGGGCTGAGGCCTGCTAGCAAGCAGTCTCATCCCCTGGGGGAGTTCCAGGGACCCCTCAGAAGTGCAAGGGAACAGTGTTAGTGTTAGTCCAGTAACACAGCCCAGACCCTGCcttccacgtgggtttgacaggagcctcctaactgctcttctgcttccatttttgccccttcagtctattctcaacagggaagccagaggcatccttaaccatgtcagatcatgtggctcctcagctcaaagccTCATCTCAGAGGAAAGCTCTGGTCCCTTAAAAATGGCCCAGGTGGTGACAGACAGACTCTATGGtgagcagactgttgctagatatctgggctcggaggactcgccactgctcaaaggcagtgaggattttcgcactagaagctggaggagagggatccttattaggtaggagcagaaagcttagaaaagtggtctcctgcagttatgtggaaaacacatcatgtaagtgataaattgggtatgcagttcaggagatttccaagtaaaatgttgaggatgctgcctggtttcttcttactgcttataatacagtgtgagagaagagagataaattgagaaagagactggtttttaaactgttaaa attgaatcaggacttgatgattttgaaaattgtcagtctccccacatggaaaaagatgctgaaattaacaaatggcttctgagcatgtggcatagggtgtaactgtacagtcttttgtgattatgcataaagatcaaaggatgggagtagcaatgagtcacacagaggtctgttgcaagagattataagggtgtaccatgcagaacctctccaccaaaccttagggcccctgggaagcttcagtgagttaccctgggggccatcttggcaggagctgaaggtagaaaggtagagtttatctctaaaagattcatgggtatggctcttgacaaatcgactataagccccactgaaacccacagaggacaggcaaagggtttgggaaagctgtttcacccacagtgctggccgattggtctgtaggggacagagtgcaaactgaaagaagtctgtcagagcccccaaactctactgtcaagaagaaggctgataaaactacttggctgcaaacacgtggatctttcatgagaaaagaaggatgacccagaggcagaagcccagaaggcagagccaagagacatggaatattcccacatcttaaaacctatttagggaacaccagcatttgtccagctggatttcagaatcaccattccttcatccctcccctgctacctctttctgaacagcaatgtctcaagctttacccaccattgtgtgttgcatatgtagggggcagatagcttgtatctttagttttccagatcagaggaacattcaaagaaatctgttctacacctaaacccgatttagatgagattcgggactgtgagcatgaagggatctcaagaggggtgaatgtgttttgcatgcacaagggacatgagtcttggggacagaggacaggctgtggtggcagatactaaggtgacccccacaacccccacctctgccattcacacccttgaataatccccttctctggttgt aagcagaacctgtggcttgcttatgaaggaggcggtatatatgtgattcatgtactgaccatattgtataagatcactggctggacgcagtggctcatgcctgtaatcccaacactctgggaggctgaggcgggtggatcacctgaggtcaggagtttgagaccaggctggccaacatggcaaaaccctgcctctactaaaaatacaaaaattagccaggcatagtggtgcacacctgtaatcacagctactcaagaggctgaagcaggagaattgcttgaactcaggaggtggaggtggcagtgagccaagatcgtgccactgcactccagcctcagtgacagagtgagactctgtctcaaaaaataaataaataaaatgttaagatcataacctgtctttctggggactctctc--gacgcctttgaagaagcaggctgccatgttgcaagctgcctcatggaggggatcagctgcgaggagctaagagccccctccagtcaatgctcaccaggaagctgaggtcttgtgtccagcaccctgcatggaactgaatgctgccatgtgagcttggaagcagagccatccacacagctgagccccagatgagaacccagtgctggctgacaccctgatggcaccttacagagaaccagttaggctgtgccaactcctgacctgcagaagctggggaacattgggtcgtatttgcagctgctggatttgtgggaatttgtcacacagcaatTGGGAGTCACACAGCCTGTGATGCCCCAACAATCCACAcctcctgcatctccctgccttcacttcctagcacactgccctgactccctctgctgtagccacgctggccctctgctgttcttcaaagccaccaggcctgcatcggctcccagcctttgctctcactgctttctcctcctagagagcccttcctgcatgtatatgtttgactcactcccttgcctccttcagacttgtactt aaaaatctcagtaagcatttccctggctacccttttaaaaattgcaacccacttccatccccatccccaacatgccatatttcctttcttcttcttcCTTCTTCCTAtttttttttttttttttttttttttgacacaggttctctctctgtcacccagcctggagtgcagtgacatgatctcggctcactgcaacctctgcctccccag + +a score=356594 +s hg18.chr1 30595 3890 + 247249719 GCAagaaaaggggaggatgccaataaaggatgcattgatttgtatttactacagtggacatcaagggcacattcttgctgtggccatcaagagactgtataaattctatgacttgtagttgtcccacttaagaaacaaagaagctgtgcatttctttactggtctagagctgctctagggcattttctctacagcaattctaggtttccccaccttgtgagtttagctttttctatattcaaagaaaagtcctcagccagagattctcaggagctta-----tagaacaatccaaactcttgggaatattaagtggagaggggtacgtgcaagacaccaacagcACTAGAAACAGTCCACATCTTTCCATGCGTGGAGGAGTTTATGCTCTATGTGAGTTCACTCCATCATTAATTCTTCAAACACAAGAGTGTTAAAGGAACAAGAGTTAATGGGTCCTGTCATTACACTTGTTCCCAGGATGACATTCTTCATCTTCCTCTTCTACAACCTGTTCTATATTCCCCTCATGTTTATCCAGTGCTTCTGCTAGTCTAGTTCACTTCCAAAGACCCATGATTACCATGGCCCTGTCAGGCTGTAATTGCTGCAATTTCCAATTTACAATTGTCATCATCTATGGTTGATAAAGgtatagcaatatttctatttcctcatgataatgaaggtcaattacaactgccagtataataacttatttctttgtctgccaacctacatacacaaggaagccaaaatgacagggagctactaaaactttattcttattggaatgcttactatgtacccagaagaagcattctccctactccagcagagcttaatgctgtaggtccaggaagctcaaattctccaagggagttttagtgagaggagccactctcaccctctgcccttggtttacaaacctgtatattctaggaccca atatcttacaatgtccattggttcaaagtataacatgttaaagcacagagccccaactctgaaaagtaccatccctaaattggcatttagttgcacctttatatccacctttaaaagaaatatcttttaatgttctatcagactgatagattctgtttaatatagtatattatagcaccagtggatcatttggttgtatgcatattattgtaccttctctgctacaaaatatattcctttgtcctaaggtgtgttacaaagaacattaggcattctatgcatctttggatagtttaatggccaagacattgatggcaggagagtcaaagccacaggtggaaaacacatttatcccagtaagaacaaattgctattcttccactgtagagagggtaaacaatgtgccattacgttgccaattgaatgcctcaatcatgtcaagggctgaacatctatgactgtttctgaaaggtcaaacattcaacagaggctgtagctagaactgccttaatgataagagatcatgctgaattacccatgcaaaaccttaatacttgacacttatcactactttattcaagagcctattgtgcaagcataagtggctgagTCAGGTTCTCAACTCTGCTCATTAATACTATGCTTGGAGTATACAGTAAGATAAGAAACATAAATAAGAAGTGTACATTTGTTTCTTCCTGTTTTCTTCTGGCTATTGGATCAATTACATCCCATCTTAAGCTGACCCCTGTGTAATTAATCAATATCCGTTTTAAGCAGCAATCCATAGTTGTGCAGAAATTAGAAAACTGACCCACACAGAAAAACTAATTGTGAGAACCAATATTATACTAAATTCATTTGACAATTCTCAGCAAAGTGCTGGGTTGATCTCTATTTACGCTTTTCTTAAACACACAAAATACAAAAGTTAACCCATATGGAATGCAATGGAGGAAATCAATGACATATCAGATCTAGAAACTAAT CAATTAGCAATCAGGAAGGAGTTGTGGTAGGAAGTCTGTGCTGTTGAATGTACACTAATCAATGATTCCTTAAATTATTCACAATAAAAAAAAAGATTAGAATAG-TTTTTTTAAAAAAAAAGCCCAGAAACTAATCTAAGTTTTGTCTGGTAATAAAGGTATATTTTCAAAAGAGAGGTAAATAGATCCACATACTGTGGAGGGAATAAAATACTTTTTGAAAAACAAACAACAAGTTGGATTTTTAGACACATAGAAATTGAATATGTACATTTATAAATATTTTTGGATTGAACTATTTCAAAATTATACCATAAAATAACTTGTAAAAATGTAGGCAAAATGTATATAATTATGGCATGAGGTATGCAACTTTAGGCAAGGAAGCAAAAGCAGAAACCATGAAAAAAGTCTAAATTTTACCATATTGAATTTAAATTTTCAAAAACAAAAATAAAGACAAAGTGGGAAAAATATGTATGCTTCATGTGTGACAAGCCACTGATACCTATTAAATATGAAGAATATTATAAATCATATCAATAACCACAACATTCAAGCTGTCAGTTTGAATAGACaatgtaaatgacaaaactacatactcaacaagataacagcaaaccagcttcgacagcacgttaaaggggtcatacaacataatcgagtagaatttatctctgagatgcaagaatggttcaaaatatggaaaccaataaatgtgatatgccacactaacagaataaaaaataaaaatcatattatcatctcaatagatgcagaaaaagcattaacaaaagtaaacattctttcataataagacatcagataaaacaaattaggaatagaaggaatgtaccgcaacacaataaaggccatatataacaagcccacagctaacatcataatagtaaaatcatcacactggtaaaaaaaatgaaagcttttcctctaaggtcagaaataatataaaggttcccactcttgctat ttctattccatatcgtactaaaagtcctagccaggacaattagacaaaataaaaataaaaacacccaaattggaaagatagaagcaaacttttctgtttacagataacataatcttatatgtagaaaccccttaaaacttcagcaaaaaaaaaaaaaaaactacagagctagtaaattcagtgaagttgcagaatacaaaatcaacatacaaaaatcagtagtgtctctatacactaataaggacttaacagagaaagaagttaagaaaacaataccactaacaatagaatccaaaaaataaaatacttaggaataaattttaccaaacatctgtacactaaaaactataaaacattgaaaaaagaagttgaataagacacatataaatagaaagctatctcatgttaatagattagaaaaagtaatattgttaagatgtcctcactacttaaagcaatttatagatctaatgcatttattgcaatctcttcaaaatcccaaaggtatttttgacagaaataaaaaaaaaattctaaaatatgcatgaaaccacaaaagactgtgaatagctaaagcaatcttgagcaagatgaacaacactggaagcatcacactaccttatttcaaaatctactacaaagctatagtgatcaaagcaacatgatactgtcataaaaacacacagataaacctatggaatggaataaagagcacagaaataagtccacacatttacattcaattgattttcaacaacaatgtcaagaagacaatggggaaaagacaatctcttcaataaatgatgctggaaaaactatatatccacatgcagaagaatgcagttgaatcctgatttcataccatatgcaaaattcaactggaaatggattaaatacaaatttaaaacatgaaatggtataactattagaacaaaacatagaaaatattcttcctgacattggtttgggc +s panTro2.chrUn 9695081 3894 + 58616431 gcaagaaaaggggaggatgccaataaaggatgcattgatttgtatttactacagtggacatcaagggcacattcttgctgtggccatcaagagactgtataaattctatgacttgtagttgtcccacttaagaaacaaagaagctgtgcatttctttactggtctagagctgctctagggcattttctctacagcaattctaggtttccccaccttgtgagtttagctttttctatattcaaagaaaagtcctcagccagagattctcaggagcttagagtatagaacaatccaaactcttgggaatattaagtggagaggggtatgtgcaagacaccaacagcACTAGAAACAGTCCACATCTTTCCATGCATGGAGGAGTTTATGCTCTATGTGAGTTCACTCCATCATTAATTCTTCAAACACAAGAGTGTTAAAGGAACAAGAGTTAATGGGTCCTGTCATTACACTTATTCCCAGGATGACATTCATCATCTTCCTCTTCTACAACCTGTTCTATATTCCCCTCATGTTTATCCAGTGCTTCTGCTAGTCTAGTTCACTTCCAAAGACCCATGATTACCATGGCCCTGTCAGGCTGTAATTGCTGCAATTTCCAATTTACAATTGTCATCATCTATGGTTGATAAAGGTATAGCAATATTTCTATTTCCTCATGATAATGAAGGTCAATTACAACGGCCAGTATAATAACTTATTTCTTTGTCTGCCAACCTACATACACAAGGAAGCCAAAATGACAGGGAGCTACTAAAACTTTATGCTTATTGGAATGCTTACTATGTACCCAGAAGAAGCATCCTCCCTACTccagcagagcttaatgctgtaggtccaggaagctcaaattctccaagggagttttagtgagaggagccactctcaccctctgcccttggtttacaaacctgtatattctaggaccca atatcttacaatgtccattggttcaaagtataacatgttaaagcacagagccccaactctgaaaagtaccatccctaaattggcacttagttgcacctttatatccacctttaaaagaaatatcttttaatgttctatcagactgatagattctgtttaatatagtatattatagcaccagtggatcatttggttgtatgcatattattgtaccttctctgctacaaaatatattcctttgtcctaaggtgtgttacaaagaacattaggcattctatgcatctttggatagtttaatggccaaggcattgatggcaggagagtcaaagccacaggtggaaaacacatttattccagtaagaacaaattgctattcttctactgtagagagggtaaacaatgtgccattatgttgccaattgaatgcctcaatcatgtcaagggctgaacatctatgactgtttctgaaaggtcaaacattcaacagaggctgtagctagaactgccttaatgataagagatcatgctgaattacccatgcaaaaccttaatacttgacacttatcactactttattcaagagcctattgtgcaagcataagtggctgagTCAGGTTCTCAACTCTGCTCATTAATACTATGCTTGGAGTATACAGTAAGATAAGAAACATAAATAAGAAGTGTACATTTGTTTCTTCCTGTTTTCTTCTGGCTATTGGATCAATTACATCCCATCTTAAGCTGACCCCAGTGTAATTAATCAATATCCATTTTGAGCAGCAATCCATAGTTGTGCAGAAATTAGAAAACTGACCCACACAGAAAAACTAATTGTGAGAACCAATATTATACTAAATTCATTTGACAATTCTCAGCAAAGTGCTGGGTTGATCTCTATTTACGCTTTTCTTAAACACACAAAATACAAAAGTTAACCCATATGGAAAGCAATGGAGGAAATCAATGACATATCAGATCTAGAAACTAAT CAATTAGCAATCAGGAAGGAGTTGTGGTAGGAAGTCTGTGCTGTTGAATGTACACTAATCAATGATTCCTTAAATTATTCACAAT--AAAAAAAGATTAGAATACTTTTTTTTTTAAAAAAAGCCCAGAAACTAATCTAAGTTTTGTCTGGTAATAAAGGTATATTTTCAAAAGAGAGGTGAATAGATCCACATACTGTGGAGGGAATAAAATACTTTTTGAAAAACAAACAACAAGTTGGATTTTTAGACACATAGAAATTGAATACGTACATTTATAAATATTTTTGGATTGAACTATTTCAAAATTATACCATAAAATAACTTGTAAAAATGTAGGCAAAATGTATATAATTATGGCATGAGGTATGCAACTTTAAGCAAGGAAGCAAAAGCAGAAACCATGAAAAAAGTCTAAATTTTACCATATTGAATTTAAATTTTCAAAAACAAAAATAAAGACAAAGTGGGAAAAATATGTATGCTTCATGTATGACAAGCCACTGATACCTATTAAATATGAAGAATATTATAAATCATATTAATAACCACAACATTCAAGCTGTCAGTTTGAATAGACaatgtaaatgacaaaactacatactcaacaagataccaacaaaccagcttcgacagcacgttaaaggggtcatacaacataatcgagtagaatttatctctgagatgcaagaatggttcaaaatatggaaatcaataaatgtgatatgccacactaacagaataaaaaataaaaatcatattatcatctcaatagatgcagaaaaagcattaacaaaagtaaacattctttcacaataagacatcagataaaacaaattaggaatagaaggaatgtaccgcaacacaataaaggccatatataacaagcccacagctaacatcataatagtaaaatcatcacaatggtaaaaaaaatgaaagcttttcctctaaggtcagaaataatataaaggtgcccactcttgctat ttctattccatatagtactaaaagtcctagccaggacaattagacaaaataaaaataaaaacacccaaattggaaagatagaagcaaacttttctgtttacagataacctaatcttatatgtagaaaccccttaaaacttcagaaaaaaaaaaaaacaaactacagagctagtaaattcagtgaagttgcagaatacaaaatcaacatacaaaaatcagtagtgtctctatacactaataaggacttaacagagaaagaagttaagaaaacaataccattaacaatagaatccaaaaaataaaatacttaggaataaattttaccaaacatctgtacactaaaaactataaaacactgaaaaaagaagttgaataatacacatataaatagaaagctatctcatgttaatagattagaaaaagtaatattgttaaaatgtcctcactacttaaagcaatttatagatctaatgcatttattgcaatctcttcaaaatcccaaaggtattttttacagaaataaaaaaaaaattctaaaatatacatgaaaccacaaaagactgtgaatagctaaagcaatctagagcaagatgaacaacactggaagcatcacactaccttatttcaaaatctactacaaagctgtagtgatcaaagcaacatgatactgtcataaaaacacatagataaacctatggaatggaataaagagcacagaaataagtccacacatttacattcaattgattttcaacaacaatgtcaagaagacaatggggaaaagacaatctcttcaataaatgatgctggaaaaactatatatccacatgcagaagaatgcagttgaatcctgatttcataccatatgcaaaattcaactcgaaatggattaaatacaaatttaaaacatgaaatggtataactattagaacaaaacatagaaaatattcttcctgacattggtttnnnc + +a score=9778 +s hg18.chr1 34485 118 + 247249719 catcatttttctgatatgactctaaaagcacaggcaaaaaaagaaaaaatagacaaatgagactatgccaaattaaaaaatttctaacaacaaaagaaacgatcaatagagtgaaaaa +s panTro2.chrUn 9699210 118 + 58616431 catcatttttctgatatgactctaaaagcacaggcacaataagaaaacatagacaaatgagactatgccaaattaaaccttttctaacaacaaaagaaacgatcaatagagtgaaaaa + +a score=709815 +s hg18.chr1 34612 7875 + 247249719 ttgaatgggagaaatatttgcaaactactcatccaaccggggattgatatccagaatatacaagtaacacaaatatgtcaaaagtaaa-------ataaataaataaataaataaataaataaattaaataaattatttaaaaatcggcagaggacaggaatagacatttctcaggagacaacatacaaagggccacagatacatcaaaaaatgctcaacatcactatttgtcagggaagtactaattaaaaccaaaatgagatgtcccctcaaacctgttagaatggctattatcaaaaagatgaaagatagcaactatcagagaggatgatagaaaagggaacccttgcatcatgtacaaattaaaaatagaactatcacatgatccaagaatcctacttctgggtatatagccaaaggaattgaaatcaatatgtcaaagggatatctgcactcctatgttattgcagcatgttcacaatggccaagatatagaatcaacctaactgttcatagacagatgaatggataaatgaaatgtgatatggaaaattattcagccttaaaaacagtaggaaattctgtcatttgagacaacgtggatgaacctagaggacattaagctaagtgaaataagctagacacagaaagacaaatattgcatgatctcacttagaatctaaaaaatctgaactcatagaagcagagaatagtatgatggttactagggttatctggcagggagaggatgaggaaatgggacattgttaataaaaggaaaaaaa-ttcaattagtaggattacattcaggggacccaatatacgacatgttgactgtaattaataatgtattgtatgcttgaaaattgctaatacagtatattgtaaatgttaatatgaggtaatatatgtgttaattaacttgatttattcattcaacaacatac acatatattaaaacatcacactgtattccacaaatatatataatttttgtcaattaaaaaaTAATTTTTAAAAATGAGAAACAAAAAAGCTGACATTTTCAGATTAAAAAAATTATACAGAAGAATTAATTCATTAAAGTAAAAACAAATGTGGGAAAATGGTTTTTAAATATAATTTAAACCAAATTTAAAATAAGCATATaaagactatggacaaaacaagaaatccaaataaaaaataaacatatgaagaatattcaaactcactttttatcaaagaaatgtaaattTTAAAATATAGCATTGCTATTGTGTTTTCATAAATAATAATATATCATGGATGAGCCTGTGAGGAAACAGACACTCATACTCTGCAAAGCAATGACTAAgataattatgtcagatcatgaattacgttaattagcttgatggtggtcactgtttcacgataaatatacatatgtatcaaaacatcacattacacaccataaagatatataacttgttatCAAAAAGAAATATAGCAGttaaaatttaaaatttttaaaaaaCGTCTTTTTGAGGTTCGTACCTCACTTAAGTCACACTGTTCAAAATATTCATGCACTCATTTCTCTCATTCATGTGTTAATGTACAGGGTACGGGCCACTATAAATTCCTTCAGCAACTGGAAAGGAAACTTTATGTACTGAGTGCTCAGAGTTGTATTAACT-TTTTTTTTTTTTtgagcagcagcaagatttattgtgaagagtgaaagaacaaagcttccacagtgtggaaggggacccgagcggtttgccCAGTTGTATTAACTTCTAATTCAACACTTTAAGATTCTTAGCATTATTGCAGACAACATcagcttcacaagtgtgtgtcctgtgcagttgaacaagatcccacacttaaaaggatcctacactttttttaatgctctgctgtttctgccttgaaattcttaacaatttttttaaccaaagtcct cacaaattcagtttacattagccctgcaatcatgtagacatcctgATTCCAGACAATGTGTCTGGAGGCAGGGTTTACAGGACTTCAAGAACCTTACCTTCTCAACTTTCATCTGCATCTTTACTCCCAACTATATATGAAGATGATGAAGATAGATATGGATGGTGCTTCTACCATACCCTCTTCCTCTGCCAAACTTCCTTGATCTAGGATAAggtcagtaaacttcttccgtaaaaggccaaaagtaaatattataggctctacaggccctagagtgtctgtcataactactcaactctt--attgtagcataaaaactgtcaacagacaatacagaaacaaatgagtgtgactgggttccagtgaaactttatttacaaaagatttgtcccatgagtcaaatttaccacctccAGATCTAGAGAAACAGTTTTGAGCCCTTTTATTTTGCTCAACAGTTAAGCATGGCTCCATGTCCCTTATATTTAGTCAGAACTCGGTATGTTTTAAGGAAAGAATGGTTACACGAAGACATACATTCATTCATTTATACAACACATTTTCAGTGTTGAATGATAAATTTTGGAATAGTTAACAGATGATAAAAGTGTTGTTTTCAGTCATCCCTATCCAATGAAGTAAAAAAAAAA-GTGTTGAATGGGAAGAAATCAAGAATAGTTATACGAATATCACCATTGCATTAAAGCTCTCTTCCTTGTTTCTAAAAGAATATCTTGACACACATTAAGCTCACTGACCCCCACACCATGAATGAGGGCATCTTCAACAATGGTGGATGACGTCTTAGTTTCCCTCAACTCAGTTAATCTAAGTAAGCTCATGGTATCACTTTCCTGTCCTAGAGGGAACATATTTCCTGCATTTTTCTTTTTTT-CCTTACTTTCCATCACCAAGTAACTCTTCTGATATTTTTTCTCTTGAGAAAATTAATATGACTCATAGATCTGGTTCCCAAGAGAAATC AATGGAGGCCTGGTTACAAGGATCTAAGAAGCATCAATGGGTCACTAACATCTAGTGGTACTAATTAACTCTGTTAATCATTGGGAAGAAAATGTATATATACTTTTGTCTTGGAGCTGATTCTACTAGAAAGCAGAAATCAAAA-TGATCAGTTTCCCAGTGTCACTACTGCACACCCTGGAACAGAACAGGTAGGTCAGAAAAACGCTCCCAAAGTTTAGCAATGTCAAGGCAATCTCTCTCTTCTTACATTTCCCTTCAACCTTCTATCTCCTCCACTTTTCTGTTTTCCTCCTATCTCCAATTATTTCAATCCTCAGAGCATTATTCTTACAATCTTAATCACTAAATTATATTACACCCGTTAAAGGAGAGATTTCTAAATGCATTGACATTTGTACTGTCTCTCTTTGGAGAATTAGTATTATAAGGATCTGTTATCTCTTGTCACCTTCCTTATGTCATATGATATGTCACATTTCCCACTGCGGAGACCAAACATGTTCACATCGTGTGCGTTCCATTTTCCTAATGGAAAGTGGGGGGAAGTGATTTTCTGTCCTCATATAGAGAATGCTGGGGCCATTCCCTCTGTATGCCATATTTGATAAAGCATTTGATAATCTTAGTCAATGCCTGGGCCAAGAATTAAAGGGGTAATTATCAGAATGAAAATGGTTTAATGAAACTGTGTCTATCAGTTCTGAAAAGGGCCTCTATCACAATGAACTAAGGTAGTTATGAATAGAGCTAAaacttaggcaacaccatcctggacataggaacgggcaaagatttcatgacaaagacacggaaaccaatcacaacaaaagcaaaaattgagaagtggaatctaataaaacaatagcttctgcacagcaaaagaagctaccaacaaagtaaacagacaacctacagaatgggagaaaatatttgccaactgtaagtctgacaaaaatctaatatctggcagctataaggaacttaa atttacaagacaaaaacaaccccattaaaaagtgggcaaagaacatgaatagacactctcaaaagaagatatacatatggttaacaagcatatgaaaaaaaagctcaatatactgagcattagagaaatgcaaatcaaaaccatattgagatatcatctcataccaggcagaatggctattattaaaaagtcaaaaataacagatatcggtgaggttacagagaaaagggaacacttatacactgttggtgggactgtaaattatttcaaccattgtggaaagcagtatgggatggcgattcctcaaaaagccaaaaacagaactatcattcaacccagcaattccattactgggtatatacccagaagaatataaatcgttctaccataaagacgcatgcatgagaatgttcattgcagcactactcacaatagcagagacatggaatcaacttaaatgcccatcagtaacagactggataaagaaagtgtggtacagatacaccgtggattactatgcagccataaaaaagaacaagatcatgtctttgacaggaacatggatggagctggaggctactatccttagcaagctaaggcaggaacagaaatccaaataccgcatgttctcacttatgagcgtgagataaatgatgagaacttgtaaacacaaagaaggaaacaacaggcagtggggtctacttgaggacgacgggaagagggagaggagcagaaaagataactactgactaccgggcgctacctgggggatgaaacaatctgtacaacgaacccccaggacatgagtttacctatgtaacaaaccttcacgtgtacccccgaacctaaaataaaagtcaaaaagaaaAAGAAAA------AAAGAAAAATCCATGCATATGATACATCAGTTAACAAGGCACTGGTGAAATTAATTTTAAGTATTATTGTCTCTTTGTGTTTTTGGTCTCAGAAAAGTTACGATTTCC CTTAGTTCCTTAGGGCAGAGAGAATCTTCAATCACTGAAGTCAGGAGACACACATTCTATCTGATTTTCTACATTATCTGTTTGAAAAGGTTACCCACTTATTAGTGTTAAAGCCAAGATATCCAGCAAGGATAGCAACCAACTCTTAAGGTACTCTCCCTTAGGAGGATTCCTGATTCTTTAATGTTTTCTAAAAAAGCAAAACAAA----CAAACAAACAAAACAAAACACTAAATGTTTTCTCTTTCAACTTATTTGAATACACTCTTTTCTCACTGCTCTGAGCATGAATTCAATATTTCAGGGCAAACTAACTGAATGTTAGAACCAACTCCTGATAAGTCTTGAACAAAAGATAGGATCCTCTATAAACAGGTTAATCGCCACGACATAGTAGTATTTAGAGTTACTAGTAAGCCTGATGCCACTACACAATTCTAGCTTTTCTCTTTAGGATGATTGTTTCATTCAGTCTTATCTCTTTTAGAAAACATAGGaaaaaattatttaataataaaatttaattGGCAAAATGAAGGTATGGCTTATAAGAGTGTTTTCCTATTGTTTTCAGTGTAGGACTCACTGTTCTAAATAACTGGGACACCCAAGGATTCTGTAAAATGCCATCCAGTTATCATTTATATTCCCTAACTCAAAATTCATTCACATGTATTCATTTTTTT-CTAAACAAATTAGCATGTAGAATTCTGGTTAAAATTTGGCATAGAACACCCGGGTATTTTTTCATAATGCACCCAATAACTGTCATTCACTAATTGAGAATGGTGATTTAACAAAGGATAATAAAGTTATGAAACCAATGCCACAAAACATCTGTCTCTAACTGgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtAAGAGGGAGAGAGAGAAAATTTCACTCCCTCCATAAATCTCACAGTATTCTTTT-CTTtttcctttcctttccttgctcttctttctctcctattgctttcctt tcatttccttCTCATAAAAGAAAAATAACAATATAGAAAATAACAAAATATAGATGGTCAACCTTTTTAATATTAAGGTTACCTAAAATGCCATTATCCAAAGTGGTTCTCTAGAGATGCTGATGTATATACTTACATATTTTACAGTGTATTCAAATAAAGAGTATATTACATAAGACATATCCTTTTGTAACCAACTTTTGTCATTAACAATTTACTGGACTTGTCAACAAACCTAAATCTGTATCGTCTATAATGGCTACGTTCATTTTGGTATGAATCTTAATTACCCCTTTCTGCATTATTTAATGATTTTCTCATATGTCACTCTTAAATGTACTTCTAATTTTTCACTTTACATCACATAATGAATGGATCCAAATATGTTATGGATAGATATCTTCAAACTTTCTACTTACAAGTAGTGATAATAACAGATGTTCTCTCTAAAGTGTAGTTGGTATCAATTTTACTGACCTTTAAAAATATCTTAATGGGACAAAGTTCAAATATTTGATGACCAGCTATCGTGACCTTTATCTCTGTGGCTCTGTGGGCCTGTAGTTTTTACGTGCTTTTAGTGTATCATGATTAAATATTTTGTTTTAGTAAAGACACCATTATTTCCCAACTTCATATTCAAATTGTCAAAGGTATTAATCCTAGAGCAGAACTCTCAAAAGCACCAACTCTGATTCCTAACAAAGCATGGAAAAGCCCTCTCTCTGAGTTTCAGATACTCTTTTTTGTGGGGGTTGAGTTTCACTTTATTTAAAGTGAGTCTTAATCCTCCAACAAGTCAACAAGTGATTGGCTGGAATCACACGTATTGGAAAACCAGCGGAAGAGTAAGTCTTTGTATTTTATGCTACTGTACCTCTGGGATTAATTGCTCTTTCCCTCATTGGCCAGTCACTCTT-AGTGTGTGATTAATGCCTGAGACTGTGTGAAGTAAGAGATGGATCAGAggccgggcgcgggggctcgc gcctgtcatcccagcactttgggaggccgaggcgggcggatcacgaggtcaggagatcgagaccatcctggctaacacggggaaaccccgtctccactaaaaatacaaaaagttagccgggcgcggtggcgggcgcctgcggtcccagctgctggggaggccgaggcgggagcatggcgggaaccgggaggcggagcctgcagtgagccgagatggcgccaccgcactccagcctgggcgacccagcgagactccgcctcaaaaaaaaaaaaagaaGATTGATCAGAGAGTACCTCCCCTAAGGGTACATGCAGATAAATACAGTTAAGGCGATTAACATTTCAAATAC-GGTGACTGTTTCTTACGTGGACGACGTTGTGTTGAACATGGGTGAGTAAGACTGAAGCAGCCGTAATTACTGCACGATGCGCATGGTAAAGAAGCACTCCGTTAGGGAAATTATATTCTTTGCCCCTCTAATCCTTCACTCCACCTGCCATATTCCCACATGATTTTTTTCTTTGCTGTTCTTGTCTAATTGttattaataattaataaataaCTTATGATCTAATTGTTATTAA----TAATAACTTATCATCACATGatttattaataaattaataaataacttattatCACCGCATTTCCCCAATTCATTTATCTTTCTTTCATTTTCTCTCTTTGTGTGTTTTCTGTCTTCATATTTCAGCACTTGCCACATATTTCCCACAAAATCATTTATGGTCAAACAACACTTCAACGTGTAGCATTTGTATTTCTCAATTCTTCCTCACTTTCTTCCTTCAGAATACTAAAGCTTCTTCTCTACTGACTGAGTCAATGGCCAATGGATAGAGTAAATAATTCTGCGGTATCTAAATTTGTATTGATTGGACTTTCAAGCTCTTGGGAGATGCATCTTTTTCTTTTTTGGTTCTTCTCTGTGTTCTACATGGGAATTATCCTGGAAAATCTCTTCATTGT GTTCACAGTAATTATTGACTCTCATTTAAATTCCCC +s panTro2.chrUn 9699336 7904 + 58616431 ttgaatgggagaaatatttgcaaactactcatccaactggggattgatatccagaatatacaagtaacacaaatatgtcaaaataaaataaataaataaataaataaataaataaataaataaataaaataaattatttaaaaatcggcagaggacaggaatagacatttctcaggagacaacatacaaagggccacagatatatcaaaaaatgctcaacatcactatttgtcagggaagtactaattaaaaccaaaatgagatgtcccctcaaacctgttagaatggctattatcaaaaagatgaaagatagcaactatcagagaggatgatagaaaagggaacccttgtatcatgtacaaattaaaaatagaactatcacatgatccaagaatcctacttctgggtatatagccaaaggaattgaaatcaatatgtcaaagggatatctgcactcctatattatggcagcatgttcacaatggccaagatatagaatcaacctaactgttcatagacagatgaatggataaatgaaatgtgatatggaaaattattcagccttaaaaatagtaggaaattctgtcatttgagacaacgtggatgaacctagaggacattaagctaagtgaaataagctagacacagaaagacaaatattgcatgatctcacttagaatctaaaaaatctgaactcatagaagcagagaatagtatgatggttactagggttatctggcagggagaggatgaggaaatgggacattgttaataaaaggaaaaaaaattcaattagtaggaatacattcaggggacccaatatatgacatgttgactgtaattaataatgtattgtatgcttgaaaattgctaatacagtatattgtaaatgttaatatgaggtaatatatgtgttaattaacttgatttattcattcaacaacatac acatatattaaaacctcacactgtattccacaaatatatatactttttgtcaattaaaaaaTAATTTTTAAAAATGAGAAACAAAAAAACTGACATTTTCCGATTAAAAAAATTATACAGAAGAATTAATTCATTAAAGTAAAAACAAATGTGGGAAAATGGTTTTTAAATATAATTTAAACCAAATTTAAAATAAGCATATaaagacaatggacaaaacaagaaatccaaataaaaaataaacatatgaagaatattcaaactcactttttatcaaagaaatgtaaattttaaaatatagcattgctattgtgttttcataaataataatatatcatggatgagcctgtgaggaaacagacactcatactctgcAAAGCAATGACTAAgataattatgtcagatgatgaattatgttcattagcttgattgtggtcactgtttcatgataaatatacgtatgtatcacaacatcacattacacaccataaagatatataacttgttatCAAAAAGAAATATAGCAGttaaaatttaaaattttttaaaaatCTCTTTTTGAGGTTCGTACCTCACTTAAGTCACGCGGTTCAAAATATTAATGCACTCATTTCTCTCATTCATGTGTTAATATACAGGGTACGGGCCATTATAAATTCCTTCAGCAACTGGAAAGGAAACTTTATGTACTGAGTGCTCAAAGTTGTATTAACTATTTTTTTTTTTTtgagcagcagcaagatttattgtgaagagtgaaagaacaaagcttccacagtgtggaaggggacctgagcggtttgccCAGTTGTATTAACTTCTAATTCAACACTTTAAGATTCTTAGCATTACTGCAGACAACAccagcttcacaagtgtgtgtcctgtgcagttgaacaagatcccacacttaaaaggatcctacactttttttaatgctctgctgtttctgccttgaaattcttaacaatttttttaaccaaagtcct cacaaattcagtttacattagccctgcaatcatgtagacatcctgATTCCAGACAATGTGTCTGGAGGCAGGGTTTACAGGACTTCAAGAACCTTACCTTCTCAACTTTCATCTGCATCTTTACTCCCAACTATATATGAAGATGATGAAGATAGATATGGATGGTGCTTCTACCATACCCTCTTCCTCTGGCAAACTTCCTTGATCTAGGATAAggtcagtaaacttcttccgtaaaaggccaaaagtaaatatcatagactctacaggccctagagtgtctgtcataactactcaactcttttattgtagcataaaaactgtcaacagacaatacagaaacaaatgagtgtgactgggttccagtgaaactttatttacaaaagatttgtcccatgagtcaaatttgccacctccAGATCTAGAGAAACACTTTTGAGCCCTTTTATTTTGCTCAACAGTTAACCATGGCTCCATGTCCCTTACATTTAGTCAGAACTCAGTATGTTTTAAGGAAAGAATGGTTACACGAAGACATACATTCATTCATTTATACAACACATTTTCAGTGTTGAATGATAAATTTCGGAATAGTTAACAGACGATAAAAGTGTTGGTTTCAGTCATCCCTATCCAATGAAGTAAAAAAAAAAAGTGTTGAATGGGAAGGAATCAAGAATAGTTATATGAATATCACCATTGCATTAAAGCTCTCTTCCTTGTTTCTAAAAGAATATCTTGACACACATTGAGCTCACTGCCCCCCACACCATGAATGAGGGCATCTTCAACAATTGTGGATGACATCTTAGTTTCCCTCAACTCAGTTAATCTAAGTAAGCTCATGGTATCACTTTCCTGTCCTAGAAGGAACATATATCCTGCATTTTTCTTTTTTTTCCTTACTTTCCATCACCAAGTAACTCTTCTGATATTTTTTCTCTTGAGAAAATTAATATGACTCATAGACCTGGTTCCCAAGAGAAATC AATGGAGGCCTGGTTACAAGGATCTAAGAAGCATCAATGGGTCACTAACATCTAGTGGTACTAATTAACTCCGTTAATCATTGGGAAGAAAATGTATATATACTTTTGTCTTGGAGCTGATTATACTAGAAAGCAGAAATCAAAAGTTATCAGTTTCCCAATGTTACTACTGCACACCCTGGAACAGAACAGGCAGGTCAGAAAAATGCTCCCAATGTTTAGCAATGTCAAGGCAATCTCTTTCTTCTTACATTTCCCTTCAACCTTCTATCTCTTCCACTTTTCTGTTTTCCTCCTATCTCCAATTATTTCAATCCTCAGAGCATTATTCTTACAATCTTAATCACTAAATTATATTACGCCCGTTAAAGGAGAGATTTCTAAACGGATTGACATTTGTACTGTCTCTCTTTGGAGAATTACTATTATAAGGATCTGTTATCTCTTGTCACCTTCCTTATGTCATATGATATGTCACATTTCCCACTGCGGAGACCAAACATGTTCACATCGTGTGCATTCCATTTTCCTAATGGAAAGTGGGGGGAAGTGATTTTCTGTCCTCATATAGAGAATGCTGGGGCCATTCCCTCTGTATGCCATATTTGATAAAGCATTTGATAATGTTAGTCAATGCCTGGGCCAAGAATTAAAGGGGTAATTATCAGAATGAAAATGGTTTAATGAAACTGTGTGTATCAGTTCTGAAAAGGGCCTCTATCACAATGAACTAAGGTAGTTATGAATAGAGCTAAaacttaggcaacaccatcctggacataggaacgggcaaagatttcatgacaaagacacgaaaaccaatcacaacaaaagcaaaaattgagaagtggaatctaataaaacaatagcttctgcacagcaaaagaagctaccaacaaagtaaacagacaacctacagaatgggagaaaatatttgcaaactataagtctgacaaaaatctaatatctggcagctataaggaacttaa atttacaagacaaaaacaaccccattaaaaagtgggcaaagaacacgaatagacactctcaaaagaagatatacatatggttaacaagcatatgaaaaaaaagctcaatatactgagcattagagaaatgcaaatcaaaaccatgttgagatatcatctcacaccaggcagaatggctattattaaaaagtcaaaaataacagatactggtgaggttgcagagaaaagggaacacttatacactgttggtgggactgtaaattatttcaaccattgtggaaagcagtatgggatggcgattcctcaaaaagccaaaaacagaactatcattcaacccagcaattccattactgggtatatacccagaagaatataaatcgttctaccataaagacgcatgcatgagaatgttcattgcagcactgctcacaatggcagagacatggaatcaacttaaatgcccatcagtaacagactggataaagaaaatgtggtacagatacaccgtggattactatgcagccataaaaaagaaccagatcatgtctttgacaggaacatggatggagctggaggctattatccttagcaaactaaggcaggaacagaaatccaaataccagatgttctcacttatgagcgtgagataaatgatgagaacttataaacacaaagaaggaaacaacaggcattggggtctacttgaggacgatgggaagaggcagaggagcagaaaagataactattgactactgggcgctacctgggggatgaaataatctgtacaacgaacccccaggacatgagtttacctatgtaacaaaccttcacatgtacccccgaaactaaaataaaagtcaaaaaaaaaAAAAAAAGAAAAAAAAGAAAAATCCATGCATATGATACATCAGTTAACAAGGCACTGGTGAAATTAATTTTAAGTATTATTGTCTCTTTGTGTTTTTGGTCTCAGAAAAGTTAGGATTTCC CTTAGTTCCTTAGGGCAGAGAGAATCTTCAATCACTGAAGTCAGGAGACACACATTCTATCTGATTTTCTACATTATCTGTTGGAAAAGGTTACCCACTTATTAGTGTTAAAGCCAAGATATCCAGCAAGGATAGCAACCAACTCTTAAGGTACTCTCCCTTAGGAGGATTCCTGATTCTTTAATGTTTTCTAAAAAAGCAaaacaaataaacaaacaaacaaaACAAAATACTAAATGTTTTCTCTCTCAACTTATTTGAATACACTCTTTTCTCACTGCTCTGAGCATGAATTCAATATTTCAGGGCAAACTAACTGAATGTTAGAACCAACTCCTGATAAGTCTTGAACAAAAGATAGGATCCTCTATAAACAGGTTAATCGCCACGACATAGTAGTATTTAGAGTTACTAGTAAGCCTGACGCCACTACACAATTCTAGCTTTTCTCTTTAGGATGATTGTTTCATTCAGTCTTATCTCTTTTAGAAAACATAGGaaaaaattatttaataataaaatttaattGGCAAAATGAAGGTATGGCTTATAAGAGTGTTTTCCTATTGTTTTCAGTGTATGACTCACTGTTCTAAATAACTGGGACACCCAAGGATTCTGTAAAATGCCATCCAGTTATCATTTATATTCCCTAACTCAAAATTCATTCGCATGTATTCATTTTTTTTCTAAACAAATTAGCATGTAGAATTCTGGTTAAAATTTGGCATAGAACACCCGGGTATTTTTTCATAATGCACCCAATAACTGTCATTCACTAATTGAGAATGGTGATTTAACAAAGGATAATAAAATTATGAAACTAATGCCACAAAACATCTGTCTCTAACTGgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtAAGAGGGAGAGAGAGAAAATTTCACTCCCTCCATAAATCTCACAGTATTCTTTTTCTTtttcctttcctttccttgctcttctttctctcctattgctttcctt tcatttccttCTCATAAAAGAAAAATAACAATACAGAAAATAACAAAATATAGATGGTCAACCTTTTTAATATTAAGGTTACCTAAAATGCCATTATCCAAAGTGGTTCTCTGGAGATGCTGATGTATATACTTACATATTTTACAGTGTATTCAAATAAAGAGTCTATTACATAAGACATATCCTTTTGTAACCAACTTTTGTCATTAACAATTTACTGGACTTGTCAACAAACCTAAATCTGTATCATCTATAATGGCTACGTTCATTTTGGTATGAATCTTAATTACCCCTTTCTGCATTATTTAATGATTTTCTCATATGTCACTCTTAAATGTACTTTTAATTTTTCACTTTAGATCACATAATGAATGGATCCGAATATGTTATGGATAGATATCTTCAAACTTTCTACTTACAAGTAGTGATAATAACAGATGTTCTCTCTAAAGTGTAGTTGGTATCAATTTTACTGACTTTTAAAAACATCTTAATGGGACAAAGTTCAAATATTTGATGACCAGCTATCGTGACCTTTATCTCTGTGGCTCTGTGGGCCTGTAGTTTTTACGTGCTTTTAGTGTATCATGATTAAATATTTTGTTTTAGTAAAGACACCATTATTTCCCAACTTCATATTCAAATTGTCAAAGGTATTAATCCTAGAGCAGAACTCTCAAAAGCACCAACTCTGATTCCTAACAAAGCATGGAAAAGCCCTCTCTCTGAGTTTCAGAGACTCTTTTTTGTGGGGGTTGAGTTTCACTTTATTTAAAGTGAGTCTTAATCCTCCAACAAGTCAACAAGTGATGGGCTGGAATCACACGTATTGGAAAACCAGCAGAAGAGTAAGTCTTTGCATTTTATGCTACTGTACCTCTGAGATTAATTGCTCTTTCCCTCATTGGCCAGTCACTCTTAAGTGCGTGATTAATGCCTGAGATTGTGTGAAGTAAAAGATGGATCAGAggctgggcgcggtggctcgc gcctgtaatcccagcactttgggcggccgaggcgggcggatcacgaggtcaggagatcgagaccatcctggctaacaccgtgaaaccccgtctccactaaaaatacaaaaaattagccgggcgcggtggcgggcgcctgtggtcccagctgctggggaggctgaggcaggagaatggcgggaacccggaggcggagcctgcagtgagccgagatggcgccaccgcactccagcctgggggacccagccagactccgcctcaaaaaaaaaaaaaaaaGATTGATCAGAGAGTACATCCTCTAAGGGTATATGCAGATAAATACAATTAAGGCTATTAACATTTCAAATACGGGTGACTGTTTCTTACGTGGACGACGCTGTGTTGAACATGGGTGAGTAAGACCGAAGCAGCCGTAATTACCGCACGATGCGCATGGTAAAGAAGTACTCTGTTACGGAAATTATATTCTTTGCCCCTCTAATCCTTCACTCCACCTGCCATATTCCCACATGATTTTTTTCTTTGCTGTTCTTGTCTAATTGTTattaataattaataaataacttatgatctaattgttattaataattaataacttatgatcacatgatttattaataaattaataaataac---ttaTCACCGCGTTTCCCCAATTCATTTATCTTTCTTTCATTTTCTCTCTTTGTGTGTTTTCTATCTTCATATTTCAGCACTTGCCACATATTTCCCACAAAATCATTTATGGTCAAACAACACTTCAACGTGTAGCATTTGTATTTCTCAATTCTTCCTCACTTTCTTCCTTCAGAATACTAAAGCTTCTTCTCTACTGACTGAGTCAATGGCCAATGGATAGAGTAAATAATTCTGCGGTATCTAAATTTGTATTGATTGGACTTTCAAGCTCTTGGGAGATGCATCTTTTTCTTTTTTGGTTCTTCTCTGTGTTCTACATGGGAATTATCCTGGAAAATCTCTTCATTGT GTTCACAGTAATTATTGACTCTCATTTAAATTCCCC + +a score=246514 +s hg18.chr1 42487 2748 + 247249719 AGGTACTGCCTACTGGCCAACATTTATCTTCTTGATCTGGGTCTTCTCCTACAGTTCTGACTTTTTCACTAACTGCAGCATCATTTCTTTTCCAAGATGCATCATACAGATATTTTTCATTTGTGTCATGCGTAAAAATTGAGATGGTGCTGCTCATAACCATGGCATAGAGCAGGTACACTGCCAATCTGTAAGCCTCCCCATTACCTGACCACAATGAACCCCAAAATGTGTGTTTCCTTTGTTGGAGGCATCCTGGATAGTCAGGATAATCCATGCTGTATCTCAGTTTGTTTTTGCCATAAACTTGCCTTTTTGTGGCCCTAATAGAGTAGGTAGTTTTCACTGTGATTTTCCTTATGTCATGAAACTTGCTTGTGTAGACACTTACAAACTAGAGGTTGTAGTCACTGCTAACAGTGGGCTTATATCCATAGCTACCTGTTTCTTATTAATAATATCCTATATTTTCATTTCGGTAACCGTCTAGAATCCTTCTTCAGGAGACTTATCTAAAGCATTTGTGTCATGTTAGATCACATCACAGTAGGGATTTTGTTTTTTATGCCATGTATATTTCTGTATGTGTAGCCTTTGCCTAAAACAACACATGATTAATATTTGTTCATTGTTCCTTTTGCTATCACCCCTGTCTAGGATCTACACATTAAGAAACAAAGACATGAACGTCTCCATGGAAAGACTGGGAAAATGGATTGCAGGTTCTAGCAGGATGTCATAATAAATGGTGCATATCCAGAGTGCAAGATGATTCAGTCTCACCAAGAACACTGAAAGTCACATGGCTACCAGCATTATTGTGATAAGAACTACTATTTTGGGAGATAGTTTAGCAAAGGTGCCATGTAGAAATTGATTAAGTCAGAGGTATCTTTAACTTGCCACCACAGAGAAGAGATTAATTTCATATACTTCCATTGAGAAGAG AGATAAGAATACAAAACCAAGCTGATTTGCAGGAGTAAACTTGATATTCAAATACTATTTCCTGAATGACATTTTCTGAGACATGCTAATTGTAATTACTTTCAGCTTCAAAACATAATAAATTTATCTCATAGTAAGCATATAGATGGAATAAATAAAATGTGAACTTAGGtaaattataaattaataaagtatatttttaaaatttCCATTTTAATTTCTGTTTAAATTAGAATAAGAAACAAAAACAACTATGTAATACGTGTGCAAAGCCCTGAACTGAGATTTGACTTTACCTTGAGCTTTGTCAGTTTACGATGCTATTTCAGTTTTGTGCTCAGATTTGAGTGATTGCAGGAAGAGAATAAATTTCTTTAATGCTGTCAAGACTTTAAATAGATACAGACAGAGCATTTTCACTTTTTCCTACATCTCTATTATTCTAAAAATGAGAACATTCCAAAAGTCAACCATCCAAGTTTATTCTAAATAGATGTGTAGAAATAACAGTTGTTTCACAGGAGACTAATCGCCCAAGGATATGTGTTTAGAGGTACTGGTTTCTTAAATAAGGTTTTCTAGTCAGGCAAAAGATTCCCTGGAGCTTATGCATCTGTGGTTGATATTTTGGGATAAGAATAAAGCTAGAAATGGTGAGGCATATTCAATTTCATTGAAGATTTCTGCATTCAAAATAAAAACTCTATTGAAGTTACACATACTTTTTTCATGTATTTGTTTCTACTGCTTTGTAAATTATAACAGCTCAATTAAGAGAAACC-GTACCTATGCTATTTTGTCCTGTGATTCTCCAAGAACCTTCCTAAGTTATTCTACTTAATTGCTTTATCACTCATATGAATGGGAATTTCTTCTCTTAATTGCTGCTAATctcccccatcttcaaatactctaccgggcttctggaacaccacagcttcctggctttttctcctacctcctgggcaagtccttccctgtgtctttt gttgagtgttcctcatctgcttaactaccaatcaacctattgcccctaatttgatctttggcctgttttcacttagattctatccctacgtatcacccattcccacagctttaatcaccatctaaacactaggggctctcaaaccttgtatttttctttctttctttctttctttctttctttctttctttctttctttctt------------tctttctttcttcctccttttctttccttttctttctttcattctttctttcttttttaaggggcagggtctcactatgttgctgaggctggtctcaaactcctgacctcaagcaatctgtctgcttcagcctcccaagtagctgagaatacagggacaagccattgcacctgaccctggtactatttcttgagttcctgatccacagatctaacctcctactttcctggatgccacacaagatcttccactcaacaagtctgcaactaaactagccttcctcttttcaaacctactcttctttcagtgttctcagtcacaataatttgtaccaactagttacctagttgcacaacccaaaatctgggaaaaataatagatttctttctccatagtacccccaaatcaataaatcatcaagtcttattctaccttccaaagagccttacatatgttcctttattttcatctgtaacaccactattcctgtctaagcctacctatgtcatttttggaagagaatatagtcacctatgcgaccttcccacttaaaatcctactatttacgcttcagtaaaagaaaaaaaatttttaatctaagtatgtaatt +s panTro2.chrUn 9707735 2758 + 58616431 AGGTACTGCCTACTGGCCAACATTTATCTTCTTGATCTGGGTCTTCTCCTACAGTTCTGACTTTTTCACTAACTGCAGCATCATTTCTTTTCCAAGATGCATGATACAGATATTTTTCATTTGTGTCATGCGTAAAAATTGAGATGGTGCTGCTCATAACCATGGCATAGAGCAGGTACACTGCCAATCTGTAAGCCTCCCCATTACCTGACCACAATGAACCCCAAAATGTGTGTTTCCTTTGTTGGAGGCATCCTGGATAGTCAGGATAATCCATGCTGTATCTCAGTTTGTTTTTGCCATAAACTTGCCTTTTTGTGGCCCTAATAGAGTAGATAGTTTTCACTGTGATTTTCCTTATGTCATGAAACTTGCTTGTGTAGACACTTACAAACTAGAGGTTGTAGTCACTGCTAACAGTGGGCTTATATCCATAGCTACCTGTTTCTTATTAATAATATCCTATATTTTCATTTTGGTAACCATCTAGAATCCTTCTTCAGGAGACTTATCTAAAGCATTTGTGTCATGTTAGATCACATCACAGTAGGGATTTTGTTTTTTATGCCATGTATATTTCTCTATGTGTAGCCTTTGCCTAAAACAACACATGATTAATATTTGTTCATTGTTCCTTTTGCTATCACCCCTGTCTAGGATCTACACATTAAGAAACAAAGACATGAACGTCTCCATGGAAAGACTGGGAAAATGGATTGCAGGTTCTAGCAGGATGTCATAATAAATGGTGCATATCCAGAGTGCAAGATGATTCAGTCTCACCAAGAACACTGAAAGTCACATGGCTACCAGCATTATTGTGATAAGAACTACTATTTTGGGAGATAGTTTAGCAAAGGTGCCATGTAGAAATTGATTAAGTCAGAGGTATCTTTAACTTGCCACCACAGAGAAGAGATTAATTTCATATACTTCCATTGAGAAGAG AGATAAGAATACAAAACCAAGCTGATTTGCAGGAGTAAACTTGATATTCAAATACTATTTCCTGAATGACATTTTCTGAGACATGCTAATTGTAATTACTTTCAGCTTCAAAACATAATAAATTTATCTCATAGTAAGCATATAGATGGAATAAATAAAATGTGAACTTAGGtaaattataaattaataaagtatatttttaaaatttCCATTTTAATTTCTGTTTAAATTAGAATAAGAAACAAAAACAACTATGTAATACGTGTGCAAAGCCCTGAACTGAGATTTGACTTTACCTTGAGCTTTGTCAGTTTACGATGCGATTTCAGTTTTGTGCTCAGATTTGAGTGATTGCAGGAAGAGAATAAATTTCTTTAATGCTGTCAAGACTTTAAACAGATACAGACAGAGCATTTTCACTTTTTCCTGCATCTCTATTATTCTAAAAATGAGAACATTCCAAAAGTCAGTCATCCAAGTTTATTCTAAATAGATGTGTAGAAATAACAGTTGTTTCACAGGAGACTAATCGCCCAAGGATATGTGTTTAGACGTACTGGTTTCTTAAATAAGGTTTTCTAGTCAGGCAGAAGATTCCCTGGAGCTTATGCATCTGTGGTTGATATTTTGGGATAAGAATAAAGCTAGAAATGGTGAGGCATATTCAATTTCATTGAAGATTTCTGCATTCAAAATAAAAACTCTAATGAAGTTACACATACTTTTTTCATGTATTTGTTTCTACTGCTTTGTAAATTATAACAGCTCAATTAAGAGAAACCGGTACCTATGCTATTTTGTCCTGTGATTCTCCAAGAACCTTCCTAAGTTATTCTACTTAATTGCTTTATCACTGATATGAATGGGAATTTCTTCTCTTAATTGCTGCTAATctcccccatcttcaaatactctaccgggcttctggaacaccacagcttcctggctttttctcctacctcctgggcaagtccttccctgtgtctttt gttgagtgttcctcatctgcttaaccaccaatcaacctattgcccctaatttgatctttggcctgttttcacttagattctatccctacgtatcacccattcccacagctttaattaccatctaaacactaggggctctcaaaccttgtatttttctttctttctttctttctttctttctttctttctttctttctttctttctttctttctgtctttctttcttcctccttttctttccttttctttctttcattctttctttcttttttaaggggcagggtctcac--tgttgctgaggctggtctcaaactcctgacctcaagcaatctgcctgcttcagcttcccaagtagctgagaatacagggacaagccattgcacctgaccctggtactatttcttgagttcctgatccacagatctaatctcctactttcctggatgccacacaagatcttccactcaacaagtctgcaactaaactagccttcctcttttcaaacctactcttctttcagtgttctcagtcacaataatttgtaccaactagttacctagttgcacaacccaaaatctgggaaaaataatagatttctttctccatagtaccccaaaatc-ataaatcatcaagtacaattctgccttccaaaGAGCAAAACAAATGTTCATTTAGCTTCGTTTGTCACACCAATACTCGAGTCTAAGCCTACAGGAATCACACATGGAGGGGAATATAGTCACCTATGTGATCTTCCCACTCAAAATCGCATTATACATGCTTCAGTAAAAGAAAAAAAAGTGCTAATCTAAGTATGTAATT + +a score=245281 +s hg18.chr1 45644 2651 + 247249719 TGCATTTTAAGTTCAACATGAGCAGGACTTTGTCGTGTTCACCTCTATCACATCATAAATATAGCAAACAGTAAAACTATTGCAACATGACTAATGTATTGAACGATGCTTCAGCTTTCTTCTTACGTTCAATCACAGGTCATATGACTAAAGAACTTCCTTTTTAATCTCCTTTTCTATTCTCAATTAATTTCTTCTGCCTGCATCACCTCAAGTCTCTGGGGTGAAATCCACTAATGAATTCCTTTTGCAGCTTAAGCCAATTCCAATCTTGAGCCAATCTCAGGTGAAGAAGCCTGTAAATTATCACTCTCAGTCCTCTCTTGTACTACTAGGTCTCATGAACTCTTCATTAACAACTCCAGCTTCTCTGTTAGCCCAAAAGCCTTTTGCTGCCTAGAAAACCCATGATTCATGCCTCAGGAAACAGCCTTCAAATCACAACATGTTCTGTATCTGGCTGGCCAACTCCCTGCAACTTATTTCTGCCTAGATTCTCCCTCATTCATTTCAATACGCTGTTCGGCCTGCTACCCCAGTTTCCCACTTAGAACAATGGCACACAGGACAGGAGCACATTGGCACATCAGAATGACTTATGTACTGCTCATTGTGTTGCAGAAGAGACCTCTGTGGGGGCAATAGAACAGATTTTCCTCTCACGTCACTGTAGTTGTGGTTTCCCTAAGCACCTACACTGTTTCACCTCATCTTAGGTAGACAATAATCCATGTAACTGACTGTGTATCCTAATTTTAAAAAATATTTCTGCCCACATTATTCTGCAGTTTTTATCTTGCTTACGTATTTTTGGAATGTTACTATTTTTCAAAAATTAATTTGGGATCAACCAACACTTCTTATTCTGCTGCTGTTCTAGAGAAAATCATTTTCCTCATTTCTGAACAAGAGAAAATGAAATACAGCTCTAAACAAATGCCACTGTAA ACCAAGGTGGAGCCTTTGCACTTTCAGGCCACCATGATAACCTGGAGATTAGATTTTTCTGTGTCTTTATATCAATAATAAAGCCAAGCTTCTCCAGGGGTATCCACTAGGCTTGTCTCAATGGCTCAATACAGGTCCTTTTGTGAATGATTACCTCACCCTCATGGAAACACACTCTTGTTACAGAAACTCAGAATGATTCTATTTTTTCTTTTATATTTGTATATGTTTTTCCAATACCTCTGAAAAAACTGATCCAAAAAAAA--TACAAATTTTAATTGTAGCCAGTCAATTCAGGAAGGATAAAGGTCAAAAACTTTCAAAGAAACCTTCAGCCCCAACACACTAAACTTTGGGAGCACAGGTTGGCATCCAGAGGTAAACATTTGCTATAACTGATAACAGGAGAAGGATCCATTTATTCACCTGTTATCAATTACAGGCATTGTATTTAAAGATCAGATGTTTTATATTTATTTCTTCAAATTTCATTCATGGTGCCATAAGTGAAGGTATCTCTGTCCACCCTGAATATATTTTCACTCCCTCATCTCAGTCATTCCGAACAATTCACACACTAAGATTACCCATGCTAAATGGGGATTCTTTTTTACTAGCCAATGTAGTACCTCAAATCCTTCCTTCCCTCCCCCTATTTCATCAGCAGGCAATTCTTTTGATACTTTTGTCAAGGGGAAATTGTGTGACTCAGAGATCTAGTCCCCAAGAGAAACTAATAATGGGCTGGGTATTGTCTGTCTCAGCAGCATCAGTGGGTCCCTCTCCTGTGCAGCTAATTAGCTTCCTTTCCAATATGAAGAATCTTATATATAGCTTTGTCTTTGGGGTATTACATAAATGAAGATTAAGCTATCTGAATTTCTCCTTCTCCTAAAAATGCACATCCTATGACTGAAAAGACAGGTAAAAGAGATGCTTTTAATTACAAAACTTTCCCTGTCGTGGTTGCTTCTCTCTATCCTTCTA AACTCCCTTTCAATTTCTTCTCTTCTGTAACATATTTGTGCCCAAAATCTTCTGCTTTCTGAAATATTTTATCTTTTTCTTCCACACTATCTCTTATTTTCCAATTTTAATCATTAAATTATATTATGTCTTATAAAACTAATCCCACATATAAACCCCTATGATAATTTCAGTTTGTCCCTAGTATGAAGTTCTTTAAAGATGTGTAGTTTTCTAACTTTCATGCTCTCCAATTAATTATAAACTTCATTTTCCACTCTGAAAAGGAGATGTCTGATCTCAGCTATTTCCATCCTATTTGAAAACCAGATTTAGTTTTAAACCAGAGGAAGGGAATCTCAAGTCTTTACCTCCCACAGTCTGGTGTGATTCTCTCTCTTTTGGTATTACCTTCCTCCACATTGGAACACTCCAGCCAATGCATAGGCTGAGAGGCTATCTCAGATTCAGAAAGATTTGGCCTCATCCCAGGGGAGGGTACAGAGGAGCTGATGACTATGAATTCTGAAATGGAACTGTTCCAGG----TTGAAGAAATAAGAAAGGGAATTGGGAAGAGCAATGCCCAGTGAAAAAGAAGAAATAATATTTTAGGAAGTGAATGCTAATTTTATTTTAAACAAAATAAGAACTCAAGGAATAAGAGGGTTCTTCCAATAGGTTAGAGTGATCCTGTCAAACATATATGCTTCTAGATTTTTTTAAAGACTGTTTCTACT +s panTro2.chrUn 9711251 2657 + 58616431 TGCATTTTAAGTTCAACATGAGCAGGACTTTGTCATGTTCACCTCTATCACATCATAAATATAGCAAAGAGTAAAACTATTGCAACATGACTAATGTATTGAACGATGCTTCAGCTTTCTTCTTACGTTCAATCACAGGTCATATGACTAAAGAACTTCCTTTTTAATCTCCTTTTCTATTCTCAATTAATTTCCTCTGCCTGCATCACCTGAAGTCTCTGGGGTGAAATCCACTAATGAATTCCTTTTGCAGCTTAAGCCAATTCCAATCTTGAGCCAATCTCAGGTGAAGAAGCCTGTAAATTATCACTCTCAGTCCTCTCTTGTACTACTAGGTCTCATGAACTCTTCATTAACAACTCCAGCTTCTCTGTTAGCCCAAAAGCCTTTTGCTGCCTAGAAAACCCATGATTCATGCCTCAGGAAACAGCCTTCAAATCACAACATGTTCTGTATCTGGCTGGCCAACTCCCTGCAACTTATTTCTGCCTAGATTCTCCCTCATTCATTTCAATACGCTGTTCGGCCTGCTACCCCAGTTTCCCACTTAGAACAATGGCACACAGTACAGGAGCACATTGGCACATCAGAATGACTTATGTACTGCTCATTGTGTTGCAGAAGAGACCTCTGTGGGGGCAATAGAACAGATTTTCCTCTCACGTCACTGTAGTTGTGGTTTCCCTAAGCACCTACACTGTTTTACCTCATCTCAGGTAGACAATAATCCATGTAACTGACTGTGTATCCTAATTTTAAAAAATATTTCTGCCCACATTATTCTGCAGTTTTTACCTTGCTTACGTATTTTTGGAATGTTACTATTTTTCAAAAATTAATTTGGGATCAACCAACATTTCTTATTCTGCTGCTGTTCTAGAGAAAATCATTTTCCTCATTTCTGAACAAGAGAAAATGAAATACAGCTCTAAACAAATGCCACTGTAA ACCAAGGTGGAGCCTTTGCACTTTCAGGCCACCATGATAACCTGGAGATTAGATTTTTCTGTGTCTTTACATCAATAATAAAGCCAAGCTTCTCCAGGGGTATCCACTAGGCTTGTCTCAATGGCTCAATACAGGTCCTTTTGTGAATGATTACCTCACCCTCATGGAAACACACTCTTGTTACAGAAACTCAGAATGATTCTATTTTTTCTTTTATATTTGTATATGTTTTTCCAATACCTCTGAAAAAACTGATCCAAAAAAAAAATACAAATTTTAATTGTAGCCAGTCAATTCAGGAAGGATAAAGGTCAAAAACTTTCAAAGAAACCTTCAGCCCCAACACGCTAAACTTTGGGAGCACAGGTTGGCATCCAGAGGTAAACATTTGCTATAACTGATAACAGGAGAAGGATCCATTTATTCACCTGTTATCAATTACAGGCATTGTATTTAAAGATCAGATGTTTTATATTTATTTCTTCAAATTTCATTCATGGTGCCATAAGTGAAGGTATGTCTGTCCACCCTGAATATATTTTCACTCCCTCATCTCGGTCATTCCGAACAATTCACACACTAAGATTACCCATGCTAAATGGGGATTCTTTTTTACTAGCCAATGTAGTACCTCACATCCTTCCTTCCTTCCCCCTATTTCATCAGCAGGCAATTCTTTCGATACTTTTGTCAAGGGGAAATTGTGTGACTCAGAGATTTAGTCCCCAAGAGAAACTAATAATGGGCTGGGTATTGTCTGTCTCAGCAGCATCAGTGGGTCCCTCTCCTGTGCAGCTAATTAGCTTCCTTTCCAATATGAAGAATCTTATATATAGCTTTGTCTTTGGGGTATTACATAAATGAAGATTAAGCTATCTGAATTTCTCCTTCTCCTAAAAATGCACATCCTATGACTGAAAAGACAGGTAAAAGAGATGCTTTTAATTACAAAACTTTCCCTGTCGTGGTTGCTTCTCTCTATCCTTCTA AACTCCCTTTCAATTTCTTCTCTTCTGTAACATATTTGTGCCCAAAATCTTCTGCTTTCTGAAATATTTTATCTTTTTCTTCCACACTATCTCTTATTTTCAAATTTTAATCATTAAATTATATTATGTCTTATAAAACTAATCCCACATATAAACCCCTATGATAATTTCAGTTTGTCCCTAGTATGAAGTTCTTTAAAGATGTGTAGTTTTCTAACTTTCATGCTCTCCAATTCATTATAAACTTCATTTTCCACTCTGAAAAGGAGATGTCTGATCTCAGCTATTTCCATCCTATTTGAAAACCGGATTTAGTTTTAAACCAGAGGAAGGGAATCTCAAGTCTTTACCTCCCACAGTCTGGTGTGATTCTCTCTCTTTTGGTATTACCTTCCTCCACATTGGAACACTCCAGCCAATGCATAGGCTGAGAGGCTATCTCAGATTCAGAAAGATTTGGCCTCATCCCAGGGGAGGGTACAGAGGAGCTGATGGCTATGAATTCTGAAATGGAACTGTTCCAGGTTGTTTGAAGAAATACGAAAGGGAATTGGGAAGAGCAATGCCCAGTGAAAAAGAAGAAATAATATTTTAGGAAGTGAATGCTAATTTTATTTTAAACAAAATAAGAACTCAAGGAAAAAGAGGGTTCTTCCCATAGGTTAGAGTGATCCTGTCAAACATATATGCTTCTAGATTTTTTTAAAGACTGTTTCTACT + +a score=547947 +s hg18.chr1 48332 5984 + 247249719 CTGGAATTTAGGAGGTCTGCCTTCTGATTCTGACTTCTTGAATGTATTGTTAGCCATTTAACCACACTGTGTTGTTTCTCATTCTACCTGTAGAATCTCAAAGTTCTTTCCCACTTCTATACAAAACTATAATTCTGAACATCCTTTTTGTTTAATATAAGTCTGCATTTCCTGTTTGAAGATATGTGTCCCAGACCCTAAATGACTGACAAATTTTAAATCTCCAATAGGAAAGATGACAAACTCTATGGAAACTTGGCTTCTGAAGAACTCCTAGAAGCTTTCCAAAGTCATCAGTGTTTCCTAAGAAGGCAGAGAAATCAAACACATGGTCTTTTCCTCCAGACAAGCTCCTTTGGGTCATCAGGATTTCTTCAACAATAAAATGTAATAATTCCAAATGTTTGTAACAGAATGGGTAGGACTTTCTTCACTTATTTAAATACTCCCTTTTTTATGCAACTGAGTTTTCATCAACAAGTACAAGCTTGTGAAGGAGTACTTTAAAATGCAATTTCTCTCTATTTTTGTGGGGGCTAATATTTTATTTCTCATATTGACAATTTATTATGCTGTTTTTAAAAAGttcattcatcaagtatttcttgagctttttctatgagacaggcactgttttaggcaagtaattatgcactgaacaatgcaaaaagtttccctgcactcatggactttaattttaCATTTATGAAAAGCTACAAATATTAGAATAAGTAAAATACTGCCTGGAGGCTAAAGCATATTTTGATCACTTATTCCCTAATTCTTTTAGAAGAGAACTCACCTGTCGGTTAGCTGAACCACTGCCAGTGATATCCAACTATACATTCAATCCCACCATACCTCATTATCACACCTATTCACTCACAAGCTTAAACTCTTAACTTTTCTCCACATATCAGTGACTATTTCCTACAGCTTTTCTTTTAC TTTCCATGTTTGCAGTGACAATATACATAAACAGTGTATGAAAACTCAAGTAAAATCTACTCTCTCAGGTGTTCATAATGTATCAATGTATATTGCTTTAAGCCTGAAGGTAACCTAAGTAAAGATGTACCATGTTCCACCAATGCTTCTTTTGATCATCATTTTATCCTGTTTTTTCTTTAGGATTCTTTCTTATTCCTTCCCCTGACCCTTCTTTTATTCTCCAAATTTCTTTCCAATTCATCTTTGTTCTTCCCTTTCCTTTTTACTCTCTTTAAACATTCTATGGACTCTGCCTCCTTCACACTGATATTGAACGCCCATAGTTTCATATTTTGGATTGCGATTGTTTTATTTTAAAATGGCAAATGTTCATGTTATAAAGAGAATTTTTCAGTCTTTAGACTAATAGGTTCATGTAGTTTGGGATTTTCCTCTTTAAGAAAATTAATTATCACTCACACTCCAAGACAAACACCATTTCAGTAGCAATATGAATTTCAGTAGTAATAGGAATCTCCAAATATGACAAAGTAATTCAGACATTAATTGCTTTTGTTTTGGAATTGCTCTTATAAGATGAAATATCACTTTCATGATGAGAGTCCTAGAGTGCTTGGTTTATATATTGTATCTTAGTTTTAACAGGATAAAACACTTGATCCTAAGCAGTAAACATGATTCTTCAGCTTCAACTTCATTTCTTTATAAATAACTATTTATGAATTGGTGTTGAGCTTAGTAAGTCACCAAACACCTTCTGCTCAGCAGCATAAAGGACATTTCCATGAAACCTCCCAGGGATAATCTTATTTACTCTATAATGTTTCCCGGGTTCAATTCCTCTCCCAAAATTCTTTGTTCTTAAGCCCCTATGATCTGGGTGATCTAAATATGGGTAAGAAGTCCAGGGATAGCACTATGAATGAAGTGAAAATAGTAAAACATAGTTAAAAATGTAcagatgctctctgacttataatagggtt acgtcctgataaatccatcataagtcaaaaatgcatttaatattcctaatgtacctcacatcatagtttggcctagcctaccttaaatgtgctcagaacactttcattagcttatataagatcacctaatacaaagcctattttataataaaatattgaatagctcacgtaatatactgactactatactcaagtacagtttcttctgaatgcatgtcactttctcaccattgtaaagtcaaacaattataagtcaaactatcacaagccagggaccatcCATATGTATTTCATTCAGAAAATGCTGGAAAGAGCATTTCGGAGAATATCTAGATGAGAGAAGGTAGAAAGCCATGCACAAATTCACTGAGAGTTTAAAAAAATACATGCATATTGTGGAGATAGAAATCAAATCTATTTGTCTCCATCTGCTGTATTCTTCCCAAAATATTATCTCTTCTTATCCCATTGTACTATATTGCATTTCTTTGACCATTTATTGTGTATCTCTTAATATTTCCCACTTCATCATTACTAACCTCACTCACTCTGAACTTGATGAGAGCACCTGAGCATTAATTTTTCTTATAATTATTTAATGATTACCAGAATTCGTTCAGTATGGCCAGCTCTGGTCAAAGTGAGGCAGGCAAGATGCTTTGTCAACTGCCTGGATGGAATGTCTCAAAAGGTTTCCATTTCATGGTAGCATTATGCAAAGTTCAAGACGTTTAATCAAGACCCTTCACTTACTTAACTATACCTCCTTGAGAATCCCATCTATGAAAAAATTCTAGTCATTATAAAAATGATTGATTAAATGAGGGAAGTAGTAGAGTTCTTCATTTCTTTAGTTGGTTTAGTCTCCTATGAGTCAATCCTA-TTTTCAAAATTCTTAATAAACCATTTATTCCTTCAACTTTCTATGCCATTTGATGTTTTGTAAAAAAAAAAATATAATATGTATACAAAAAGATATTTCAAAATC TAGAAAGAGAGCTTTAGAGCTTTGTAAAGCTCTTTTAAAAATCAAAAACAACTACTGTTAATTAACATGTTGTACTATGCAATTTGTTTACCATTATTACTCTTGGTATTTTTAAGAAAAGTCTTTCCATTGTTATTATAAATGCTTCTATTGATATTTATTTTAATAACTGTTATTACAGTCCGTCATGTACATACACTATACTTAAACCTAATGTTTGGTATTTAAATCGTTTCAAGATTTTATCACTGTCAACAAAGTATGATGAATATTTTTATGCTGAAAACTTCTGTAAAAatagaattccaagagtattattgcaccaaaaggcatggacttaaaattcttgatacatgatttcaaaatattttctttaaggtttgaatcagtctatattccctccagcagcgtataaaagtgccaatttctctgatccttaGCCAGTTTGGGTAATAATAATTGTAAAACttttttttcttttttttt-gagacagagtctccctctgtcgccaggctgaagtgcagtggcgcaatctcggctcactgcaacctccgcctcccggggtcaagctattctcctgcctcagcctcccaagtagctgggactacaggcatgcaccaccatgcccagctaatttttgttatttttagtagagatggagtttccccatgttggacaggatggtctcgatctcttgacctcgtgatccaccctcctcggcctcccaaagtgctgggataacaggcgtgaacaaccatgcccggccTGTAAAACTTTTTCCTAATTTAACAGAAAAATAATAGTATTATATTTTATCATATTTCTTTGATTTCTAAGacacacatacacacacacacacacaTATCTGTATATACAAATACACGTATAGCTTACATTTTAATTCTTCATTTCATTTGTTCATTTATTAGGTCTTGGAGATTTTGTGAAACTGTTTAAATTCTTTTTTATACTATGAAGATATCAACCT TTTGTCTCTACAGCATTTCAAATTCAAGTATGATTCACGTGTTGGTTTGGGGTAGATCATTATAGGCACATGTAGGAAACAGCTTTCAGAGATGCCTTAACCGTAATTATGCATTTGTATTCTAATTTTTATTTAATGTTATTATTGATTGCATTTTTAAAGATTCTGTATTTTTTAAACCATTTATTTGTATATGTTGGTATACAATCTTGCCATTTTCTGGGATTTCATATTTCCTTATTTTTGTTTTTTACCTTTTTTGGCTTGAATTTTTTGAGTTTTTATGCATTCTTTTCCAGTTTCTTAAGATGCTAATAAGTTCATGTATTTGAGCAATTGAGAACATTTAAAGCAATAGACTGCCTCTGAGCACAGCTTTGTCCATATTACATTAACCTTTTATACCCTGGGTTCCCACTAGTTTTTAAATAATCTACTATCAAATAAAAGATTTGTTAATAATAAATTTTAAATCATTAACACTTAACGCATTATTTTCAGTCACACTAAGTTGATTCCTTCGTTTCTTTCAGGTTGCTTCAGAGTCTTCCCTTCTATCTGATTCAGTGGACCAAGTAAATGACTCTCTGGTAACAGAATTTGTATTACTTGGACTTGCACAATCCTTGGAAATGCAGTTTTTCCTTTTTCTCTTCTTCTCTTTATTCTATGTGGGAATTATCCTGGGAAAACTCTTCATTGTGTTCACAGTGATCTTTGATCCTCACTTACACTCCCCCATGTATATTCTGCTGGCCAACCTATCGCTCATTGACTTGAGCCTTTCATCTACCACAGTTCCTAGGTTGATCTACGATCTTTTTACTGATTGTAAAGTTATTTCCTTCCATAATTGCATGATACAAAAGTTCTTTATCCATGTTATGGGAGGAGTTGAAATGGTGCTGCTGATAGTCATGGCATATGATAGGTACACTGCGATCTGCAAGCCTCTCCACTATCCAACTATTATGAATCCCAAAATGTGC ATGTTTTTGGTAGCAGCAGCTTGGGTCATTGGGGTGATTCATGCTATGTCTCAGTTTGTTTTTGTCATAAATTTACCCTTCTGTGGCCCTAATAATGTGGGGAGCTTTTATTGTGATTTTCCTCGGGTTATTAAACTTGCATGCATGGACACTTATGGGCTAGAATTTGTGGTCACTGCCAACAGTGGATTCATATCGATGGGCACCTTCTTTTTCTTAATTGTATCATACATTTTTATTCTGGTCACTGTCCAACGACATTCCTCAAATGATTTATCCAAAGCATTCTTCACTTCGTCGGCTCACATCACCGTAGTGGTTTTGTTTTTTGCTCCATGCATGTTTCTCTACGTGTGGCCTTTCCCTACTAAGTCATTGGATAAATTTTTTGCCATCATGAACTTTGTTGTCACCCCTGTCGTAAATCCTGCCATCTATACTTTAAGGAACAAAGATATGAAGTTTGCAATGAGAAGGCTGAATCAACATATTTTAAATTCTATGGAGACGACATAACACATTTGGTTGATGAGAGCACAGGATAAATGCCATGGACCATCAAGACTCCTGTGATCACCATGATCACTATGGAACGCGCACATTTTTAGTATTGCCTGAAAAAACTGAAAAATCTGCAAAAAGGATGCATTAAATCTAAGAATTGTATTTCAGATAAAGTTGCAACATTTTTTGTTAATCATAAAAAGTATATATTTCTATCTAATGTGTGTATCTAATTAACAGCAATGACTACCTTTAATTTTGATGTAGTTATTTTATATCTGTATATAAGCACATACACATATATATGACCTAGGTTTATTTATCAGTATTTTTATGCTGATAATAAGCATCACTGGAAATTAATTTTCTTATGGAAATTATGTGGATCCAATGGATAAAATATGAGTTTATATAAATTAGTAAATGCCAAAATCAAGGAAGAAACAATTTTTATTTTAATTGTACTTTAAGTTAGATAAATGGTA AGGTCAACAGCTTGTTACAACCCTTAAGTATTATTTTCAGGCTGATTGTCAATATGTTTTGTACAatgttctcacttataggtgggaattgaa +s panTro2.chrUn 9714242 5977 + 58616431 CTGGAATTTAGGAGGTCTGCCTTCTGATTCTGACTTCTTGAATGTATTGTTAGCCATTTAACCACACTGTGTTGTTTCTCATTCTACCTGTAGAATCTCAAAGTTCTTTCCCACTTCTATACAAAACTATAATTCTGAACATCCTTTTTGTTTAATATAAGTCTGCATTTCCTGTTTGAAGATATGTGTCCCAGACCCTAAATGACTGACAAATTTTAAATCTCCAATAGGAAAGATGACAAACTCTATGGAAATTTGGCTTCTGAAGAACTCCTAGAAGCTTTCCAAAGTCATCAGTGTTTCCTAAGAAGGCAGAGAAATCAAACACATGGTCTTTTCCTCCAGACAAGCTCCTTTGGGTCATCAGGATTTCTTCAACAATAAAATGTAATAATTCCAAATGTTTGTAACAGAATGGGTAGGACTTTCTTCACTTATTTAAATACTCCCTTTTTTATGCAACTGAGTTTTCATCAACAAGTACAAGCTTGTGAAGGAATACTTTAAAATGCAATTTCTCTCTATTTTTGTGGGGGCTAATATTTTATTTCTCATATTGACAATTTATTATGCTGTTTTTAGAAAGttcattcatcaagtatttcttgagctttttctatgagacaggcactgttttaggcaagtaattatgcactgaacaatgcaaaaagtttccctgcactcatggactttaattttaCATTTATGAAAAGCTACAAATATTAGAATAAGTAAAATACTGCCTGGAGGCTAAAGCATATTTTGATGACTTATTCCCTAATTCTTTTAGAAGAGAACTCACCTGTCGGTTAGCTGAACCACTACCAGTGATATCCAACTATACATTCAATCCCACCATACCTCATTATCACACCTATTCACTCACAAGCTTAAACTCTTAACTTTTCTCCACATATCAGTGACTATTTCCTACAGCTTTTCTTTTAC TTTCCATGTTTGCAGTGACAATATACATAAACAGTGTATGAAAACTCAAGTAAAATCTACTCTCTCAGGTGTTCATAACGCATCAATATATATTGCTTTAAGCCTGAAGGTAACCTAAGTAAAGATGTACCATGTTCCACCAATGCTTCTTTTGATCATCATTTTATCCTGTTTTTTCTTTAGGATTCTTTCTTATTCCTTCCCGTGACCCTTCTTTTATTCTCCAAATTTCTTTTCAATGCATCTTTGTTCTTCCCTTTCCTTTTAACTCTCTTTAAACATTCTATCGACTCTGCCTCCTTCACACTGATATTGAATGCCCATAGTTTCATATTTTGGATTGCGATTGTTTTATTTTAAAATGGCAAATGTTCATGTTATAAAGAGAATTTTTCAGTCTTTAGACTAATAGGTTCATGTAGTTTGGGATTTTCCTCTTCAAGAAAATTAATTATCACTCACACTCCAAGACAAACACCATTTCAGTAGCAATATGAATTTCAGTAGTAATAGGAATCTCCAAATATGATAAAGTAATTCAGA-ATTAATTGCTTTTGTTTTGGAATTGCTCTTATAAGATGAAATATCACTTTCATGATGAGAGTCCTAGAGTGCTTGGTTTATATATTGTATCTTAGTTTTAACAGGATAAAACACTTGATCCTAAGCAGTAAACATGATTCTTCAGCTTCAACTTCATTTCTTTATAAATAAATATTTATGAATTGGTGTTGAGCTTAGTAAGTCACCAAACACCTTCTGCTCAGCAGCATAAAGGACATTTCCATGAAAACTCCCAGGGATAATCTTATTTACTCTATAATGTTTCCCGGGTTCAATTCCTCTCCCAAAATTCTTTGTTCTTAAGCCCCTGTGATCTGGGTGATCTAAATATGGGTAAGAAGTCCAGGGATAGCACTATGAATGAAGTGAAAATAGTAAAACATAGTTAAAAATGTAcagatgctctctgacttataatagggtt atgtcctgataaatccatcataagtcaaaaatgcatttaatattcctaatgtacctcacatcatagtttagcctagcctaccttaaatgtgctcagaacactttcattagcttatataagatcacctaatacaaagcctattttataatacaatattgaatagctcacgtaatatactgactactatactcaagtacagttt--tctgaatgcatgtcactttctcaccattgtaaagtcaaacaattataagtcaaactgtcacaagccagggaccatcCATATGTATTTCATTCAGAAAATGCTGGAAAGAGCATTTAGGAGAATATCTAGACGAGAGAAGGTAGAAAGCCATGCACAAATTGACTGAGAGTTTAAAAAAATGCATGCATATTGTGGAGATAGAAATCAAATCTATTTGTCTCCATCTGCTGTATTCTTCCCAAAATATTATCTCTTCTTATCCCATTATACTATATTGCATTTCTTTGACCATTTATTGTGTATCTCTTAATATTTCCCACTTCATCATTACTAACCTCACTCACTCTGAACTTGATGAGAGCACCTGAGCATTAATTTTTCTTATAATTATTTAATGATTACCAGAATTCGTTCAGTATGGCCAGCTCTGGTCAAAGTGAGGCAGGCAAGATGCTTTGTCAACTGCCTGGATGGAATGTCTCAAAAGGTTTCCATTTCATGGTAGCATTATGCAAAGTTCAAGACGTTTAATCAAGACCCTTCACTTACTTAACTATACCTCCTTGAGAATCCCATCTATGAAAAAATTCTAGTCATTATAAAAATGATTGATTAAATGAGGGAAGTAGTAGAGTTCTTCATTTCTTTAGTTGGTTTAGTCTCTTATGAGTCAATCCTAGTTTTCAAAATTCTTAATAAACCATTTATTCCTTCAACTTTCTATGCCATTTGATGTTTTGTCAAAAAAATA-TATAATATGTATACAAAAAGATATTTCAAAATC TAGAAAGAGAGCTTTAGAGCTTTGTAAAGCTCTTTTAAAAATCAAAAGCAACTACTGTTAATTAACATGTTGTACTATGCAATTTGTTTACCATTATTACTCTTAGTATTTTTAAGAAAAGTCTTTCCATTGTTATTATAAATGCTTCTATTGATATTTATTTTAATAACTGTTATTACAGTCCGTCATGTACATACACTATACTTAAACCTAATGTTTGGTATTTAAATCGTTTCAAGATTTTATCACTGTCAACAAAGTATGATGAATATTTTTATGCTGAAAACTTCTGTAAAAatagaattccaagagtattattgcaccaaaaggcatggacttaaaattcttgatacacgatttcaaaatattttctttaaggtttgaatcagtctatattccctccagcagcgtataaaagtgccagtttctctggtccttagccagtttggATAATAATAATTGTAAAACttttttttcttttttttttgagacagagtctccctctgtcgccaggctgaagtgcagtggcgcaatctcggctcactgcaacctccgcctcccggggtcaagctattctcctgcctcagcctcccaagtagctgggactacaggcatgcaccaccatgcccagctaatttttgttatttttagtagagacggagtttccctatgttggacaggatggtctcgatctcttgacctcgtgatccaccctcctcggcctcccaaagtgctgagataacaggtgtgaaccaccatgcccggccTGTAAAACTTTTTCCTAATTTAACAGAAAAATAATAGTATTACGTTTTATCATATTTCTTTGATTTCTAAGacacacatacacacacacaca----tatctgtatatacaaatacacgtataGCTTACATTTTAATTCTTCATTTCATTTGTTCATTTATTAGGTCTTGGAGATTTTGTGAAACTGTTTAAATTCTTTTTTATACTATGAAGATATCAACCT TTTGTCTCTACAGCATTTCAAATTCAAGTATGATTCACGTGTTAGTTTGGGGTAGATCATTATAGGCACATGTAGGAAACAGCTTTCAGAGATGCCTTAACCGTAATTATGCATTTGTATTCTAATTTTTATTTAATGTTATTATTGATTGCATTTTTAAAGATTCTGTATTTTTTAAACCATTTATTTGTATATATTGGTATACAATCTTGCCATTTTCTGGGATTTCATATTTCCTTATTTTTGTTTTTTACCTTTTTTGGCTTGAATTTTT-GAGTTTTTATGCATTCTTTTCCAATTTCTTAAGATGCTAATAAGTTCATGTATTTGAGCAATTGAGAACATTTAAAACAATAGACTGCCTCTGAGCACAGCTTTGTCCATATTACATTAACCTTTTATACCCTGGGTTCCCACTAGTTTTTAAATAATCTACTATCAAATAAAAGATTTGTTAATAATACATTTTAAATCATTAACACTTAACGCATTATTTTCAGTCACACTAAGTTGATTCCTTCCTTTCTTTCAGGTTGCTTCAGAGTCTTCCCTTCTATCTGATTCAATGGACCAAGTAAATGACTCTCTGGTAACAGAATTTGTATTACTTGGACTTGCACAATCCTTGGAAATGCAGTTTTTCCTTTTTCTCTTCTTCTCTTTATTCTATGTGGGAATTATCCTGGGAAACCTCTTCATTGTGTTCACAGTGATCTTTGATCCTCACTTACACTCCCCCATGTATATTCTGCTGGCCAACCTATCGCTCATTGACTTGAGCCTTTCATCTACCACAGTTCCTAGATTGATCTATGATCTTTTTACTGATTGTAAAGTTATTTCCTTCCATAATTGTATGATACAAATGTTCTTTATCCATGTTACGGGAGGAGTTGAAATGGTGCTGCTGATAGTCATGGCATATGATAGGTACACTGCGATCTGCAAGCCTCTCCACTATCCAACTATTATGAATCCCAAAATGTGC ATGCTTTTGGTAGCAGCAGCTTGGGTCATTGGGGTGATTCATGCTATGTCTCAGTTTGTTTTTGTCATAAATTTACCCTTCTGTGGCCCTAATAATGTGGGGAGCTTTTATTGTGATTTTCCTCGGGTTATTAAACTTGCATGCATGGACACTTACGGGCTAGAATTTGTGGTCACTGCCAACAGTGGATTCATATCTATGGGCACCTTCTTTTTCTTAATTGTATCATACATTTTTATTCTGGTCACTGTCCGACGACATTCCTCAAATGATTTATCCAAAGCGTTCTTCACTTCGTCGGCTCACATCACCGTAGTGGTTTTGTTTTTTGCTCCATGCATGTTTCTCTACGTGTGGCCTTTCCCTACTAAGTCATTGGATAAATTTTTTGCCATCATGAACTTTGTGGTCACCCCTGTCTTAAATCCTGCCATCTACACTTTAAGGAACAAAGATATGAAGTTTGCAATGAGAAGGCTGAATCAACATATTTTAAATTCTATGGAGACGACATAACAGATTTGGTTGATGAGAGCACAGGATAAATGCCATGGACCATCAAGACTCCTGTGATCACCATGATCACTATGGAACGCGCACATTTTTAGTATTGCCTGAAAAAACTGAAAAATCTGCAAAAAGGATGCATTAAATCTAAGAATTGTATTTCAGATAAAGTTGCAACATTTTTTGTTAATCATAAAAAGTATGTATTTCTATCTAATGTGTGTATCTAATTAACAGCAATGACTATCTTTAATTTTGATGTAGTTATTTTATATCTGTATATAAGCACATACACATATATATGACCTAGGTTTATTTATCAGTATTTTCATGCTGATAATAAGCATCACTGGAAATTAATTTTCTTATGGAAATTATGGGGATCCAATGGATAAAATATGAGTTTATATAAATTAGTAAATGCCAAAATCAAGGAAGAAACAATTTTTATTTTAATTGTACTTTAAGTTAGATAAATGGTA AGGTCAACAGCTTGTTACAACCCTTAAGTATTATTTTCAGGCTGATTGTCAATATGTTTTGTACAatgttctcacttataggtgggaattgaa + +a score=104160 +s hg18.chr1 54316 1163 + 247249719 caatgagaacacatggacacaggaaggggaacatcacacaccggggcctgttgtggggtggggggaagggggagggatagcattaggagatataactagtgttaaatgacgagttaatgggtgcagcacacccacatggcacatgtatacatatgtaactaacctgcacattgtgcacatgtaccctagaacttaaagtataataa--aaaaaaaTAGACTCTAGTACTCTGTATTATGCAAAATTTGTCTATGTTACACTTTTTTAACAACACAATCCTATTGCCCTTGAAATCTTCTTCAAAGCATTTCTCGAGTCACTCTTAAAAAGCATCTACAACCTAAAAGTATAGGAAGAGATTTATTTCCTGGAGAAGAGACCCCATTGAGATCTTAAAAGCACATTTAATGTGCCTGTGCTTAACTTAAGGT----GCTTAGGACAAAGAAGGCGATTGACATCTTTCAGGTAAAACCTGGTAAGTTTGGTGGTCAAGGAACACAACTGAGACATCACTTGGATGTATTCCTATGACTATTTTAAGAAACATAAATTGTGGTGACTCACTCAGCTCACTTTTAACTACTGCATGGTAATTAAAGATGCAAAATAAAATAAGTTACAAGAAGTGAGGTTTTTTATTGGTTAAAGCAATTTTTCTATATTTTCTCCGCAAGTTGGTCATAAAAGTTCTAAGCATTCCTCTTTTTATAAAATCGAAGCATTATTACTTACTCTCTTGTTAACCTATCTGGATTTTAATTTTGTAACTTTATTATATTTGTTTTGCTGTGATTCTTTAAAAAGCACCTTTAGACTCAGTGAGATAGCAAAAATATCCAAATAGGCCAAAAAATTGTGGCAATGTCCTCTCACTCAGGAAAATTCTGTGTGTTTTCTCTAATGGCCAAGGGAAAACTTGTGAGACTATAAAAGTTAGTCTCAGT ACACAAAGCTCAGACTGGCTATTCCCAGATCTCTTCAGGTACATCTAGTCCATTCATAAAGGGCTTTTAATTAACCAAGTGGTTTACTAAAAAGGACAATTCACTACATATTATTCTCTTACAGTTTTTATG-----------------------------------CCTCATTCTGTGAAAATTGCTGTAGTCTCTTCCAGTTATGAAGAAGGTAGGTGGAAACAAAGACAAAACACATATATTAGAAGAATGAA +s panTro2.chrUn 9720505 1203 + 58616431 caatgagaacacatggacacaggaaggggaacatcacacaccggggcctgttgtggggtgggggaaggggggagggatagcattaggagatatacctaatgttaaatgacgagttaatgggtgcagcacacccacatggcacatgtatacatatgtaacaaacctacacattgtgcacatgtaccctagaacttaaagtataacaacaaaaaaaaaaGACTCCAGTACTCTGTATTATGCAAAATTTGTCTATGTTACACTTTTTTAACAACACAATCCTATTGCCCTTGAAATCTTCTTCAAAGCATTTCTCGAGTCACTCTTAAAAAGCATCTACAACCTAAAAGTATAGGAAGAGATTTATTTCCTGGAGAAGAGACTCCATTGAGATCTTAAAAGCACATTTAATGTGCCCGTGCTTAACTTAAGGTAGGTGCTTAGGACAAAGAAGACGATTGACATCTTTCAGGTAAAACCTGGTAAGTTTGGTGGTCAAGGAACACAACTGAGACATCACTTGGATGTATTTCTATGACTATTTTAAGAAACATAAATTGTGGTGACTCACTCAGCTCACTTTTAACTACTGCATGGTAATTAAAGATGCAAAATAAAATAAGTTACAAGAAGTGAGGTTTTTTATTGGTTAAAGCAATTTTTCTATATTTT-TCCGCAAGTTGGTCCTAAAAGTTCTAAGCATTCCTCTTTTTATAAAATCGAAGCATTATTACTTACTCTCTTGTTAACCTATCTGGATTTTAATTTTGTAACTTTATTATATTTGTTTTGCTGTGATTCTTTAAAAAGCACCTTTAGACTCAGTGAGATAGCAAAAATATCCAAATAGGCCAAAAAATTGTGGCAATGTCCTCTCACTCAGGAAAATTCTGTGTGTTTTCTCTAATGGCCAAGGGAAAACTTGTGAGACTATAAAAGTTAGTCTCAGT ACACAAAGCTCAGACTGGCTATTCCCAGATCTCTTCAGGTACATCTAGTCCATTCATAAAGGGCTTTTAATTAACCAAGTGGTTTACTAAAAAGGACAATTCACTACATATTATTCTCTTACAGTTTTTATGCTTCAAGGCAGTGCAAATAAAGGGAAATTTGTACTCCTCATTCTGTGAAAATTGCTGTAGTCTCTTCCAGTTATGAAGAAGGTAGGTGGAAACAAAGATAAAACAAATATATTAGAAGAATGAA + +a score=43935 +s hg18.chr1 55740 675 + 247249719 TCTTTCCCCAGGTCCGGTGTTTTCTTACCCACCTCCTTCCCTCCTTTTTATAATACCAGTGAAACTTGGTTTGGAGCATTTCTTTCACATAAAGGTACAaatcatactgctagagttgtgaggatttttacagcttttgaaagaataaactcattttaaaaacaggaaagctaaggcccagagatttttaaatgatattcccatgatcacactgtgaatttgtgccagaacccaaatgcctactc-----------------------------------ccatctcactgaGACTTACTATAAGGACATAAGGCatttatatatatatatattatatatactatatatttatatatattacatattatatatataatatatattatataatatatattatat-tatataatatataatataaatataatataaattatattatataatatataatataaatataatataaattatataaatataatatatattttattatataatataatatatattatataaatataatatata---aattatataatataatatatattatat-aatata--atatattttattatataaatatatattatatt------atataatatatattttattatataatatatattatatatttatagaatataatatatattttattatataatatatattatataatatatattatatttatatataacat +s panTro2.chrUn 9721736 704 + 58616431 TCTTTCCTCAGGTCCGGTGTTTTCTTACCCACCTCCTTCCCTCCTTTTTATAATACCAGTGAAACTTGGTTTGGAGCATTTCTTTCACATAAAGGTACAaatcatactgctagagttgtgaggatttttagagcttttgaaagaataaactcattttaaaaacaggaaagctaaggcccagagatttttaaatgatattcccatgatcacactgtgaatttctgccagaacccaaatgcctactcccaatatatattatataaatataacatatattttaCCATCTCACTGAGACTTACTATAAAAACATAATACATTTTtatatatatatataatatatataata----taaatataatacatattat-tatattatatatattatataa---atattatatatatttattatat--tatatatattatataa---atataatatattttattatataaatataatatatattatctaaatataatatatattttattatataatgt--tatatattatctaaatataatatatattttattatataa-atataatatattatctaaatataatatatattttattatataaatataatatatattatctaaatataatatatattttattatata--atataatatatattatctaaatataatatatattttattatatga-atataatatatattatatattatatttatatttattat + +a score=772400 +s hg18.chr1 56415 8433 + 247249719 atattattatataaaatatgtataatatatattatataaatatatttatatattatataaatatatatattatatataatTCTAATGGTTGAATTCCAAGAATAATCTATGGCATGAAAGATTTTACCTGTCAACAGTGGCTGGCTCTTCATGGTTGCTACAATGAGTGTGTAAGATTCTGAAGGACTCCTTTAATAAGCCTAAACTTAATGTTCAACTTAGAATAAATACAATTCTTCTAATTTTTTTTGAATAATTTTTAAAAAGTCAGAAATGAGCTTTGAAAGAATTATGGTGGTGAAGGATCCCCTCAGCAGCACAAATTCAGGAGAGAGATGTCTTAACTACGTTAGCAAGAAATTCCTTTTGCTAAAGAATAGCATTCCTGAATTCTTACTAACAGCCATGATAGAAAGTCTTTTGCTACAGATGAGAACCCTCGGGTCAACCTCATCCTTGGCATATTTCATGTGAAGATATAACTTCAAGATTGTCCTTGCCTATCAATGAAATGAATTAATTTTATGTCAATGCATATTTAAGGTCTATTCTAAATTGCACACTTTGATTCAAAAGAAACAGTCCAACCAACCAGTCAGGACAGAAATTATCTCACAATAAAAATCCTATCGTTTGTACTGTCAATGATTAGTATGATTATATTTATTACCGTGCTAAGCAGAAGAGAAATGAAGTGAATGTTCATGATTTATTCCACTATTAGACTTCTCTTTATTCTTAAAAATATTTAAGATCACTAAATTTTTATAGGACTTTAAAAACAGTAATGTGCTGCTTTGAGTGTGTAGGACTAAGAAATGGGATTCAGAGTAGTAAAGAGAAAAGTGGAATTTCCAAGCACTATGAATTACTGTTCTTTAAAAAACAGCAAAAATCAAATAACAGTATTCCTCCAAAAAAGATGGCAAGTGTAAACTCTATACCTTC ATGTCTCCCGTGGAATGTTAGTGATCAATTTCCACTTCTCTCTTTTACATCTTACTTGCCCATTAACTCTTATACCTAATCCAAAGATTGTTAATATGGCTATGTCTCACTTTCAGGACACCTTTTATTTGTTACTTCTCTTCACTGCAAAACTTCTTGAAACAGTACTTATTTTCTCTCCTCCATACACAATTGAAATGGCTCTCAACTCATGCCCAGAAGTCAGTGTTCAGTCTCTCACCTGGCAGATAGCAACTTACAAAGATGCCCCAACAATACCTCCTTGTGTCTAGACAGTCATCATTATCCTTTACCTTTTTCTGTATTTATTTCTGCTCCTAAAAGGGATCTCTATGTAAAGTATTGTTATACTAGTGCTTGTTATAATTATTATCAGAGTTAAAGCCATCACAATGTTCCCAATTACTTAAAGACATTGGAATAACATTTTTTTTATTTTCCACATCTTGCCAAAAAATATTTTGTTATCAGTACCTTaataatggctattatatattgaccattactatttgctagaaaatttatatacctggtcgtatccaatcctcacagaacttctataaagttgtgctattatcacctatattttccagatgtggccgtaagactgaaatcacttaggtgacttgtctaaggtcattcagatacatagtagataacccaggatttgaacacaggcctcctagcacacaagctcatatcttaactactttaatacgttgctcGATGGGATCTTACAGGTCTTCATTCACCCCTTTCCTGCTCACACAACCACAACCTGCAGCTATTACCTATTGTTAGGCTTAAAATAATTACTTGGCTTCATTTCCAAGCTCCCTCCCTTCCAATTCACATTGAGTCCAGAGCTAAATTAAACAATCATTCAAAATTTTTCAGTAGTTCTTGTCTCTATAATAAAACAGAAATGCTTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTC CTATGAAAGTCCTTCACactttctctcatttaaactttattgcattttcctcactttttctcacttcacttttgaattccctattcttttatcctctgttaatttttaagtattatatttgtgatattattttttctttttttctattttttatctttcatttcattttggcctatttttttctcttAAGAACTTTAATATCACCAAATAACATGTGTGCTACAAACTGTTTTGTAGTTCAAAGAAAAAGGAGATAAACATAGAGTTATGGCATAGACTTAATCTGGCAGAGAGACAAGCATAAATAATGGTATTTTATATTAGGAATAAACCTAACATTAATGGAGACACTGAGAAGCCGAGATAACTGAATTATAAGGCATAGCCAGGGAAGTAGTGCGAGATAGAATTATGATCTT-----GTTGAATTCTGAATGTCTTTAAGTAATAGATTATAGAAAGTCACTGTAAGAGTGAGCAGAATGATATAAAATGAGGCTTTGAATTTGAATATAATAATTCTGACTTCCTTCTCCTTCTCTTCTTCAAGGTAACTGCAGAGGCTATTTCCTGGAATGAATCAACGAGTGAAACGAATAACTCTATGGTGACTGAATTCATTTTTCTGGGTCTCTCTGATTCTCAGGAACTCCAGACCTTCCTATTTATGTTGTTTTTTGTATTCTATGGAGGAATCGTGTTTGGAAACCTTCTTATTGTCATAACAGTGGTATCTGACTCCCACCTTCACTCTCCCATGTACTTCCTGCTAGCCAACCTCTCACTCATTGATCTGTCTCTGTCTTCAGTCACAGCCCCCAAGATGATTACTGACTTTTTCAGCCAGCGCAAAGTCATCTCTTTCAAGGGCTGCCTTGTTCAGATATTTCTCCTTCACTTCTTTGGTGGGAGTGAGATGGTGATCCTCATAGCCATGGGCTTTGACAGATATATAGCAATATGCAAGCCCCTACACTACACTACAAT TATGTGTGGCAACGCATGTGTCGGCATTATGGCTGTCACATGGGGAATTGGCTTTCTCCATTCGGTGAGCCAGTTGGCGTTTGCCGTGCACTTACTCTTCTGTGGTCCCAATGAGGTCGATAGTTTTTATTGTGACCTTCCTAGGGTAATCAAACTTGCCTGTACAGATACCTACAGGCTAGATATTATGGTCATTGCTAACAGTGGTGTGCTCACTGTGTGTTCTTTTGTTCTTCTAATCATCTCATACACTATCATCCTAATGACCATCCAGCATCGCCCTTTAGATAAGTCGTCCAAAGCTCTGTCCACTTTGACTGCTCACATTACAGTAGTTCTTTTGTTCTTTGGACCATGTGTCTTTATTTATGCCTGGCCATTCCCCATCAAGTCATTAGATAAATTCCTTGCTGTATTTTATTCTGTGATCACCCCTCTCTTGAACCCAATTATATACACACTGAGGAACAAAGACATGAAGACGGCAATAAGACAGCTGAGAAAATGGGATGCACATTCTAGTGTAAAGTTTTAGATCTTATATAACTGTGAGATTAATCTCAGATAATGACACAAAATATAGTGAAGTTGGTAAGTTATTTAGTAAAGCTCATGAAAATTGTGCCCTCCATTCCCATATAATTTAGTAATTGTCTAGGAACTTCCACATACATTGCCTCAATTTATCTTTCAACAACTTGTGTGTTATATTTTGGAATACAGATACAAAGTTATTATGCTTTCAAAATATTCTTTTGCTAATTCTTAGAACAAAGAAAGGCATAAATATATTAGTATTTGTGTACACCTGTTCCTTCCTGTGTGACCCTAAGTTTAGTAGAAGAAAGGAGAGAAAATATAGCCTAGCttataaatttaaaaaaaaatttatttGGTCCATTTTGTGAAAAACATAAAAAAAGAACTGTCACATCTTAATTTAAAAAATATATGCTTAGTGGTAAGGAGATATATGTCAACTTTTAAGA GGTTGAAAAACAAACGCCTCCCATTATAAGTTTATACTTCACCTCCCACCACTATAACAACCCAGAATCCATGAGGGCATTATCAGGAGTGAGTGGAAGAGTAAGTTTGCCAATGTGAAATGTGCCTTCTAGGTCCTAGACGTCTGTGGTATAACTGCTCATAAGCAGTAGAAAGAATTTAGAGGGATCCAGGCTCTCATCACGTTGGCACAAAGTATATTACTTGGATCCATCTATGTCATTTTCCATGGTTAATGTTTaaaagcacaggctttaaagtaaaaaacaaagagctggattcaactctactgactcttattaatcatgattttgggcacattacgtagctttcatgagctttagtttctacatttataaacaggagattatacctattatgcatggttattatgaaggaaaatgacaaaatagatataaatcaaatagcccacttcgagacatattaagcatgaataaacattagatactattaAAATCCTATATATTAACAAAGCCAAAAGTTTCAAACTTTACTTTTTCCCAACATTCTTGTGAAATATGACACATCCCAATCTTAACAGATGCTCATTTGGGATACTGTACTTGTGAGTGGAAGTGTGTATATTTGTGTGCAAGTGTGTACTCATATACTTCCACCTTACCACCCTAGAAAGGCATGATGAAAATTTAAGATAGAAGGAAAATATAAATTGAAAAAAAAAAACCTTAACAAATGATTCTGACAAATATCTTCTCTTTCCAGGGAGAATCACTGAGCCAGAATAAAATTGAACACTAAATATTCTAAGAAAAAAGGAATCTAGTTTGTCAAAATGTGACTTGAATTAATAGATAAGGAGAGTCAGATGATAAGAGGGTCAAAATTATGTTTATCTTAGGAAAAGTAGAATAGAAAATTTATAAGCAGATTAAAAACACATAATAAAAGTAGTAAATAATAATGACAGTATCTCAAATcagtgcagggg ggaaaggcctactaatgtgatggtgggataattggatagcaatatgggaaaagatatatttaatttatttgctacaccaaatgccaggacaatctctaagtgaattcaagacataactcttttttcaaaaaaactatgcaaatattaaaagaaaacaagttaatgtttttataatctatgaatatggtaaagatGGATAACATTGACTATCAAATTAATTTTTAATGCGTAATAAAACTATGAGAAAATTTAAAAGTGAGAAGAAACTACTTGTAACTCACATAATAGActagtacttctaacacatagggaacttctaaaacaaaacccaaaatattaataggaaaatgggcaaaacagttaaacttacagttcataCATAAGGAGAATCAGTCTTTTTTTTTTTTTTTACAGTTGTAGGCAGAAAACTTTTATTTTTCATTTATTTGTAAAATTTACCCCTAATTTATTCATAATTCATTTAACTGCTAAGGGCATTAATGTGTACAACGCCATGGGAGAAACCAGTATATTCAGAATTTCTCCTGAAATTTGACCAGAAGTTATGGGCATCCCTCCCCTGGGAAGGAGGCAGGCAGAAAAGTTTGGAATCTATGTAGTAAAATATGTTACTCTTTtatatatatacatatatgtgtgtatatgtgtatatatatatacac--------------acatatatacatacatacatacatacatatTATCTGAATTAGGCCTGGTCttttttaatactttaagttctgggatacatgtgcagaatgtacaggtttgttacacaggtatacacctgccatggttgtttgctgcacccatcaactcaccatctacattaggtatttctcctaacgttatccctctccttgcctcccacctcccgacaggccctggtgtgtgatattcccttccctgtgcccatatgttctcattggtcaactcccatttatgagtgagaacatgcggtgt ttggttttctgttcttgtgttagtttgcggagaatgatggtttccagcttcatccatgtccctgcaaaggacatgaactcattcttttttatggctgcaagaaatgcaaatcaaaaccacaatgagatgccatctcacaccagttagaatggcaatcattaaaaagtcaggaaacaatagatgctggagaggatgtggagaaataggaatgcttttacactgttggtgggagcgtacattagttcaaccattgtggaagacagtgtggtgtttcctcaaggatctaaaactagaaataccatttgacccagcaatcccattactgggtatatacccaaacgattgtaagtcattctactacaaagacacatgcacaggtatgtttattgcagcactattcacaatagggaagacttggaaccaacccaaatgcccgtcaatgttagactagataaaatgtggcacatagacCTGGTCTTAAAATCAAGAACAGAGATTGTTACTTTTACATCCATTCCTAATTGATAAACCATTCAGTTATACCACATCTTAGCTTCTGGACTACAATGACCATATTTGGGGttttctttctaatttcattataggttcagagggtacatgtgcaggtttgagacaaaggtatattgcatgatactaaggtttggagtacaaatgattccacctcccaggtagcaagaataatacccaatatgtagtttttcaactctttcccctcttcctccatcctccctctgctactctgtggtgtctgtttttctcatctttatgtccatgtgtactcgatgtttagctcccccttgttaggtgagaacatgtggtatttggttttctgtttcagtgttaattcacttaggataatggcctccaactgcattcatgctgctgcaaaggatgtgactttcttcttattagctgcatatattttgtggtggatttgtaccacatttactttatctagtccaaagttg ttgggcacccaggtggattccatgtctttgctattgtgaatagcactgggacaacccatacaagttcatgtgtctttttggtaaaacaatgtattttcctttgggcatatatgcggtgatggaattgctggatcgagtggtagtttaactcttagttctttgagaaatccccagactgttctccacagtggctggactaagttgcattcccaccagcagtgtagaagtgttccccattctctgtagcctcaccagcacatgttAAACTATCTttaaatatatgaaaaaaatgttcaagtctctcagattaagatgcatgcaaagtaaaatgatacttaaatatcagttctaacctataaaatatcaaatatctgacctcaatatttgataatccaacctgttgatgaagctgtagagagaggcaccctTtttttttttttt-----aattatactttaagttttagggtacatgtgcaccttgtgcaggttagttacatatgtatacatgtgccatgctggtgcgctgaacccactaactcgtcatctagcattaggtatatctcccaatgctatccctcccccctccccccaccccacaacagtccccagagtgtgatattccccttcctgtgtccatgtgatctcattgttcacttcccacctatgagtgagaatatgcggtgtttggttttttgttcttgcgatagtttactgagaatgatgatttccagtttcatccatgtccctacaaaggacatgaactcatcattttttatggctgcatagtattccatggtgtatatgtgccacattttcttaatccagtctatcattgttggacatttgggttggttccaagtctttgctattgtgaataatgccgcaataaacatacgtgtgcatgtgtctttatagcagcatgatttatagtcctttgggtatatacccagtaatgggatggctgggtcaaatggtatttccagttcg agatccctgaggaatcgccacactgacttccacaatggttgaactagtttacagtcccaccaacagtgtaaaagtgttcctatttctccacatcctctccagcacctgttgtttcctgactttttaatgattgccattctaactggtgtgagatgatatctcattgtggttttgatttgcatttctctgatggccagtgatgatgagcattttttcatgtgttttttggctgcatagatgtcttcttttgagaagtgtctgttcatgtccttcgcccacttgttgatggggttgtttgtttttttcttgtaaatttgtttgagttcattgtagattctggatattagccctttgtcagatgagtaggttgcaaaaattttctcccattttctgggttgcctgttcactctgatggtagtttcttttgctgtgcagaagctctttagtttaattagatcccatttgtcaattttgtcttttgttgccattgcttttgTCccaccgatcccacagaaatacaaactaccatcagagaatactacaaacacctctacgcaaataaactagaaaatctagaagaaatgga +s panTro2.chrUn 9723596 8444 + 58616431 atattattatataaaatatgtac--tatatattatataaatatatttatatattatataaatatatatattatatataATTCTAATGGTTGAATTCCAAGAATAATCTATGGCATGAAAGATTTTACCTGTCAACAGTGGCTGGCTCTTCATTGTTGCTACAATGAGTGTGTAAGATTCTGAAGAACTCCTTTAATAAGCCTAAACTTAATGTTCAACTTAGAATAAATACAATTCTTCTAAATTTTTTTGAATAATTTTTGAAAAGTCAGAAATGAGCTTTGAAAGAATTATGGTGGTGAAGGATCCCCTCAGCAGCACAAATTCAGGAGAGAGATGTCTTAACTACGTTAGCAAGAAATTCCTTTTGCTGAAGAATAGCATTCCTGAATTCTTACTAACAACCATGATAGAAAGTCTTTTGCTACAGATGAGAACCCTCGGGTCAACCTCATCCTTGGCATATTTCATGTGAAGATATAACTTCAAGATTGTCCTTGCCTATCAATGAAATGAATTAATTTTATGTCAATGCATATTTAAGGTCTATTCTAAATTGCACACTTTGATTCAAAAGAAACAGTCCAACCAACCAGTCAGGACAGAAATTATCTCACAATAAAAATCCTATCATTTGTACTGTCAATGATTAGTATGATTATATTTATTACCGTGCTAAGCAGAAGAGAACTGAAGTGAATGTTCATGATTTATTCCACTATTAGACTTCTCTTTATTCTTAAAAATATTTAAGATCACTAAATTTTTATAGGACTTTAAAAACAGTAATGTGCTGCTT-GAGTGTGTAGGACTAAGAAATGGGATTCAGAGTAGTAAAGAGAAAAGTGGAATTTCCAAGCACTATGAATTACTGTTCTTTAAAAAACAGCAAAAAACAAATAACAGTATTCCTCCAAAAAAGATGGCAAGTGTAAACTCTATACCTTC ATGTCTCCCGTGGAATGTTAGTGATCAATTTCCACTTCTCTCTTTTACATCTTACTTGCCCATTAACTCTTATACCTAATCCAAAGATTGTTAATATGGCTATGCCTCACTTTCAGGACACCTTTTATTTGTTACTTCTCTTCACTGCAAAACTTCTTGAAACAGTACTTATTTTCTCTCCTCCATACACAATTGAAATGGCTCTCAACTCATGCCCAGAAGTCAGTGTTCAGTCTCTCATCTGGCAGATAGCAACTTACAAAGATGCCCCAACAATACCTCCTTGTGTCTAGACAGTCATCATTATCCTTTACCTTTTTCTGTATTTATTTCTGCTCCTAAAAGGGATCTCTATGTAAAGTATTGTTATACTAGTGCTTGTTATAATTATTATCAGAGTTAAAGCCATCACAATGTTCCCAATTACTTAAAGACATTGGAATAACATTTTTTTTATTTTCCACATCTTGCCAAAAAATATTTTGTTATCAGTACCTTaataatggctattatatattgaccattactatttgctagaaaatttatatacctggtcgtatccaatcctcacagaacttctataaagttgtgctattatcatctatattttccagatgtggccataagactgaaatcacttaggtgacttgtctaaggtcattcagatacatagtagataacccaggatttgaacacaggcctcctagcacacaagctcatatcttaactactttaatacgttgctcGATGGGATCTTACAGGTCTTCATTCACCCCTTTCCTGCTCACACAACCACAACCTGCAGTTATTACCTATTGTTAGGCTTAAAATAATTACTTGGCTTCATTTCCAAGCTCCCTCCCTTCCAATTCACATTGAGTCCAGAGCTAAATTAAACAATCATTCAAAATTTTTCAGTAGTTCTTGTCTCTATAATAAAACAGAAATGCTTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTC CTATGAAAATCCTTCACactttgtctcatttaaaatttattgcattttcctcactttttctcacttcacttttgaattccctattcttttatcctctgttaatttttaagtattatatttgtgatattattttttctttttttctattttttatctttcatttcattttggcctatttttttctcttAAGAACTTTAATATCACCAAATAACATGTGTGCTACAAACTGTTTTGTAGTTCAAAGAAAAAGGAGAAAAACATAGAGTTATGGCATAGACTTAATCTGGCAGAGAGACAAGCATAAATAATGGTATTTTATATTAGGAATAAACCTAACATTAATGGAGACACTGAGAAGCCGAGATAACTGAATTATAAGGCATAGCCAGGGAAGTAGTGCGAGATAAAATTATGATCTTTGGTTGTTGAATTCTGAATGTCTTTAAGTAATAGATTATAGAAAGTCACTGTAAGAGTGAGCAGAATGATATAAAATGAGGCTTTGAATTTGAATATAATAATTCTGACTTCCTTCTCCTTCTCTTCTTCAAGGTAACTGCAGAGGCTATTTCCTGGAATGAATCAACGAGTGAAACGAATAACTCTATGGTGACTGAATTCATTTTTCTGGGTCTCTCTGATTCTCAGGAACTCCAGACCTTCCTATT-ATGTTGTTTTTTGTATTCTATGGAGGAATCGTGTTTGGAAACCTTCTTATTGTCAGAATAGTGGTATCTGACTCCCACCTTCACTCTCCCATGTACTTCCTGCTAGCCAACCTCTCACTCATTGATCTGTCTCTGTGTTCAGTCACAGCCCCCAAGATGATTACTGACTTTTTCAGCCAGCGCAAAGTCATCTCTTTCAAGGGCTGCCTTGTTCAGATATTTCTCCTTCACTTCTTTGGTGGGAGTGAGATGGTGATCCTCATAGCCATGGGCTTTGACAGATATATAGCAATATGCAAACCCCTACACTACACTACAAT TATGTGTGGCAACGCATGTGTCGGCATTATGGCTGTCGCATGGGGAATTGGCTTTCTCCATTCGGTGAGCCAGTTGGCCTTTGCCGTGCACTTACCCTTCTGTGGTCCCAATGAGGTCGATAGTTTTTATTGTGACCTTCCTAGGGTAATCAAACTTGCCTGTACAGATACCTACAGGCTAGATATTATGGTCATTGCTAACAGTGGTGTGCTCACTGTGTGTTCTTTTGTTCTTCTAATCATCTCATACACTATCATCCTAATGACCATCCAGCATCGCCCTTTAGATAAGTCGTCCAAAGCTCTGTCCACTTTGACTGCTCACATTACAGTAGTTCTTTTGTTCTTTGGACCATGTGTCTTTATTTATGCCTGGCCATTCCCCATCAAGTCATTAGATAAATTCCTTGCTGTATTTTATTCTGTGATCACCCCTCTCTTGAACCCAATTATATACACACTGAGGAACAAAGACATGAAGACGGCAATAAGACGGCTGAGAAAATGGGATGCACATTCTAGTGTAAAGTTTTAGATCTTATATAACTGTGAGATTAATCTCAGATAATGACACAAAATATAGTGAAGTTGGTAAGTTATTTAGTAAAGCTCATGAAAATTGTGCCTTCCATTCCCATATAATTTAGTAATTGTCTAGGAACTTCCACATACATTGCCTCAATTTATCTTTCAACAACTTGTGTGTTATATTTTGGAATACAGATACAAAGTTATTATGCTTTCAAAATATTCTTTTGCTAATTCTTGGAACAAAGAAAGGCATAAATATATTAGTATTTGTGTACACCTGTTCCTTCCTGTGTGATCCTAAGTTTAGTAGAAGAAAGGAGAGAAAATATAGCCTAGCttataaa-ttaaaaaaaaatttatttGGTCCATTTTGTGAAAAACATAAAAAAAGAACTGTCACATCTTAATTTAAAAAATACATGCTTAGTGGTAAGGAGATATATGTCAACTTTTAAGA GGTTGAAAAACAAACGCCTCCTATTATAAGTTTATACTTCACCTCCCACCACTATAACAACCCAGAATCCATGAGGGCATTATCAGGAGTGAGTGGAAGAGTAAGTTTGCCAATGTGAAATGTGCCTTCTAGGTCCTAGACATCTGTGGTATAACTGCTCATAAGCAGTAGAAAGAATTTAGAGGGATCCAGGCTCTCATCATGTTGGCACAAAGTATATTACTTGGATCCATCTATGTCATTTTCCATGGTTAATGTTTaaaagcacaggctttaaagtaaaaaacaaagagctggattcaactctactgactcttattaatcatgattttggacacattatgtagctttcatgagctttagtttctacatttataaacaggagattatacctattatgcatggttattatgaaggaaaatgacaaaatagatataaatcaaatagcccactttgagacatattaagcatgaataaacattagatactattaAAATCCTATATATTAACAAAGCCAAAAGTTTCAAACTTTACTTTTTCCCAACATTCTTGTGAAATATGACACATCCCAATCTTAACAGATGCTCACTTGGGATACTGTACTTGTGAGTGGAAGTGTGTATATTTGTGTGCAAGTGTGTACTCATACACTTCCACCTTACCACCCTAGAAAGGCATGATGAAAATTTAAGATAGAAGGAAAATATAAATTG-AAAAAAAAAACCTTAACAAATGATTCTGACAAATATCTTCTCTTTCCAGGGAGAATCACTGAGCCAGAATAAAATTGAACACTAAATATTCTAAGAAAAAAGGAATCTAGTTTGTCAAAATGTGACTTGAATTAATAGATAAGGAGAGTCAGATGATAAGAGGGTCAAAATTATGTTTATCTTAGGAAAAGTAGAATAGAAAATTTATAAGCAGATTAAAAACACATAATAAAAGTAGTAAATAATAATGACAGTATCTCAAATcagtgcagggg ggaaaggcctactaatgtgatggtgggataattggatagcaatatgggaaaagatatatttaatttatttgctacaccaaatgccaggacaatctctaagtgaattcaagacataactcttttttcaaaaaaactatgcaaatattaaaagaaaacaagttaatgtttttataatctatgaatatggtaaagatGGATAACATTGACTATCAAATTAATTTTTAATGCGTAATAAAACTATGAGAAAATTTAAAAGTGAGAAGAAACTACTTATAACTCACATAATAGActagtacttctaacacatagggaacttctaaaacaaaacccaaaatattaataggaaaatgggcaaaacagttaaacttacagttcataCATAAGGAGAATCAGTC--TTTTTTTTTTTTTACAGTTGTAGGCAAAAAACTTTTATTTTTCATTTATTTGTAAAATTTACCCCTAATTTATTCATAATTCATTTAACTGCTAAGGGCATTAATGTGTACAACGCCATGGGAGGAACCAGTATATTCAGAATTTCTCCTGAAATTTGACCAGAAGTTATGGGCATCCCTCCCCTGGGAAGGAGGCAGGCAGAAAAGTTTGGAATCCATGTAGTAAAATATGTTACTCTTTtatatatatacatatatgtgtgtatatgtgtatatatatatacacacacacatatacatacatacatacatacatacatacatacatatTATCTGAATTAGGCCTGGTCttttttaatactttaagttctgggatacatgtgcagaatgtacaggtttgttatacaggtatacacgtgccatggttgtttgctgcacccatcaactcatcatctacattaggtatttctcctaacgttatccctctccttgcctcccaccccccgacaggccctggtgtgtgatattcccttccctgtgcccatatgttctcattggtcaactcccacttatgagtgagaacatgcagtgt ttggttttctgttcttgtgttagtttgcggagaatgatggtttccagcttcatccatgtccctgcaaaggacatgaactcattcttttttatggctgcaagaaatgcaaatcaaaaccacaatgagatgccatctcacaccagttagaatggcaatcattaaaaagtcaggaaacaatagatgctggagaggatgtggagaaataggaatgcttttacactgttggtgggagcgtacattagttcaaccattgtggaagacagtgtggtgtttcctcaaggatctaaaactagaaataccatttgacccagcaatcccattactgggtatatacccaaacgattgtaagtcattctactataaagacacatgcacaggtatgtttattgcagcactattcacagtagggaagacttcgaaccaacccaaatgcccatcaatgttagactagataaaatgtggcacatagacCTGGTCTTAAAATCAAGAACAGAGATTGTTACTTTTACTTCCATTCCTAATTGATAAACCATTCAGTTATACCACATCTTAGCTTCTGGACTACAATGACCATATTTGGGGttttctttctaatttcattataggttcagagggtacatgtgcaggtttgagacaaaggtatattgcatgatactaaggtttggagtacaaatgattccacctcccaggtagcaagaataatacctaatatgtagtttttcaactctttcccctcttcctccatcctccctctgctgctctgtggtgtctgtttttctcatctttatgtccatgtgtactcgatgtttagctcccccttg-taggtgagaacatgtggtatttggttttctgtttcagtgttaattcagttaggataatggcctccatctgcattcatgctgctgcaaaggatgtgactttcttcttattagctgcatatattttgtggtggatttgtaccacatttactttatctagtccaaagttg ttgggcacccaggtggattccatgtctttgctattgtgaatagcactgggacaacccatacaagttcatgtgtctttttggtaaaacaacgtattttcctttgggcatatatgcggtgatggaattgctggatcgagtggtagtttaactcttagttctttgagaaatccccagactgttctccacagtggctgaactaagttgcattcccatcagcagtgtagaagtgttccccattctctgtagcctcaccagcacctgttAAACTATCTttaaatatatgaaaaaaa-gttcaagtctctcagattaagatgcatgcaaattaaaatgatacttaaatatcagttctaacctataaaatatcaaatatctgaccccaatatttgataatccaacctgttgatgaagctgtggagagaggcactctTTTTtttttttttttttaaattatactttaagatttagggtacatgtgcaccttgtgcaggttagttacatatgtatatatgtgccatgctggtgcgctgaacccactaactcgtcatctagcattaggtatatctcccgatgctatccctcacccctccccccaccccacaacagtccccagagtgtgatattccccttcctgtgtccatgtgatctcattgttcaattcctacctatgagtgagaatatgcggtgtttggttttttgttcttgtgatagtttactgagaatgatgatttccaatttcatccatgtccctacaaaggacatgaactcatcctttttaatggctgcatagtatgccatggtgtatatgtgccacattttcttaatccagtctatcattgttggacatttgggttggttccaagtctttgctattgtgaataatgccgcaataaacatacgtgtgcatgtgtctttatagcagcatgatttatagtcctttgggtatatacccagtaatgggatggctgggtcaaatggtatttccagttct agatccctgaggaatcgccacactgacttccacaatggttgaactagtttacagtcccaccaacagtgtaaaagtgttcctatttctccacatcctctccagcacctgttgtttcctgactttttaatgattgccattctaactggtgtgagatggtatctcattgtggttttgatttgcatttctctgatggccagtgatgatgagcattttttcatgtgttttttggctgcataaatgtcttcttttgagaagtgtctgttcatgtccttcgcccactttttgatggggttgtttgtttttttcttgtaaatttgttttagttcattgtagattctggatattagccctttgtcagatgagtaggttgcgaaaattttctcccattttgtaggttgcctgttcactctgatggtagtttcttttgctgtgcagaagctctttagtttaattagatcccatttgtcaattttgtcttttgttgccatttgctttGTCccaccgatcccacagaaatac-aactaccatcagagaatactacaaacacctctacacaaat-aactag-aaatctagaagaaatgga + +a score=362262 +s hg18.chr1 66429 4062 + 247249719 aaaaatcaattcaagatggattaaagacttaaacgttagacctcaaaccataaaaaccctagaagaaaacctaggctttaccattcaggacataggcatgggcaaggacttcatgtctaaaacaccgagagaggcactcttatgcattgttggtgagaatacaaaatggtacaactcttggcaatatcttaaaaaatttacatggtactgacttttggtctagcaatcctacttctatcctaaagatatattggcaaaaatacaaaataattgatgcactcaagtctattcattgaagcattgtttttcatagtaaa---cggaaagtaggccgggcgtggtggctcatgcctgtgatcccagcattttgggaggctgaggcgggcagatcacttgaggccaggaattcaagaccagcgtggctaacatggcgaaaccccatctctaccaaaaatacaaaaattagctgggcgtggtggtgcacacttgtaattccagctacttgagaggctgaggtgggaggatcgcttgaacctgggaggcagaagtttcagtgagcccagaacgtgcctctgcactccagccaggatgacagagcaagactccatctcaaaaaaaaaaaaaaaaaaaaaggaaaataaccaaatgacaattagtgagtactacttgcaaaacttgtacgcaatagagtatgaagcaactataaaatgagagagaaatatctccaaatactactctaaagtaatctacaaggtataccttaactgaaaagaaacaaaaaagtgacaccagaatgctatttttatgttaaaacagggataaataCATTGGATTTACATGCatatataagtatatattttataaatgtttaaataaGCATACTTAAAATGGCAAAAACGTAATACATATATAATTTTCTTATGGCAGGAGGAGGAAACAGGGCAAGGC ACAGGGATAAAAGTTATTCTGAATACATCTTATTTTATATTTTTGACTTTGAAATCCTGTAGCTGTTTTATGTAATATAAAAATGTAATTAAATTAACAGAAAAAAATTACAACTGCTAAAAATCAAGATCTGGCATTTTAATTAAGTTATAAAACATCGGAGAAAAGAATTGTTTCATGGGACACTAACATACAGACAAATTCATTTGGAACCCAATGAATTAATGGGCCTAAGATAACAACCAATAGAAGCTAAAATGACGAATAACTGTTTCAGAAGAAAACATATATGGAATGAATCAGCTGAAAATACCTGAACCTACTGATCAATTTTTATATCACATGAAGTGAATACACATAAAGTATAATATGGAGCACATAGAACCAACTAGAAATGAGCCTAATTGTTAAATATTCTCTATTTTATGAcaatatacaggaaatatgtcgaagagagaaacatgcaagaacaccgtagggtttaataagataatcacaaggtatggaatattcaacaggatgagtatcctggattattcagcaaatacacagagctaaaaagcaggagaaaggaattcatatatatttttaaaaactaaaaagatatattagctgatgcaactttgaaacttctttagatcctgattcaaatagagcaaatttaacaaatatatttgaaactattaaaataatttaaaaatgaccaagtatttgattatatcaaatatagacaataataaccttgaatgtacatggattaaatgtccacttaGGggctgggtgtggtggctcatgactataattccagcactttgggaggccaaggcagaaggattgcttgaggtcagaggttcaagtgcagcctggtcaacacagtgaaaccctatctctacaaaaaacaaacaaaaataaaaaaTT-AACtaattttaaaaaatatatatttCTTCtaaattctccacctgaaagatatagactgactgaatgaatt ttaactatgatctgactatgtgcttccctgaacaaatgcactttacctgt-aaaacacatattaactaaaagaaaagagatggaaaaaggtattccatgaacagaaaccaaaatgagtaggagtagctatacttctgtcagacaaaacagactttaagtcaaaactagctttagaaaaaagacaaaaatgcttattatacaacgataaaggaatcaatccagaaagaggatataacaattttaaatatatatgcagccaacactggagcagccagattcataaagcaaatactactagatcaaaacagagaggtagactcaaatataataatagtgaaggacttcaacaccccactttcagcattaaacagatcatctaataagaaaaccaatctcgcagccctcaccctggagagtccacaggtaccaggggttggtctgaacccccagcacagagcacctgcctcacagaagagtggctgcatttttcttcctgcagttttcagtcctcacttctccttaccaagcagggccacctggcctgggactccggtacaactaccctgccccccacctgacgacttcaataagaagtagcccagcatttctccaaggaggaaataccagagtcaattcacaaccactgcaattgcagtggtaccaccataacagcccttgggctgcagaaggaactaagagtctagtcactacagtggcaccttcagcacaccacagccaccatacagagaggaatccagccccctcccctgggaacccccaccacccactccaccaggcacagcacccagctcataactgcagatcagttgccccacccacagctgagcttacctactggcagtggcccagactttccctagggagaggctcccagaggcaaacggcagcctctctgcccgtgtcacagcagcagttctatccatgctgtcctcaggcttggaaagaaacaaagcgcctgaaggctgcac ctgaacttacagcatgccacagttcccatatggagaggagaccagtctctcctcccagtgagccctaaaccccctgatccccaacaagcagagccctaacctcacaccagcagtacagctgccccatcccccaggctgaacattcccagtaatagcagctccacctggagatggaacccccagggtcaactaaaagcccctctgccactgcctctacagtggtactacccctgctacccttgaactaacaaaggagcaaagaccccagtgctttatccacacctccaacaagctgcagtcgaccacaaagaagaaacacgtctgtctcccatgggtcctacccacaccccctgctgttcaccatggatgatagagtcaacagtgtgaaaacgaccatactgccaaaagcaacctacaaattcaatgcaattcccatcaaaataccaccatcattcttcacagaactagaaaaaacaaggctaaaattcacatggaaccaaaaaagagcccacatagccaaagcaagactaagcaaaaagaataaatctagaggcatcacattactcgacttcaaactatactataaggccatagtcaccaaaacagcatggtactggtataaaaataggcatatagaccaatggaatagaataaagaacccagaaataaagccaaatactttcagccaactgatctttgacaaagcaagcaaaaacataaagtggggaaaggacaccctattcaacaaatggtgctggtataattggcaagccacatgtagaagaatgcaactggatcctcatctctcaccttataaacaaatcaactcaagatggttcacagacttaaatctaagacctgaaaccataaaaattctagaagataagattggaaaaacccttctagacattggcttaggcaaagacttcacaatcaagaacccaaaagcaaacacaacaaaacaaagataaatagatgggacttaatta aactgaaagccttctgcacatcaaaataaataatcagcagagtaaacagacaacccacagagtgggagaaaatcttcacaaactatgcatccaacagaggactaatatccagaatctacaaagaattggaacaaatcagcaagaaaaaaaac +s panTro2.chrUn 9734145 4062 + 58616431 aaaaatcaattcgagagggattaaagaattaaacattggacttaaaaccataaaaaccctagaagaaaacctaggcattaccattcaggacataggcatgggcaaggacttcatgtttaaaacactgagagaggcccttttatgcattgttggtgagaatacaaaatggtacaactcttggcaatattttaaaaaatttacatggtactgacttttggtctagcaatcctacttttatcctaaagatatactggcaaaaatacaaaataattgatgcacacaagtttattcattgaagcattgtttttcatagtaaagaatggaaagtaggccgggtgtggtggctcatgcctgtaatcccagcattttgggaggctgaggtgggcagatcacttgaggccaggaattcaagaccagcgtggctaacatggcgaaaccccatctttaccaaaaatacaaaaattagccaggcatggtggtgcacacttgtaattccagctacttgagaggctgaggcgggaggatcgcttgaacctgggaggcagaggtttcagtgagcccagaacatgcctttgcactccagccaggatgacagagcaagactccatctcaagaaaaaaaaaaaaaaaaa-ggaaattaaccaaatgacaagtagtaagtactacttgcaaaacttgtacgcaatagagtatgaagcaaccataaaatgagtgagaaatatctccaaatactactctaaagtaatctacaaggtataccttaactgaaaagaaacaaaaaagtgacaccagaatgttattttt--gttaaaacagggataaataCACTGGATTTACATGCatatataagtatatattttataaatatttaaataaGCATACTTAAAATGGCAAAAACATAATACATATATAATTTTCTTATGGCAggaggaggaaacagggcaaggc acagggataaaagttattctgaatacatcttattttatatttttgactttgaaatcatgtagctgttttacataatttaaaaatgtaattaaagtaacagaaaaaaattacaactgccaaaaATCAAGATCTGGCATTTTAATTAAGTTATAAAACATCGGAGAAAAGAATTGTTTCATGGGACACTAACATACAGTCAAATTCATTTGGAACCCAATGAATTAATGGGCCTAAGATAACAACCAGCAGAAGCTAAAATGACGAGTAACTGTTTCAGAAGAAAACATATATGGAATGAATCAGCTGAAAATACCTGAACCTACTGATCAATTTTTATATCACATGAAGTGAATACACATAAAGTATAATATGGAGCACATAGAACCAACTAGAAATGAGCCTAATTGGTAAAGATTCTCTATTTTATGAcaatatacaggaaatatgtcgaagagagaaacatgcaagaacaccgtaggatttaataagataatcacaaggtatggaatattcaacaggatgaatatcctggattattcagcaaatacacagagcgaaaaagcaggagaaaggaattcatatatatttttaaaaactaaaaagatatattagccaatgcaactttgaaacttctttagatcctgattcaaatagagcaaatttaacaaatatatttgaaactattaaaataattttaaaatgactaagtatttgattatatcaaatatagacaataataaccttgaatgtacatggattaaatgtccacttaGGggctgggtgtggtggctcatgactataattccagcactttgggaggccaaggcagaaggattgcttgaggtcagaggttcaagtgcagcctggtcaacacagtgagaccctatctctacaaaaaacaaacaaaaataaaaaaTTAAACtaatttttaaaaaaatatatttCTTCtaaattctccacctgaaagatatagactgactgaatgaatt ttaactatgacctgactatgtgcttccctgaacaaatgcactttacctgtaaaaacacatattaactaaaagaaaagagatggaaaaaggtattccatgaacagaaaccaaaatgagtagaagtagctatacttatgtcagacaaaacagactttaagtcaaaactagctttagaaaaaagacaaaaatgcttattatacaatgataaaggaatcaatccagaaagaggatataacaattttaaatatatatgcagccaacactggtgcagccagattcataaagcaaatactactagatcaaaacagagaggtagactcaaatataataatagtgaaggacttcaacaccccactttcagcattaaacagatcatctaataagaaaaccaatctcgcagccctcaccctggagagtccacagggaccaggggttggtctgaacccccagcacagagcacctgcctcacggaagagtggctgcatttttcttcatgcagttttccgtcctcacttctccttaccaagcagggccgcctggcctgggactcctgtacaactaccctgcccctcacctgaccacttcaataagaagtagcccagcatttctccaaggaggaaataccagagtcaattcacaaccactgcaattgcagtggtaccaccataacagcccttgggctgcagaaggaactaagagtctagtcactacagtggcaccttcagcacaccacagccaccatacagagaggagtccacccccctcccctgggaacccccaccacccactccaccaggcacagcccccagctcataactacagatcagttgccccacccacagctgagcttacctactggcagtggcccagactttccccagggagaggctcccagaggcaaacggcagcctctctgcccctgtcacagcagcagttctatccatgctgtcctcaggcttggaaagaaacaaagcgcctgaaggctgcat ctgaacttacagcatgccacagttcccatatggagaggagaccagtctctcctcccagtgagccctaaaccccctgatccccaacaagcagagccctaacctcacaccagcagtacagctgccccatcccccaggctgaacattcccagtaatagcagctccacctggagatggagcccccagggtcaaccaaaagcccctctgccactgcctctacggtggtactactcctgctacccttgaactaacaaaggagcaaagaccccagtgctctatccacacctccaacaagcttcagtcgaccacaaagaaaaaaccagtctgtctcccatgggtcctacccacaccccctgctgttcaccatggatgatagagtcaacagtgtgaaaacaaccatactgccaaaagcaacctacaaattcaatgcaattccaatcaaaataccaccatcattcttcacagaactagaaaaaacaatgctaaaattcacatggaaacataaaagagcccacatagccaaagcaagacttagcaaaaagaacaaatctagaggcatcacattacttgacttcaaactatactataaggccatagtcaccaaaacagcatggtactggtataaaaataggcatatagaccaatggaatagaatagagaacccagaaataaagccaaatacttacagccaacttatctttgacaaagc-agcaaaaacataaagtggggaaaggacaccctattcaac-aatggtgctggtataattggcaagccacatgtagaagaatgcaactggatcctcatctctcaccttataaaaaaatcaactcaagatggttcacagacttaaatctaagacctgaaaccataaaaattcttgaagataacattggaaaaacccttctagacattggcttaggcaaagacttcacaatcaagaacccaaaagcaaacacaacaaaacaaagataaatagatggcacttaatta aactgaaaagcttctgcacagcaaaataaataatcagcagagtaaacagacaacccacagagtgggaggaaatcttcacaaaccatgcatccaacagaggactaatatccagaatctacaaagaattggaacaaatcatcaagaaaataaac + +a score=285297 +s hg18.chr1 70493 3253 + 247249719 aacaCAAGGATGACAGTGGAAATACAAAAACAAGACATAAATATTCTGAATAGTGATAATAAAACAGTGCATACCAGAATAcaaactgtttccaagttacaatggttcaaccatttttcagctttatggtggtgtgaaagtgatatccattcattagaaaccatgctccaggatgggcgcagtgggtcacgcctgtaatcctagcactttgggaggccgaggagggcggatcacaaggtcaagagatcaagaccatcctggccaacatggtgaaaccccgtctctcctaaaaatacaaaaattagctgggcattgtggtgcgtgcctgtaatcccagctattcgggaggctgaggcaggagaatcacttgaaccagggagtcggaggtgttgcagtgagccgagatcgtgccactgcctccagcctggcaacagagtgagactccatctcaaaaaaaagaaagaaaccctactccgaattttgaattttgatattttcctggactaccaatatgtggcacaatgctctctcacaatgttgtgcaacagcggtgagctgcagcttccagtcagctaaatgataataaaggtagataatccatcttgatatcttcctgaagaacataatgcctgcctaccatcaacaggcatcaatactttctaccagctattctcaaccctcatgatcggaagagacagagactgactgtgtcaaagtattagtcccatcattcagcaattaactttagctcaatgcttcaaaaattcttcaggccctgtgtaatttcagctacgtacattaatgatgagtacccatacaaccattctgtttcttattttcagtaccatatttaataaatatcagttattcaatactttatttagacattttgttagattattttgaccaactgaagtctaatctaaatgttctgagcatgttcaaagt aagctaggccaacctataattttcggtgtgctaaatgcatttttaacttatgatattttcagtttacgggggtttgttgagacataacttcatcatacatcaaggagcatctgTAtatgggatatagttaaagcagtgatcagaggaaaatctatagccttaacacatttattaataaaagtgtaggaattaaattatcagctgaaaaatgtaaaaagtatctaaaagagtaagcagaaagtacaagaaagaacccaaagtagaaaaaagtgaaaattaataaaataagaagccaaaaaacagatcaaatcagtaaaccaaaaatcttgttctttaaacaaatcaacaaagttgacaaaaaaattagatcttttaatcatgaataaaaaaaagagaaagcacaaaaatgaataaggaatggtgagagaaataactattgataatcagcaaataaaaaatcattaaaaacaatgttgttcacatctatgaaaaacattgaaagctagagggaatgggtaattttctagaaaaatacaattcaccacaactgacttcaaaaaaaaaaaaaaaaAAAAAGAAGTACCGCACTTATGTGAGCAATTTCCATAGAGAAATACAGTTGTCATGGAATTATAACACACACACAAACACTAGGTTTAGATGTTTTCACAGAGAATTCCACCAAACCTTTAGAAATCAGATCGTCCAaaggcaaattaacaactctcagccatttgaggcaaaatattacaattgaggcaagatatactgtactgaaaacttgaggaaaaagcaggagagaaagttcctttgggaaattcgaatactcaaaagtgcttacatacaatgaaaaatttggaaatccataagcatggccaaggtgggacacatgctcagaaaaggcctgagaagacactaataactcacctttagtaattcctaggctcacagc---aagaaaaaatgaaggctaaggcagaattatatat ggctccgctaagtgttgagggagccccaatacagagtcagtaagcaaagtctgggagaagtttttcata-tttttttctttcttggctccttgcagtcaaggaaatcatttttaaatcactaaatgctaaatgaacacaagctaaaggaaccgagccttcaaacatcaaatataaaaaagaatgcagatattacaaaaccagtttacaaaagttactaaacaaataaaaactacatcccacagtgggtaacaaaaataaccttgaagaagggaaaaatttggtttccagaataaacacattataatatccaaaatgtccagttttcaacaaaaattaagaagcatgcaaataaacacaaaactatggcccatttacagaagaaataaatgagactctccctgagtaag--cagatattgaaaatattagacaaaaactttatataactgtcttaaataaacttaaagagctaaagaaacccaagagaatgacatataaataaataagaaatatgaatttttttaaaggtacaaaaaaattctgaggctgaaaagtacaa----taagtaaaaagttactttttacttagggttccaatagaagatttgagcagctggaaaaaagaatcagtgaacttgatagatcaaatgaaatgattcagtctgaagagcaggaaaatgaaagaatgacaacaaaaaagaatagagcctaaagacctgtgtaacaacatcaagaatgcctacatacagaatcctggtggggagtgaggggcaggaagactatttgaagaaatgtgtttgaaagcttcccaaatttcactaaaaacaaatatatacattcaaaaagctcagtgaacttcatcaaggaaatatacaaagatattcacaccaagacacactatgtttcaaattgtcaaaaggcaaagcgaatgtttgaaagcagcaagagaaaggcaacgcgtcatttacaaaggatcctcaataagtttg acagcagatagtgcattataagccatggatgccagaagagcttaggaaaaaggcaacgcgtcatttacaaaggatcctcagtaagtttgacagcagagagctcattataaaccatgggtgccagaagagcttaggatgacattttaaagttctgaaagaaaaaaacactgtcaaccaaaaattctataacttggaagatgccccttcaagtattaaggataaattacacattcccagattaaaaaaaagaaagagagagagagagaaagagaaagaaagaaag--agaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaagagaaagaaa +s panTro2.chrUn 9741371 3254 + 58616431 AACACAAGGATGACAGTGGAAATATAAAAACAAGACATAAATATTCCGAATAGTGATAATAAAACAGTGCATACCAGAATAcaaactgtttccaagttacaatggttcaaccatttttcaactttatggtggtgtgaaagtgatagccattcattagaaaccatgctccaggatgggcacagtgggtcacgcctgtaatcctagcactttgggaggccgaggaaggcagatcatgaggtcgagagatcaagaccatcctggccaacatggtgaaaccccgtctctcctaaaaatataaaaattagctgggcattgtggtgcgtgcctgtaatcccagctatttgggaggctgaggcaggagaatcacttgaaccagggagttggaggtattgcagtgagccaagatagcaccactgcctctagcctggcaacagggtgagactccatctcaaaaaaaaggaagaaaccctactccgaattttgaattttgatattttcctggactaccaatatgtggcacaatgctctctcacaatcttgtgcaacagcggtgagctgcagcttccagtcagccaaatgataataaaggtagataatccatctttatatcttcctgaagaacataatgcctgcctaccatcaacaggcatcaatactttctaccagctattctcaaccctcatcatcggaagagacagacactgactgtgtcaaagcattagtcccatcattcagcaattaactttagctcaatgcttcaaaaattcttcaggccctgtgtaatttcagctacatacattaatgatgagtacccatacaaccattctatttcttattttcagtaacatatttaataaatatcagttattcaatactttatttagacattttgttagattattttgaccaactgaagtctaatctaaatgttctgagcatgttcaaagt aagctaggccaacctataattttcggtgtgctaaatgcatttttaacttatgatattttcagtttacgggggtttgttgagacataacttcatcatacatcaaggagcatctgTAtatgggatatagttaaagcagtgatcagaggaaaatctatagccttaacacatttattaataaaagtgtaggaattaaattatcagctgaaaaatgtaaaaagtatctaaaagagtaagcagaaagtacaagaaagaacccaaagtagaaaaaagtgaaaattaataaaataagaagcc-aaaaacagatcaaatcagtaaaccaaaaatcttgttctttaaacaaatcaacaaagttgac-aaaaaattagatcttttaatcatgaataaaaaaaagagaaagcacaaaaatgaatacggaatggtgagagaaataactattgataatcaacaaataaaaaatcattaaaaacaatgttgttcacaactatgaaaaacattgaaagctagagggaatgggtaattttccagaaaaatacaattcaccaaaattgacttc-------aaaaaaaaaaaaaagaagtacagcacttatgtgagcaatttccatagagaaatacagttgtcatggaattataacacacacacaaacactaggtttagatgttttcacagagaattccaccaaacctttaGAAATCAGATcatccaaaggcaaattaacaaccctcagccatttgaggcaaaatattacaattgaggcaagatatactgtactgaaagcttgaggaaaaagcatgagagaaagttcctttgggaaattcgaatattcaaaagtgtttacatgtaatgaaaaatttggaaatccatgagcatggccaaggtgggacacatgctcagaaaaggcctgagaaaacactaataattcacctttagtaattcctaggctcacggcaaaaaaaaaaaacgagggccaaggcagaattatatat ggcttggctaagtgttgagggagccccaatacagagtcagtaagcatagtctgggagaggtttttcatattttttttcttttttggctccttgcagtcaaggaaatcatttttaaatcactaaatgctaaatgaacacaagctaaaggaactgagccttcaaacagcaaacataaaaaagaatgcagatattaaaaaaccagtttacaaaagttactaagcaaataaaaactacatcccacagtgggtaacaaaaataaccttgaag-agggggaaatttggtttccagaataaacacattatactatccaaaatgtccagttttcaataaaaattaagaagcatgcaaataaacacaaaagtatggctcatttacagaagaaataaatgagactctccctgagtaagcacagatattggaaatattagacaaaaactttatataactgtcttaaataaacttaaagagctaaagaaacccaagagaatgacatatgaataaataggaaatgtgaattttttaaaaagtacaaaaaaattctgaggctgaaaagtacaataactaagtaaaaagtaactttttacttggggttccaatggaagatttgagcaggtggaaaaaagaatcagtgaacttgatagatcaaatgaaatgattcattctgaagagcaggaaaacgaaagaatgacaacaaaaaagaatagagcctaaagacctgtgtaacaacatcaagaatgcctacatgcagaatcctggtggggagtgaggggcaggaagactatttgaagaaatgtgtttgaaagctccccaaatttcactaaagacaaatatacacattcaaaaagctcagtgaacttcatcaaggaaatatacaaagatattcacaccaagacacactatgtttcaaactgtcaaaaggcaaagtaaatgtttgaaagcagcaagagaaaggcaatgcatcatttacaaaggatcctcaataaatttg acagcagatagcacattataagccatggatgccagaagAGCTTaggagaaaggcaacacatcatttacaaaggatcctcagtaagtttgacagcagagagctcattataaaccatggatgccagaagagcttaggatgacattttaaagttctgaaagaaaaaaacactgtcaaccaaaaattctataacctggaatatgccccttcaagtattaaggataaattacacattcccagattaaaaaaaAAaaaga-agagagggagagagagaaataaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaaagaaagaaa + +a score=24006 +s hg18.chr1 73836 305 + 247249719 aaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag-aaagaaagaaagaaagaaagaa--aagcaagcaagctttaaaagttcatgtttggtaggctgtacttcaagatacacttttaaaaaaaagactccttcagatacaaactaaaaaacactagaaagtaactcaaaaccacataaagaaataactccagtaaagataactacataggtaaatataaaagcaattatcacattttttgtaagtcttttttaatattctatat--gttttaaaacaaatgtgtaaaataatgactata +s panTro2.chr15 87759 308 - 100063422 aaaagaaagaaagaaagaaagaaaagaa--aagaaaaaaggaaaggaaaggaagaaaaagaaaagcaagcaagcaagcaagctttaaaagttcatgtttggtaggatgtacttcaagatacactttaaaaaaaaagactcctgcagatacaaactacaaaacactagaaagtaactcaaaaccacataaagaaataactccagtaaaggtaactacataggtaaatataaaagcaattatcacattttttgtaagtcttttttaatattctatataagttttaaaacaaatgcgtaaaataatgactata + +a score=250753 +s hg18.chr1 74141 2820 + 247249719 aatctatgttaatgaagcatgatgtatacagatgtggtttgtgaaattaccaacataaagaaattcataggaaactaaataataatagagattttgtata-ctattgaagtt--gtttcaatttactctaaattgttccaaattaagaatgttaattgtaaatccccatggtaacc-actaagttaatatcttttgaaaatacagaaaaggaaagcacagggtaaacacagtgatatgctacaaaatagcaactaaacacaaaagaaggcgataattgaggaaattaggaacaaaggaggtataagacatacagaaaacaaaagcaaaatggtaggagtaagcccctctttatcagtaattacattaaatacaaatgaattaaactctccaatccaaagaaagagattaacagaatggattttttaaaaatgatccaactatattgtccacaagatactcactttagatcaaaatacacaatgagttgaaatgaaaggatgggagaaaatattccatgtaagtaataaccaaaggagatctgaggcaaatatacttatatcagacaaaatagactttaagtcaaaaactgttacaaaatacaaagaacagtatatattgatttcaaaattaattaagaagatataacaattataaatatatgtacaccaactaacagggctccaaaatatataatgtaaccattgagagaattaaagggagagacagacaattccacgaaaattgttgggcatttgaaaacccaactttaaataaaagataaaacatctagagcaaatatcaagggaggaattagaggatttgaataaaactataagcaataactatagataacacttctctcaaaaactgcagagtacacattcttctcaagtgaacatggaacattctccagcacagatgatatgttaggccataagataagctca ataaacttaaaaagattgaaatcatgcaaagtatcttcactggccacaatggaatgaaataagatatcaataacaaaagaaaaactagaaaatttacaaatatttggaaattaaacaacacagtatttaccaaccaatgaatcaaagaacaaatcatgagggaaattagaaaatgtttagagacgattgaaaacaaatatataacaagatgggtgtgatatatcaaaagcagtgctcagagttgtaacacctacattttaaaaaagaaacatgtcaaatcaataaccaaactttactcaataaaccgtaaaaggaagagcaaacaaaatccagagctagcagaaggaaggaaatgaagattagagcagagataaatgaaattgagaattaaaaaattatacagagatcaacaaaattaaaagttggttcttttaaaatatcaataaaattaatatacttttacatagactaagcaaaacatctctattcagctgactttttttacaagggagccaacattattcagtggggaataatagctttttcaacaaaaagtgctgggaatactgaatattcatatgcaaaaaaaatgaagctggacccctacctcacattatatacaaaatctagattggatcaataatgtaaatataagagtgaaaaccatacatgcttagaagaaaacatggaaataaaacattgctgtggattggcaatgcgttcttagataatacaccaaaaatacaagcatgaaacaaacaaatGCAGCCAAAATGTACCAGAATCTGAAAACATCTATTATCTATGAAGAATTAGAGGGGAATTTGGTGAAAGAAATatgggagaatgggacattgctctgtgaatgcttttgtgcataattgtacatttttaattaagttaatcttttacactctcaaagtgtgatattaagcaagcaaagataagttattacaagactctaaaaccgaatgcaatgagaaacaagt gaatccaaatatatttcaaatgaatgaatgacataatcaaacttaaggggaaaataataattaatctgattaatttttgactgttcttttagttcaaattgacttttgaacatacttggactacataccattgcttgaaaaaataaaatatctgcaaaaaattattaaatcttcatgataggcttttttctttttatattagtataaatataacaattctgaaacaaatgtatgtgcattgtaagattaagccaatgagtaaatattaatatatttgtattgctagaaccccagattctcactgtgaaaggacagagatacagatatggaataagacaaggaaagaagcagcccactgagttacattagaatcagtattatcaacataaaTATGCAATGTGCTCTCTCACATGCTCTTTCCTTCTCTTAAAAAAATATA--ATATGGACATATTATATATTATATGCATAGACACACGTGTGTCTATACATATCCTATCTATACATATTGAGGATTAACAGGTGCTAGTAGAAAATATTAACTTTCTTTGTATTAACAGGTGTTAGTAGAAAGTAGTAGTAGGTGCTAAGATAAAAGCCATAATTAAAcctcctggtgaatgaacacaccatcacctacaatcttaccaaaaatagaatcaagcacgtgtcctagtcaaacctctggattcaactgtcatttggataaaacgcaaaggatagtgaaaatgtcgatcttcactgagagtctaaccagcaaatttcacagtgtggacatcaagtgacaaaaatcccaaatttttcaacaaatatattgtatgggaaagaaaactttgaaaagaaacctgtatgttagaagagattttaaaaacatgacaaATGAAAAAAAA +s panTro2.chrUn 9745125 2821 + 58616431 AATCTTTGTTAATggagcatgatgtatcaagatgtggtttgtgaatttagctacatcaagaaattcgttggcagctaggtaataatnccgattttgtataactattgaaggttggtttcaatttatgctaaattgttccaaattaagaatgttaattgtaaatccccagggtaacccactaagttaatatcttttgaaaatacagaaaaggaacgcagagggtaaacacagtgatatgctacaaaatagcaactaaacacaaaagaaggcgataattgaggaaattaggaacaaaggaggtataagacatacagaaaacaaaagcaaaatggtaggagtaagcccctctttatcagtaatgacattaaatacaaatgaattaaactctccaatccaaagaaagagattgacagaatggatttttaaaaaatgatccaactatattgtccacaagatactcactttagatcaaaatacacaatgagttgaaatgaaaggatgggagaaaatattccatgtaagtaataaccaaaggagatctgaggcaaatatacttatatcagacaaaacagactctaagtcaaaaactgttacaaaatacaaagaacagtatatattgatttcaaaattaattaagaagatataacaattataaatatatgtacaccaactaacagggctccaaaatatataatgtaaccattgagagaattaaagggagagacagacaattccacgaaaattgttgggcatttaaaaatccaactttaaataaaggataaagcatctagagcaaatatcaagggaggaattagaggatttgaataaaactataagcaataactataggtaacacttctctcaaaaactgcagaatacacattcttctcaagtaaacatggaacattctccagcatagatgatatgttaggccataagataagctca ataaacttaaaaagattgaaatcatgcaaagtatcttcactgaccacaatggaatgaaataagatatcaatatcaaaagaaaaactagaaaatttataaatatttggaaattaaacaacacagtatttaccaaccaatgaatcaaagaacaaaccatgaggcaaattagaaaatgtttagagacgattgaaaacaaagatataacaagatgggtgtgatatatcaaaagcagtgctcagagttgtaacacctacattttaaaaaagaaacatgtcaaatcaataaccaaactttactcaataaaccataaaaggaagagcaaacaaaatccagagctagcagaaggaaggaaataaagattagagcagagataaatgaaattgagaattaaaaaattatacagagatcaacaaaactaaaagttggttcttttaaaatatcaataaaattaatatacttttacatagactaagcaaaacatctctattcagctgactttttttacaagggagccaacattattcagtggggaataatagctttttcaacaaaaagtgctgggaatactgaatattcatatgcaaaaaaaatgaagctggacccctacctcacattatatacaaaatctagattggatcaataatgtaaatataagagtgaaaaccatacatgcttagaagaaaacatggaaataaaacattgctgcagattggcaatgcgttcttagataatacaccaaaaatacaagcatgaaacaaacaaatGTAGCCAAAATGTACCAGAATCTGAAAACATGTATTATCTATGaagaattagagaggaatttggtgaaagaaatatgggagaatgggacattgctctgtgaatgcttttgtgcataattgtacatttttaattaagttaatcttttacactctcaaagtgtgatattaagcaagcaaagataagttattacaagactctaaaaccgaatgcaatgagaaacaagt gaatccaaatatatttcaaatgaatgaatgacataatcaaacttaaggggaaaataataattaatctgattaatttttgactgttctcttatttcaaattgacttttgaacatactttgactacataccattgcttgaaaaaataaaatatctgcaaaaaactattaaatcttcatgataggcttttttctttttatattagtataaatataacaactctgaaacaaatgtatatgcattgtaagattaagccaatgagtaaatattaatatatttgtattgctagaaccccagattctcactgtgaaaggacagagatacagatatggaataagacaaggaaagaagcagcccactgagttacattagaatcagtattatccacataaaTATGCAATGTGCTCTCTCACATGCTCTTTCCTTCTCTTAAAAAAATATATAATATGTGCATAT-----ATTATATGCATAGACACACGTGTGTCTATACATATCCTATCTATACATATTGAGGATTAACAGGTGCTAGTAGAAAATATTAACTTTCTTTGTATTAACAGGTGTTAGTAGAAAGTAGTAGTAGGTGCTAAGATAAAAGCCATAATTAAAcctcctggtgaatgtacacaccatcacctacaatcctaccaaaaatagaatcaagcacgtgtcctactcaaacctctggattcaactgtcatttggataaaacgcaaaggatagtgaaaatgtcgatcttcactgagagtctaaccagcaaaattcacagtgtggacatcaagtgacaaaaatcccaaatttttcaacaaatatattgtatgggaaagaaaactttgaaaagaaacctgtatgttaaaagagattttaaaaatatgacaaATGAAAAAAAA + +a score=163295 +s hg18.chr1 76976 1815 + 247249719 CTTTTAAAAAAGtttgagacagggtctcactctgtcacccaggctggagtgcagtggtgtgaccatggctcactgtggcctcaacctcctggctcaagtgatcctaccacctcagtcttccatgtagctgggactacagctgcgtgccaccacatctggctcatttttttttcttttttaagtagagacggggacttgctatgttgcccaggctagtctcaaactcctaagcacaagcgatcctcccgcctcggcccctgaaagtgctgggattgcaggcatgagccaccacacccggccAAAAGTTGCTTTTGAGGAGTTATTGCTGTGTGGATGTGATATAACCCTTTCTGTCATCTCTTCACAAAACTTTCTGTAAAACATAAAAATCACCTGGACCTTCAGAGATGAGTTTGtttatttttttattttttaaaaaattGCTAATTTACAGAACATGGAGATGAGTATGTTTTGAAGGCTTGGAAGCATGCAAGTGGGAGAAGAAAGGAGTCAGCTACATTCTGGCTGTGTGCAGAGGCAGGTCACTGTGGTGGGAGTGTTCCTGTTTCATGGACTCTGCAAATCGCAATGCTTGGCATGGCCTCCCGACCCTGATGGCAGAGAAGCAAACACCAGTCGGAGAGCTGGGGTCCTCCCAGCCCTCTTGGCCCTGTGGCCAATTTTTTCTTCAATAGCCTCATAAAATCACATTATTTGAGTGCCCATGGCTCCAAAACAAGCAGGGATGCCCATGGACCCTGATTATCCATTGTCACCCTTCCCTCCAAACAGCCACCTCTCCCCTGGAGACAGCCCCATACTCCACTCAGACCTGTGCACTTTCTGGTATCCTTGTCACCTGCTTTTTATGTCTCATTTTACAAACACCAAATTGGAAGACAGCAGGAGCTGCCCCATAATACCAGTAAAGTGAGAAGCAGAGA TAAACTAGTCCTAGACAGCCGACTCATGTTGGGGGCAGCCCACTCACAGTGGCCCTGACCCAACTCTGACTAGAGGCCACTTGctctcaacaccagggtgctcaatggcccgtcctggtactctgctcttctctctccaccttcgctttcctgcaatctatgcagcctgtgactccatccatgggctagtgacccccagaccttctcctgggaccacaggcctgtgtctctatctgctgctcaatacctcccctcgaacatccatggctaaaactgagctcctgatactctctccctacccgcttctctgtggattccccacctccgcgaaggacagcttcatcctttcagctactcaggccagaagattgaagtcatctccttctccaggaaatcgtattgagggagctacaaatatccaaaatccgatcgcttctcctccactacacccgaggcccgccacccatttttgcctgaattgctgcagcagcctcctaaccgatctctgctttcacgtgggcacctcagttttttccagaacaacaaccagagagatctgctcacacccaagtcagaccaggttactcctctgctctcatagcatttggaggaaa-----------------------------------------------------------------------------------------------acccagagtgctcgtgttggccggcagagccggcccccatctcctctgacctcctccccacctcttgccctcagcacccagagtgctcgtgacggccagcagagccagcctccatctcctctgacctcccacctctcgccctcagcaccCAGAGTGCTCGTGTTGGCCAGCAAAGCCGGCCCCCATCTCCTCTGACCTCCCACCTCTCGCCCTCTGCACCCAGAGTGCTCGTGACGGCCAGCAGAGCCGGcccc +s panTro2.chrUn 56815378 1906 - 58616431 cTTTTAAAAAAGtttgagacagggtctcactctgtcacccaggctggagtgcagtggtgtgatcatggctcactgtagcctcaacctcctggctcaagtgatcctaccacttcagtcttccatgtagctgggactacagctgcgtgccaccacatctggctcttttttttttcttttttaagtagagatggggacgtgctatgttgcccaggctagtctcaaactcctaagcacaagcgatcctcccgcctcggcccctgaaagtgctgggattgcaggcatgagccaccacacccggccAAAAGTTGCTTTTGAGGAGTTATTGCTGTGTGGATCTGATATAACCCTTTCTGTCATCTCTTCACAAAACTTTCTGTAAAACATAAAAATCACCTGGACCTTCAGAGATGAGTTTGtttatttttttattttttaaaaaattGCTAATTCACAGAACATGGAGATGAGTATGTTTTGAAGGCTTGGAAGCATGCAAGTGAGAGAAGAAAGGAGTCAGCTACATTCCGGCTGTGTGCAGAGGCAGGTCACCGTGGTGGGAGTGTTCCTGTCTCATGGACTCTGCAAATCGCAATGCTTGGCATGGCCTCCCGACCCTGATGGCAGAGAAGCAAACACCAGTCGGAGAGCTGGGGTCTTCCCAGCCCTCTTGGCCCTGTGGCCAATTTTTTCTTCAATAGCCTCATAAAATCACATTATTTGAGTGCCCATGGCTCCAAAACAAGCAGGGATGCCCATGGACCCTGATTATCCATTGTCACCCTTCCCTCCAAACAGCCACCTCTCCCCTGGAGACAGCCCCATACTCCACTCAGACCTGTGTACTTCCTGGTATCCTTGTCACCTGCTTTTTATGCCTCATTTTACAAACACCAAATTGGAAGACAGCAGGAGCTGCCCCATAATACCAGTAAAGTGAGAAGCAGAGA TAAATTAGTCCTAGACAACCGACTCATGTTGGGGGCAGCCCACTCACAGTGGCCCTGACCCAACTCTGACTAGAGGCCACTTGctctcaacaccagggtgctcaatggcccgtcctggtactctactcttctctctccaccttcgctttcctgcaatctatgcagcctgtgactccatccatgggctagagacccccagaccttttcctgggaccacaggcctgtgtctctatctgctgctcaacacctccccttgaacatccatggctaaaactgagctcctgacactctctccatacccgtttctctgtggattccccacctccacgaaggacagcttcatcctttcagctactcaggccagaagattgaagtcatctccttctccaggaaatcgtattgggggagctacaaatatccaaaatccgatcgcttctcctccactacacccgaggcccgccacccatttttgcctgaattgctgcagcagcctcctaaccaatctctgctttcacgtgggcacctcagttttttccagaacaacaaccagagagatctactcacacccaagtcagaccaggttactcctctgctctcatagcatttggaggaaaacccagagtgctcttgccctcagcacccagagtgctcgtgacggccagcaaagccggcccccatctcctctgacctcccacctctcgccctctgcacccagagtgctcgtgacggccagcagagccggcccccgtctcctctgacctcc----cacctctcgccctctgcacCCAGAGTGCTCGTGACGGCCAGCAAAGCCGGCCCCCGTCTCCTCTGACCTCCCACCTCTCGCCCTCAGCACCCAGAGTGCTCGTGACGGCCAGCAAAGCCGGCCCCCATCTCCTCTGACCTCCCACCTCTCGCCCTCTGCACCCAGAGTGCTCGTGACGGCCAGCAAAGCTGGcccc + +a score=108492 +s hg18.chr1 78793 1178 + 247249719 tctcctctgacctcccacctctctccctcagctagtcctcgaacatgtctgatgtggtcccaccttgggacccacattgctactcctctgcctgtaggggtacccacagttatccacacagttcactcctgtctttcaggtctttgtgcaaatatcaccttctcagtggagacTACaccttcaggacttaggctgtgcctggcacatagtaggtgctcagtagacactggttgtaggaaggaatCTACAGGTTGAAATAAGGAGATCATTTCCCTGAGGTTCCGAAGCTCATATTTACTCACCATTTGTTGTTTACTGCTAATATTGAGCACTATCAGTAAAATACATAAAACCCtttgccaatccaggaagtgaaaatgacactttactgttttagtttgcatttctctgcttacaaatggattacacgcattttcatgtgctgttggctacttATTCATTCAGAAAACATACTAAGTGCTGGCTCTTTTTCATGTCCTTTATCAAGTTTGGATCATGTCATTTGCTGTTTTCTTTCTGATGTAAACTCTCAAAGTTTGAAGGGTATTGTCTTTTCCTGACACATACGTTGTAAATAATTTTCTGGCTTACATTTTGACTTTTAATTTCATTCACGATGTTTTTAATGAATAATTTTAATTTTTATGAATGCAAGTTAAAATAATTCTTTCATTGTGGTTTCTGACATGTCATGCCAATAAGGGTCTTCTCCTCCAAGAGCACAGAAATATTTGCCAATACTGTCCTTAAAATCGGTCACAGTTTCATTTTTTATATATGCATTTTACTTCAATTGGGGCTTCATTTTACTG---GCCCTATTTGAAGCAAGTTTCTCAGTTAATTCTTTTCTCAAAGTGCTAAGTATGGTAGATTGCAAACATAAGTGGCCACATAATACTCCCACCTCctttgcctcctctccc aggaggagatagcctccatctttccactccttaatctgggcttggccaagtgacttacactggccaatgggatattaacaagtctgatgtgcacagaggctgtagaatgtgcactggggcttggtctctcttgctgccctggagaccagctgccCCACGAAGGAAACAGAGCCAACCTGCTGCTTCCTGGGGGGAGACAGTCCCTCAGTCCCTCTGTCTCTGCCAATCAGTTAA +s panTro2.chrUn 56817286 1178 - 58616431 tctcctctgacctcccacctctctccctcagctagccctccaacatgtctgatgtggtcccaccttgggacccacattgctactcctctgcctgtaggggtacccacagttatccacacagttcactcctgtctttcaggtctttgtgcaaatatcaccttctcagtggagacTACaccttcaggacttaggctgtgcctggcacatagtaggtgctcagtagacactggttgtaggaaggaatCTACAGGTTGAAATAAGGAGATCATTTCCCTGAGGTTCCGAAGCTCATATTTACTCACCATTTGTTGTTTACTGCTAATATTGAGCACTATCAGTAAAATACATAAAACCCtttgccaatccaggaagtgaaaatgacactttactgttttagtttgcatttctctgcttacaaatggattacacacattttcatgtgctgttggctacttATTCATTCAGAAAACATACTAAGTGCTGGCTCTTTTTCATGTCCTTTATCAAGTTTGGATCATGTCATTTGCTGTTTTCTTTCTGATGTAAACTCTCAAAGTTTGAAGGGTATTGTCTTTTCCTGACACATACGTTGTA---AATTTTCTGGCTTACATTTTGACTTTTAATTTCATTCACGATGTTTTTAATGAATAATTTTAATTTTTATGAATGCAAGTTAAAATAATTCTTTCATTGTGGTTTCTGACATGTCATGCAAATAAGGGTCTTCTCCTCCAAGAGCACAGAAATATTTGCCAATACTGTCCTTAAAATCGGTCACAGTTTCATTTTTTATATATGCATTTTACTTCAATTGGGGCTTCATTTTACTGAATGCCCTATTTGAAGCAAGTTTCTCAGTTAATTCTTTTCTCAAAGTGCTAAGTATGGTAGATTGCAAACATAAGTGGCCACATAATACTCCCACCTCctttacctcctctccc aggaggagatagtctccatctttccactccttaatctgggcttggccatgtgacttacactggccaatgggatattaacaagtctgatgtgcacagaggctgtagaatgtgcactggggcttggtgtctcttgctgccctggagaccagctgccCCACGAAGGAAACAGAGCCAACCTGCTGCTTCCTGGAGGAGGACAGTCCCTCAGTCCCTCTGTCTCTGCCAACCAGTTAA + +a score=133824 +s hg18.chr1 79971 1468 + 247249719 CCTGCTGCTTCCTGGAGGAAGACAGTCCCTCAGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGAAGACAGTCCCTCAGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCATGGAGGAAGACAGTCCCTCAGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGAAGACAGTCCCTCTGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGAAGACAGTCCCTCTGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGAAGACAGTCACTCTGTCTCTGCcaacccagttgaccgcagacatgcaggtctgctcaggtaagaccagcacagtccctgccctgtgagccaaaccaaatggtccagccacagaatcgtgagcaaataagtgatgcttaagtcactaagatttgggCAAAAGCTGAGCATTTATCCCAATCCCAATACTGTTTGTCCTTCTGTTTATCTGTCTGTCCTTCTCTGCTCATTTAAAATGCCCCCACTGCATCTAGTACATTTTTATAGGATCAGGGATCTGCTCTTGGATTTATGTCATGTTCCCACCTCGAGGCAGCTTTGTAAGCTTCTGAGCACTTCCCAATTCCGGGTGACTTCAGGCGCTGGGAGGCCTGTGCATCAGCTGCTGCTGTCTGTAGCTGAGTTCCTTCACCCCTCTGCTGTCCTCAGCTCCTTCGCCCCTGGGCCTCAGGAAATCAATGTCATGCTGACATCACTCTAGATCTAAAACTTGGGTTCTTGgaccaggtgcggtggctcacatctgtaatcccagcaatttgggaggccgaggcgggtggatcacaaggtcaggagatcaagacgatcctggctaacacggtgaaaccccgtctctactaaaaatacaaaaaaatt agccgggtttggtggcaggtgcctgtagccccagctacttgggaggctgaagcaggagaatggcgtgaacctgggaggtggagctggcagtgagccaagatcacgccactgcactccagactgggagagagagcgagactttctcaaaaaa----aaaaaaaTCTTAGGTTCTTGGATGTTCGGGAAAGGGGGTTA-TTATCTAGAATCCTTGAAGCGCCCCCAAGGGCATCTTCTCAAAGTTGGATGTGTGCATTTTCCTGAGAGGAAAGCTTTCCCACATTATACAGCTTCTGAAAGGGTTGCTTGACCCACAGATGTGAAGCTGAGGCTGAAGGAGACTGATGTGGTTTCTCCTCAGTTTCTCTGTGTGGCACCAGGTGGCAGCAGAGGTCAGCAAGGCAAACCCGAGCCCAGGGATGCGGGGTGGGGGCAGGTACATCCTCTCTTGAGCTACAGCAGATTAACTCTGTTCTGTTTCATTGTGGTTGTTTAGTTTGCGTTTTTTTTTCTCCAACTTTGTGCTT +s panTro2.chrUn 56818581 1471 - 58616431 CCTGCTGCTTCCTGGAGGAAGACAGTCCCTCTGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGAGGACAGTCCCTCAGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGAAGACAGTCCCTCAGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGG-GGAGGACAGTCCCTCTGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGAGGACAGTCCCTCTGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGAAGACAGTCACTCTGTCTCTGCcaacccagttgaccgcagacatgcaggtctgctcaggtaagaccagcacagtccctgccctgtgagccaaaccaaatggtccagccacagaatcgtgagcaaataagtgatgcttaagtcactaagatttgggCAAAAGCTGAGCATTTATCCCAATCCCAATACTGTTTGTCCTTCTGTTTATCTGTCTGTCCTTCTCTGCTCATTTAAAATGCCCCCACTGCATCTAGTATATTTTTATAGGATCAGGGATCTGCTCTTGGATTTATGTCATGTTCCCACCTCGAGGCAGCTTTGTAAGCTTCTCAGCACTTCCCAATTCCAGGTGACTTCAGGCGCTGGGAGGCCTGTGCATCAGCTGCTGCTGTCTGTAGCTGAGTTCCTTCACCCCTCTGCTGTCCTCAGCTCCTTCACACCTGGGCCTCAGGAAATCAATGTCATGCTGACATCACTCTAGATCTAAAACTTGGGTTCTTGgaccaggtgcggtggctcacacctgtaatcccagcaatttgggaggccgaggtgggtggatcacaaggtcaggagatcaagacgatcctggctaacacggtgaaaccccgtctctactaaaaatacaaaaaaatt agccgggtgtggtggcaggtgcctgtagccccagctacttgggaggctgaggcaggagaatggcgtgaacctgggaggtgtagcttgcagtgagccaagatcatgccactgcattccagactgggagagagagcgagactttctcaaaaaaaaacaaaaaaaaCTTAGGTTCTTGGATGTTCGGGAAAGGGGGTTCTTTATCTAGGATCCTTGAAGCGCCCCCAAGGGCATCTTCTCAAAGCTGGATGTGTGCATTTTCCTGAGAGGAAAGCTTTCCCACATTATTCAGCTTCTGAAAGGGTTACTTGACCCACAGATGTGAAGCTGAGGCTGAAGGAGACTGATGTGGTTTCTCCTCAGTTTCTCTGTGTGGCACCAGGTGGCAGCAGAGGTCAGCAAGGCAAACCCGAGCCCAGGGATGCGGGGTGGGGGCAGGTACGTCCTCTCTTGAGCTACAGCAGATTAACTCTGTTCTGTTTCATTGTTGTTGTTTAGTTTGCG-TTTTGTTTCTCCAACTTCGTGCTT + +a score=75360 +s hg18.chr1 81439 811 + 247249719 CATCGGGAAAAGCTTTGGATCACAATTCCCAGtgctgaagaaaaggccaaactctggaaaaaatttgaatattttgagccaaatgtgaggaccacaacctgtgagaacggaaaataaatcctgggaccccagactcactaagccaaagggaaaagccaagctgggaactggcttatgcaaacctgcttcccatctggttcctaaataagatagctattacacaaagacaaaaaagctacatccctgcctctacctccatcgcatgcaaaatgtgtattcagtgaacgctgaccaaagacagaagaatgcaaccatttgcctctgatttacccacacccattttttccacttcttcccctttccccaatacccgcacttttcccctttacttactgaggtccccagacaacctttgggaaaagcacggaccacagtttttcctgtggttctctgttcttttctcaggtgtgtccttaaccttgcaaatagatttcttgaaatgattgagactcaccttggttgtgttctttgattAGTgcctgtgacgcagcttcaggaggtcctgagaacgtgtgcacagtttagtcggcagaaacttagggaaatgtaagaccaccatcagcacataggagttctgcattggtttggtctgcattggtttggtctggaaggaggaaaattcaaagtaatggggcttacaggtcatagatagattcaaagattttctgattgtcaattggttgaaagaattattatctacagacctgctatcaatagaaaggagagtctgggttaagataagagactgtgg +s panTro2.chr1_random 1070246 811 - 9420409 CATCCGGGAAAGCTTTGGATCACAATTCCCAGtgctgaagaaaaggccaaactctggaaaaaatttgaatattttgagccaaatgtgaggaccacaacctgtgagaatggaaaataaatcctgagaccccagactcactaagccaaagggaaaagccaagctgggaactggcttatgcaaacctgcttcccatctggttcctaaataagatagctattacacaaagataaaaaagctacatccctgcctctacctccatcgcatgtaaaatgtgtattcagtgaacgctgaccaaagactgaagaatgcaaccatttgcctctgatttacccacacccattttttccacttcttcccctttccccaatacccacacttttcccctttacttactgaggtccccagacaatctttgggaaaagcacggaccatagtttttcctgtggttctctgttcttttctcaggtgtgtccttaaccttgcaaatagatttcttgaaatgattgagactcaccttggttgtgttctttgattAGTgcctgtgacgcagcttcaggaggtcctgagaacgtgtgcacagtttagtcggcagaaacttagggaaatgtaagaccaccatcggcacataggagttctgcattggtttggtctgcattggtttggtctggaaggaggaaaattcaaagtaatggggcttacaggtcatagatagattcaaagattttctgattgtcaattggttgaaagaattattatctacagacctgctatcaatagaaaggagagtctgggttaagataagagactgtgg + +a score=13698 +s hg18.chr1 82250 144 + 247249719 agaccGTGCATAGTTGCTTCCTGATCAGCTCTTTATTTGATTGAGAGTGAGGCAGGGAAGATTAGAGGGAAGCTTACAGTGGAATTCAGGGCTGAGGCTGCTATTCTTTTGCTCCTTGTAACTTCCTACAGTGTTGTCAGCATC +s panTro2.chr1 223987967 144 + 229974691 AGACCGTGCATAGTTGCTTCCTGATCAGCTCTTTATTTGATTGAGAGTGAGGCAGGGAAGATTAGAGGGAAGCTTACAGTGGAATTCAGGGCTGAGGCTGCTATTCTTTTGCTCCTTGTAACTTCCTACAGTGTTGTCAGCATC + +a score=27022 +s hg18.chr1 82394 321 + 247249719 CACATACTTCTCTG-TGGGGTTggtctcagagccaggttaccttgtcttaggtccagtggcaccctgactggcttggtgtccttgaacaagttacctaacctctccaaacctcagtccctcagttgtaaaattaaaaaaaaaaaaaagaagaagaagagtacctactgtatagcattgatttgaagattgaatgagctggtattatacaacgtttagaagcagtgcctgacacgcaaaaggctctcaacaaatACTATCCTTTACTAATATCCTGTGTGTCTGTATCAGAGCTGGTGGGGTGGAGGGACAGAAACAAGTGGG +s panTro2.chr1_random 7070572 317 + 9420409 CACATAATTCTCTGGTGGGGTTGGTCTCAgagccaggttaccttgtcttaggtccagtggcaccctgactggcttggtgtccttgaacaagttacctaacctctccatacatcagtccctcagctgtaaaatttaaaaaaaaaaaaa--agaagaagagtacctactgtatagcattgatttgaagattgaatgagctggtattatac---gtttaaaagcagcgcctgacacgcaaaagactctcaacaaatACTATCCTTTACTAATATCCTGTGTGTCTGTATCAGAGCTGGTGGGGTGGAGGGACAGAAAGAAgtggg + +a score=198719 +s hg18.chr1 82715 2225 + 247249719 AGAAGGTaaagagatggacaaatgatctctaaagtctctctggcactaacaCAATTCTTTATTATGTGTTTTGTCTGGCTCTTTATATTGATAGCTGTTCCAGAGGCAATCAATAGCTATTAGTCGGTTTTATTCTTATTTTTCTGTCTGATCTTACAGGGGAGCAAACTGTGGCAAAGTATGAACTTACTTCTCAGGAAATTAACCATTATATTGGCAATCACTGTGATTATTTGAACTTCAGCGTCTGGACAAATTTAGTCACATGAAATACAGAAGAGAGATTTCTCATGGTTAAAACGAAGCTCTCTTTATTTGCTTCTGCTAATTAAAAAATCAGAGCTAAAGATACTTAAACACTACAGTTAAAATGCCATGGTTGTCTATTGGCTTAACGAATTCTCTTATGAAATCAACTCTAAAATGCTATCCATCATAAATCATGAAACGCAATTTTTCTTATTCTCTTTAGAGCTTTACAATTCATCTTAAAGACCAGTGTTTACACTCTCTTCTGTAGGTTGTACAATAACTTTTGGCGAGAAAAAATAAAAGTCTGGCTTTCTGACTCATAGGTGTGTTCCCTTTAACAGAAAAAGAAAATATGTCCTCTTTAAAACTGATGATCATTGGTCACCTCAATTTTATTGAAGTTCACTTCTGACCTCTTTAGATGTAGTTCTCTACATAAAACTGCCCAACAGAATTCTCTGTCTGAATGTCTCCTCCACAAACAAAATTTTAAGAACTAAAATTATCATCTTTCCTTCCAAATATGCTCTCCCTATGTCCCCAGGGCTCTCCATGTGTAGAGCTGAGACCATTTGCCACTCAGTTTCCTCACCCAATTAATTACAAGTCCCAACAATTTTCCGGtttttttgtttttgtttttgtttttagacggagtcttgctctgtcaccaggctggtgtgcggtggtgcaat ctcagctcactgcaacctccgctgcctgtgttcaagcgattctcctgcctcagcttcccaagtagctgggattataggtgtgtgccactacatccagataatttttgtatttttagtagagaggggatttcaccatattggcccagatgatctcaatctcttgacctcatgatctgcccaccttggcctcccaaagtgctgggattacaggtgtgagccgccatccctggccCAGTTTTGCCTTTTTAACATCCCTCAGCTCTTCAAATCCATTTTCTcttctctaacacctccccattccccagctcgtaatgaactcgtaagtagattactacaatcacctcccaaatggtcttcctggctccatcagccttgtgaccttcaagttcattttccacatggatgtcagagtaactttctaaaatgaaaatctgaccacgttactctcttgcctaaatccgcctatggccgctgttaggatcaagtctaaactcccgaccctggaacatcaggtcttcgtgctctgttcactgcttctctacctcacctgcaaccaACACCACTCCCACATCCATATGCTGCTCACCGTGTATCAACATGAACAGGAGGTGGGTGTTTCAGTCCCCAGGAAGACACTGGGCCTTTTCAATCATCTACTGCTGTGTAATAACCACCCCGCAAACTGACCACATGATTTCATTTTGCAAGGGTTCCTTCCTTgggctgtgttcagcaaaagggtttactgagctggcaggtccaagatggcctcactcacaggactggctgttgatgggagccttgatgctcttgggctcaccccttatcctccagtaggttagagcttcttacagtggtttcaggcagcatctgaagacagtaaaagcagaagctccaaggcttcttacattctagcctggaaaatcacatcacattgcttccttcata-tttttttggcaaatcaggttgcaaggcttgcccagattag ggtaaagaggcaaagaggctccttttcttTTCttttctttttttttttttttttttttttgagtcagaatctcgctctgttgcccaggctggagtgcagtggtgcaatctaggctcactgcaagctctgcctcctgggttcacgtcattctcctgcctcaggctcccaagtagctgagactacaggcacctaccaccacgcctggctaatttttttttattttt------tattttttagtagagactgtgtttcactgtgttagccaggatggtctccatctcctgacctcgtga +s panTro2.chr1 223988426 2212 + 229974691 AGAAGGTAAACAGATGGGCAAATGATCTCTAAAGTCTCTCTGGCACTAACACAATTCTTTATTATGTGTTTTGTCTGGCTCTTTATATTGATAGCTGTTCCAGAGGCAATCAATACCTATTAGTCGGTTTTATTCTTATTTTTCTGTCTGACCTTACAGGGGAGCAAACTGAGGCAAAGCATGAACTTACTTCTCAGGAAATTAACCATTATGTTGGCAATCGCTGTGATTATTTGAACGGCAGCATCTGGACAAATTTAGTCACATGAAGTACAGAAGAGAGAGTTCTCATGGTTAAAACGAAGCTCTCTTTATTTGCTTCTGCTAATTAAAAAATCAGAGCTAAAGATACTTAAACACTACAGTTAAAATGCCATGGTTGTCTATTGGCTTAATGAATTCTCTTATGAAATCAACTCTAAAATGTTATCCATCATAAACCATGAAACACAATTTTTCTTATTCTCTTTAGAGCTTTACAATTCATCTTAAAGACCAGTGTTTACACTCTCTTCTGTAGGTTGTACAATAACCTTTGGCGAGAAAAAATAAAAGTCTGGCTTTCTGACTCATAGGTGTGTTCCCTTTAACAGAAAAAGAAAATATGTCCTCTTTAAAACTGATGATCATTGGTCACCTCAATTTTATTGAAGTTCACTTCTGACCTCTTTAGATGTAGTTGTCTACGTAAAACTGCCCAACAGAATTCTCTGTCTGAATGCCTTCTCCACAAACAAAATTTTAAGAACTAAAATCATCATCTTTCCTTCCAAATGTGCTCTCCCTATGTCCCCAGGGCTCTCCATGTGTAGAGCTGAGACCATTTGCCACTCAGTTTCCTCACCCAATTAATTGCAAGTCCCAACAAttttcc------------tttttttttttttttaaatggagtcttgctctgtcaccaggctggtgtgcggtggtgcaat ctcagctcactgcaacctccgctgcctgggttcaagcgattctcctgcctcagcttcccaagtagctgggattataggtgtgtgccactacatccagataatttttgtatttttagtaaagaggggatttcaccatattggcccagatgatctcaatctcttgacctcatgatctgcccaccttggcctcccaaagtgctgggattacaggcatgagccaccatccctggccCACTTTTGCCTTTTTAACATCCCTCAGCTCTTCAAATCCATTTTCTcttctctaacacctccccattccccagctcgtaatgaactcttaagtagattactacaatcacctcccaaatggtcttcctggctccatcagccttgtgaccttcaagttcattctccacatggatgtcagagtaactttctaaaatgaaaatctgaccacgttactctcttgcctaaatctgcctatggccgctgttaggatcaagtctaaactcccgaccctggaacatcaggtcttcgtgctctgttcactgcttctctacctcacctgcaaccaacaccactcccacatccatattctgctcACCGTGTATCAACATGAACAGGAGGTGGGTGTTTCAGTCCCCAGGAAGACACTGGGCCTTTTCAATCATCTACTGCTGTGTAATAACCACCCCGCAAACTGACCACATGATTTCATTTTGCAAGGGTTCCTTCCTTgggctgtgttcagcaaaagggtttactgagctggcaggtccaagatggcctcattcacaggactggctgttgatgggagccttgatgctcttgggctcaccccttatcctccagtaggttagagcttcttacagtggtttcaggcagcatctgaagacagtaaaaacagaagctccaaggcttcttacattctagcctggaaaatcacatcacattgcttccttcatattttttttggcaaatcaggtttcaaggcttgcccagattag ggt--------aaagaggctccttttcttttcttttcttttcttttctttttttttgtttgagtcagaatctcgctctgttgcccaggctggagtgcagtggcacgatctaggctcactgcaagctctgcctcctgggttcacgccattctcctgcctcaggctcccaagtagctgagactacaggcacctgccaccacgcccggctaattttttttttttttttttttgtattttttagtagagactgtgtttcactgtgttagccaggatggtctccatctcctgacctcgtga + +a score=51505 +s hg18.chr1 84940 586 + 247249719 tccTTGCAAAGGGACATGCAGACCACATTAGTGAGAATATGTGCCTGTATTTTGCAATCTGTAACATGGGCATAAACTAAATGTTTTCCAAAGGGAATAGGGCAAAACAAAAAGGACCTTGACCACTCCTT-GGCCCTGAATAAATCCAGGAAGCCTAAGAGTATGACTATCCTGAGGTAGAAAGAGGGTCACATGCTGGATAAGAGGTACCTGGGCTCTCCACTTACAAGAAGAGAGCATGGTTACATTTATAATCACCATTCCCAACATGCTGTGAGTGCAGGCAGCTACCAGGAGGAGAACAAAGGAAATAACCAGGACACTCATCTCTAAACCTGTTAATTTAATCACACGGAACACTTCTATTTAAAATTCCCGAGAGTTAAGATGTAAGAATGCTTATCAAGGTAAATGCTGTTCACACTGCTTGGAGTGTCAGGCCTAGATCTCTATCCATCAGAaacaacaatatcaataacaacaacagcaacaTGATGATGGGGCAATTTCTTAAAAGCACCATGTATTTTATCGATACATGTCCGTTGCAGAAAATCCAGGTGAATCCAAAGAAGAAATAAATGTC +s panTro2.chr1_random 7071473 587 + 9420409 TCCTTGCAAAGGGACATGCAAACCACATTAGTGAGAGTATGTGCCTGTATTTTGCAATCTGTAACATGGGCATAAACTAAATGTTTTCCAAAGGGAATAGGGCAAAACAAAAAGGACCTTGACCACTCCTTTGGCCCTGAATAAATCCAGGAAGCCTAAAAGTATGACTATCCTGAGGTAAAAAGAGGGTCACATGCTGGATAAAAGGTACCTGGGCTCTCCACTTACAAAAAGAAAGCATGGTTACATTTATAATCACCATTCCCAACATGCTGTGAGTGCAGGCAGCTACCAGGAGGAGAACAAAGGAAATAACCAGGACACCCATCTCTAAACCTGTTAATTTAATCACATGGAACACTTCTATTTAAAATTCCCGAGAGTTAAGATGTAAGAATGCTTATCAAGGTAAATGCTGTTCACACTGCTTGGAGTGTCACGCCTAAATCTCTATCCATCAAAAACACCCATATCAGTAACAACAACAGCAACCTGATGATGGGGCAATTTCTGAAAAGCCCCATGTATTTTATCAAAACATGTCCGTTGCAAAAAATCCAGGTGAATCCAAAAAAAAAATAAATGTC + +a score=89302 +s hg18.chr1 85526 984 + 247249719 TTCCACAATCCCATAGCCCAGAGCTAACTAACCACTATAAAGAACCCAGCGTGGTTTTAACTAATGGATCAAAAGATGCTCATCAAAGGCTCTGAGCTTTCCTGAGTGCTAACAGGAAACATCCAGCATCACTGGTCTCTCCAAGGCTGCAGGTGTCTTTGCCCATAGTGCCTGTTTTGTGTCAGGGAAAGAATCAACCTGGGAGCCAAGCCCAGGAATCAGGATGACCAAGACATACTGCACAAGGAGGGAACAAACCCATCCAAGGACACTCAAGGACAAATCAAGCAAATGAATTTAAGGGAGACGTGCTCATGGTCTGCTTTGCTGCTCAGCATGGCTGGGAGGCACAGTGGAAGATCATGCATCCTGCCCCTGGGACTCCTCTGCCAGAGCCTGAGAGCTTTCTCCTGCCCACAGGCTAGGGGTAGGGCAGTTGGAATTGATCCATGCCTTCTAGCTAGACTGTGGGTCCCCTCAGTCTTGGGCATGGTGACAGCCCAGCATCAGACAGAGGTCAGTATCAAACTAGAAAATTTAATAAATACTGTCAGATTTGTAGACCCAAGAAAATATAAACTGCCAATCACGGAGGAAAAAAA-TCTCTCAATGATCTTATCTTTATATGATTCCCTTGCTGCCTGGAGATTGACATTTCCTTGGGGATAATCTGGTCATAGGATTGGTGAAGGTGGAAGGGAGGCAACCTCCAAAGGTGGGGCCCTCTGCTCACCTGGGACAGGGAGGGCCTGAGGTAGGTGTCTGTGTGGGCTGGGGAGGAGGATGGGAGCAGTGCTTCTAGATGTTTCCACTTTCTCCTCATTAGATAATAACGAATGGGTGATTTCCCTAGTCACTGCAGTGTGAGGAAATCTACAAAATTAATTTCACAATACGCTTTACAGGATAGGTGGAGAAACACATGAAGTACAACTGCAGTGGGTTAT AAAAAACGGCCTTTCGAGTTGAGCAATAAATTCGTTC +s panTro2.chr1 223991333 983 + 229974691 TTCCACAATCC-ATAGCCCAGAGCTAACTAACCACTATAAAGAACCC-GTGTGGTTTTAACTAATGGATCAAAAGATGCTCATCAAAGGCTCTGAGCTTTCCTGAGTGCTAACAGGAAACATCCAGCATCTCTGGTCTCTCTAAGGCTGCAGGTGTCTTTGCCCATAGTGCCTGTTTTGTGTCAGGGAAAGAATCAACCTGGGAGCCAAGCCCAGGAATCAGGATGACCAAGACATACTGGACAAGGAGGGAACAAACCCATCCAAGGACACTCAAGGACAAATCAAGCAAATGAATTTAAGGGAGACCTGCTCATGGTCTGCTTTGCTGCTCAGCATGGCTGGGAGGCACAGTGGAAGATCATGCATCCTGCCCCTGGGACTCCTCTGCCAGAGCCTGAAAGCTTTCTCCTGCCCACAGGCTAGGGGTAGGACAGTTGGAATTGATCCATGCCTTCTAGCTAGACTGTGGGTCCCCTCAGTCTTGGGCATGGTGACAGCCCAGCATCAGACAGAGGTCAGTATCAAACTAGAAAATTTAATAAATGCTGTCAGATTTGTAGACCCAAGAAAATATAAACTGCCAATCACAGAGGAAAAAAAATCTCTCAATGATCTTATCTTTATATGATTCCCTTGCTGCCTGGAAATTGACATTTCCTTGGGGATAATCTGGTCATAGGATTGGTGAAGGTGGAAGGGAGGCAACCTCCGAAGGTGGGGCCCTCTGCTCACCTGGGACAGGGAGGGCCTGAGGTAGGTGTCTGTGTGGGCTGGGGAGGAGTATGGGAGCAGTGCTTCTAGATGTTTCCACTTTCTCCTCATTAGATAATAACGAATGGGTGATTTCCCTAGTCACTGCAGTGTGAGGAAATCTACAAAATTAATTTCCCAATACACTTTACAGGATAGGTGGAGAAACCCATGAAGCACAACTGCAGTGGGTTAT AAAAAATGGCCTTTCAAGTTGAGCAATAAATTCATTC + +a score=248118 +s hg18.chr1 86510 2747 + 247249719 AAGCAGCCATTCTGAAGGACAAAC-TGGCTCTGTATTTAAGAGGGGCATTCCAGCACTTCTCTAGCCACTGGGTTGACAATGACTCACCAAAGCCTCTGGTAGCCACCACAGGACACCCAGAGCATATGTTTTAAAGCTGAACACCAAACTGCGGACTTCGGGAGTAAGTGAACTGACTGGTTTTTATTTTGTTTTACTGCTTTTAACATTACAGTAACTGTTACAGGTTCCAGCAGGCTAACTGGGTGGAAATGAGTTTGGTTTCACTTAGTCTCTCTAAAGAGAAAGCAAGTCGGTAGACTAATACCTAATAAAAGCAAAGCTGCCAACAATTGAAATTGCCTAGGCTGCTCTGTGTGTCCCACAtgcatgggtgtgggtgccagtgtgtgtgcgtgtgtgcatgcatgtgcatgtgtgtTGGGATAGAGTGGTAAGAAAATGGGAAATAATAAGAATGTTCAGTCCATAGCCCTTCATTATAAAAAGGTGAGCTGTAATAAATACTAGTGCCACATTTAGCCAAAACTTTACTCCAGCCAAAGGTGATATTTTCATGATAACATCCTGTGATTGCTTTGTTCTTCGTCTTTTATGTTCTTCCTAGATGGGCTCAGAACATACAAGAATTAAGTACACATCTTATTTTCCAGTGATAATGCTACCGGCAAATTCTGTTGTTTGTATAAACATCAGCCATGTTTATATAACTAAACTAGTGTTTTGTTTTGTCAATTCAGCAAGAAATTAGACCAAATGGTGGCTTAATGCTGCATTGATTTGGCTATCAATTTGTTTTCACTTTTCTGCAAAATAATTAATACATTATTAAATTGAATTGTGCTGATGCCACAGTTGTTCTTATCTCAAGTGTCTTAAAATTCATTTAATTTGTTTTTCCTTTGGTTTCATTATTCAAATTTTAACTTCAGTTCTCAAGA TTTTATCTGATGGAAGAGATGGAGTCCATTACTAAGGACTCCATTGTGCTCCATCATGCCAGAGTTGTAAAATAGATCTTTTAAAGGAAATTTACTGTGATTTTTTTTCTATTTAAGAGCTTCCTCTCCAGTTGAGCATGTAAGAAAATTATACCAGGAGAATACAGTAAACTCTATGAGGCAAGCTATAAACATGTAGCATTGTGATTAGGGctggttctccttctagagacatggtaggattgcaatttcataccatccttgaagttagagagagccacgtgactcatttagccaatgaactgtgagcagaatgacatgtcacttccagctgaagctttaaCAATCTGAGAGACATTCATACATTTTCCATGTGCTGTAGCCTTATACCCAAAGCCTGGGTCCCAAGTGACCATGACAGGCAGAGCTCCCTGttgagccacagagatttagagaatggctgttaacacagcataatccagcccatcctgactaatCTGATATTAACATGTATAATAAAGAATTCTATCAATGCTGAGGGAAGATGACTAGTTAAGGTCCTAGGTTGCAAGTCTCAAAACCTCTTCTAAGGATTGTAGACAGGAAATTAAATGACTTCTAGTCCCTAGAGTTCCCAATCTCCTACCATCCCATCCTAATATGACAGAAGTAATTCCTGAGTTGCTTCTGAAACCAGAGCTTCCCTCAGAACCCTTAGCCTGCCAGATGGCTTCTTGGAGAGCCCTCACTCACTTTTCTCCTTCTGCTATTGCTGCTCATTCATTCCAGTTTTTAAAAATTCATCTTTATCCAGGAACCTCGCTTCTAGAAAAGTCATACAGGTGCTTCCAGGAGGCTACATGGGCACCCATATTTTTCTAGCCACTTTCATTAGACCAATGCAGCAGAGAAGAAAAGCCTCAATAATTATTATGACATGGCATGTTAGGATACCAAGTAAATTGCATTTGTAAAATGTGATTTTCTGT TGGTGTTCACTTCAGCTCTACTGACATTTGGTAAGTATTATTGACTGACTGACTAACTAATGTGGTCATTAGTCTTCATAAAGAAAGGCTCTCTACAAAAACGGAGGGATGCCCTTTTTCTGGCATTTAATACGTAAGAAATTGCCTCCAATAGAAACCAGAGTTGCCTGATTACTATCAGCACAGGAGAAATGTATTAATGTGCCTTTCTAGTAACAGGTTTTTAGAAAGTCAAATATAAACAAATCTGTCTATTTGTGTGTGTGCATGTGGTAGTGGGGAGGGAAGAAAAAAGGAGGGGGAGAGAAAGAGAAATAAGAACCAAGTTTATTATACTGTATTCAGGGGGAAAAAATTTTCCCAAGGTCCTAACAGAAGAGCAAAGTGCCACTGTCAATAGCCTCAGTAGTGTTAGGGTTGCTtttatttatttatttatttatttatttatttatttatttatttttcc--ttttttttctttctctttttttcttcttttttttttcttttctttc------ttttttttttttttttttttttttggacagagtctcacactgtcacctgggctggagtgcattggtgcaatctcgactcactgcaacttctgcctcccaggttcaagtgattctcctgcctcagccgcccaagtagctgggattacaggtgtctgccaccgtgcctagctaatttttttgtatttttagtagagatgaggtttcactatgttggccaggctggtctcaaactcctgacctcatgatccacccacgttggcctcccaaagtgctgggattacaggcgtgagccaccgcccctg +s panTro2.chr1_random 7073124 2744 + 9420409 AAGCAGCCATTCTGAAGGACAAACGTGGCTCTCTATT-AAGAGGGGCATTCCAGCACTTCTCTAGCCACTAGATTGACAATGACTCACCAAAGCCTCTGGTAGCCACCACAGGACACCCAGAGCATATGTTTTAAAGCTGAACACCAAACTGCGGACTTCGGGAGTAAGTGAACTGACTGGTTTTTATTTTGTTTTACTGCTTTTAACATTACAGTAACTGTTACAGGTTCCAGCAGGCTAACTGGGTGGAAATGAGTTTGGTTTCACTTAGTCTCTCTAAAGAGAAAGCAAGTCGGTAGACTAATACCTAATAAAAGCAAAGCTGCCAACAATTGAAATTGCCTGGGCTGCTCTGTGTGTCCCACAtgcatgggtgtgggtgccagtgtgtgtgcgtgtgtgcatgcatgtgcatgtgtgtTGGGATAGAGTGGTAAGAAAATGGGAAATAATAAGAATGTTCAGTCCATAGCCCTTCATTATAAAAAGGTGAGCTGTAATAAATACTAGTGCCACATTTAGCCAAAACTTTACTCCAGCCAAAGGTGATATTTTCATGATAACATCCTATGATTGCTTTGTTCTTCGTCTTTTATGTTCTTCCTAGATGGGCTCAGAACATACAAGAATTAATTACACATCTCATTTTCCAGTGATAATGCTACCGGCAAATTCTGTTGTTTGTATAAACATCAGCCATGTTTATATAACTAAACTAGTGTTTTGTTTTGTCAATTCAGCAAGAAATTAGACCAAATGGTGGCTTAATGCTGCATTGATTTGGCTATCCATTTCTTTTCACTTTTCTGCAAAATATTTAATACATTATTAAATTGAATTATGCTGACGCCACAGTTGTTCTTATCTCAATTGTCTTAAAATTCATTTAATTT-TTTTTCCTTTGGTTTCATTATTCAAATTTTAACTTCAGTTCTCAAGA TTTTATCTGATGGAAGAGATGGAGTCCATTACTAAGGACTCCATTGTGCTCCATCATGCCAGAGTTGTAAAATAGATCTTTTAAAGGAAATTTACTGTGATTTTTTT-CTATTTAAGAGCTTCCTCTCCAGTTGAGCATGTAAGAAAATTATACCAGGAGAATACAGTAAACTCTATAAGGCAAGCTATAAACATGCAGCATTGTGATTAGGGctggttctccttctagaaacatggtaggattgcaatttcataccatccttgaagttagagagagccacgtgactcatttagccaatgaactgtgagcagaatgacatgtcacttccagcagaagctttaagaatctgagagacattcatacgttttccatgtgctgtagccttatacccaaagcctgggtcccaagtgaccatgacaggcagagctccctgttgagccacagagatttacagaatgtctgttaacacagcataatccagcccaacctgactaatCTGATGTTAACATGTATAATAAAGAATTCTATCAATGCTGAGGGAAGATGATTAGTTAAGGTCCTAGGTTGCAAGTCTCAAAACCTCTTCTAAGGATTGTAGACAGGAAATTAAATGACTTCTAGTCCCTAGAGTTCCCAATCTCCTACCATCCCATCCTAATATGACAGAAGTAATTCCTGAGTTGCTTCTGAAACCAGAGCTTCCCTCGGAACGCTTAGCCTGCCAGATGGCTTCTTGGAGAGCTCTCACTCACTTTTCTCCTTCTGCTATTGCTGCTCATTCATTCCAGCTTTTAAAAATTCATCTTTATCCATGAACCTCGCTTCTAGAAAAGTCATACAGGTGCTTCCAGGAGGCTACATGGGCACCCATATTTTTCTAGCCACATTCATTAGACCAATGCAGCAGAGAAGAAAAGCCTCAATAATTATTATGACATGGCATGTTAGGATACCAAGTAAATTGCATTTGTAAAATGTGATTTTCTGT TGGTGTTCACTTCTGCTCTACTGACATTTGGTAAGTATTATTGACTGACTGACTAACTAATGTGGTCATTAGTCTTCATAAAGAAAGGCTCTCTACAAAAACGGAGGGATGCCCTTTTTCTGGCATTTAATACGTAAGAAATTGCCTCCGACAGAAATCAGAGTTGCCTGATTACTATCAGCACAGGAGAAATGTATTAATGTGCCTTTCTAGTAACAGGTTTTTAGAAAGTCAAATATAAACAAATCTGTCTATTTGTGTGTGTGCATGTGGTAGTGGGGAGGGAAGAAAAAAGGAGGGGGAGAGAAAGAGAAATAAGAACCAAGTTTATTATACTGTATTCAGGGGGAAAAAATTTTCCCAAGGTTCTAACAGAAGAGCAAAGTGCCACTGTCAATAGCCTCAGTAGTGTTAGGGTTGC--------atttatttatttatttatttatttatttatttatttttccttttttttttctttctctttttttcttcttttttttttcttttctttctttcttttttttttttttttttttttttttggacagagtctcacactgtcgcctgggctggagtgcattggtgcaatcttgactcactgcaacctctgcctcccaggttcaagtgattctcctgcctcagccgcccaagtagctgggattacaggtgtctgccaccatgcctagctaatttttttgtatttttagtagagatgaggtttcactatgttgg-caggctggtctcaaactcctgacctcgtgatccacccaccttggcctcccaaagtgctgggattacaggcgtgagccaccgcccctg + +a score=206892 +s hg18.chr1 89257 2260 + 247249719 gccAGGATTGCTTTTACAGCCAGTCTTCAGGTGCCCACTGTAGGAACAATGTCATTTAACCCTCGGGATTATTCTGTGCCAAATATGGATAATGACTAATATCCAACACAGATATTCTCAGCTCAGAAGAGCAATTAGCAAATTCATAAATTAAGTGCTTGCTTCCTCTTTAGTCAAATACAAACGTTTGTTAAAAGATATTATTTTGCTTTACACTTTTTCTCTCAGAAATAAGCAGATGCTTGAATTCCCACAGTGCTGCTTGAGCCTCACACCATGTCATCCTGCCAGGCACCCAGATCCAGTTCTAGAGTTTCACATGATCGTGAgtgttggttaataagtcaatgtgaactgggaggggagatttttcaggagtgccacagggctctccctttaatcACATACACTCCCTGCTTTCATTGGAAAGTGTATAATGATGTCAGAGTGCCCCAGAATGGAGCTAGTTGGAAGACTGCCGTCATAGGGATGCCTTAGTGAATTAATAAGGTTTTAATTTCTGGCTCTCAACTTTGTAGATGTAAAAGTTGATTTATCAATATGTGAGAAAGGATGAATCTTTCTGAAGGTTATGTCATCACACTCACTAAGCACACAGAGAATAATGTCTAGAATCTGAGTGCCATGTTATCAAATTGTACTGAGACTCTTGCAGTCACACAGGCTGACATGTAAGCATCGCCATGCCTAGTACAGACTCTCCCTGCAGATGAAATTATATGGGATGCTAAATTATAATGAGAACAATGTTTGGTGAGCCAAAACTACAACAAGGGAAGCTAATTGGATGAATTTATAAAAATATGCCTCAGCCAAAATAGCTTAATTCACTCTCCCTTATCATAAGGATAATCTTGCCTAAAGGGACAGTAATATTAAAGACACTAGGAATAACCTCTGTACTTTGGACAGTAGACCTGC ATAGCCCATTAGGCCTCAATGAAGTCTTATGCAAGACCAGAAGCCAATTTGCCA-TTTAAGGTGATTCTCCATGTTTCTGCTCTAACTGTGCTTCACAATACTCAAAACACTAAATCAGGATGTTTCCTGGAGTTCAGGGAGCTGTCCGTGTTACTGAGCAGTTCTCAGCAACACAAAGATCCTACTGACTCCTCATCAGACTTCTTTCTCACTGGAATTTTACACCTGGGCTGTTAACACCAGGCCAGGTCAAATTCAAAGGAGAGAAAAAAGCTCATTATGAAGGGTAAAATCCAAAACACTGTGCATAAAGATATG---GCACAATTTTTATACATAAAGATTTCATAAAACCAAAGCATCAGGAAATGAAAAGAGATACAGAAAGAAAAATGATGGTAAATGAGACATTAATTTACCCTTCTAATCTCTATCACAGCAAAAAGATAATTAAAAAATCTATATGAGGACCACAAAATACACAAAAATTATGTAGCAAAGCCTATAGCCTGAAAAAGTAAACATTGAAATTTGTATGTCCATAAAATGTTTACAAAATTCAGTACATATTACACACCCCACCCTAAAAACATCTAAGCAAAGTAGAGAATGTAGAAATGCTACAGATTATATTCTCTGATTATGACACAACAAAACTAGAAATTACAGCATGGAAATTTAAAAGCTTTCTCTTAAATAATTCTATGTCAAAAAGAAATCCAggccgggtacagtggctcatgcctgtaattccagtactttgggaggccaaggtgggcaggtcacttgaggtcagcagttcaagaccagcctcgtcaacatggtaacaccctgtctctactaaaaatacaaaaattagctgggcctggtggctcatgcctgtaatcccagctacttaggaggctgaggcaggagaattccttgaacccagaaggtggaggttgcagtgagctgagattgcaccactgcactccagcctaggtgacac agcaagactctgtcaaaaaaaaaa--aaagaaaTCCAAATAAAATTTCCAGAATATGTGGAAAATAGTGACAATAAAAATATTAcacatgtgtaatcccagcattttgagatgccaaggtggcaggatcacttgagaccaggagttcgcaaccagcctggacaacatagggagactccatctccacacacgcc-aaaaaaaattttaaatagccaggtatagtggtacttcctgtaatcccatctacttgggaggctaaggtgggagaatcacccaacctcaggagttcagggcttcagcaagccatgatcatatcactgcactccagcctcagca +s panTro2.chr1_random 7087943 2267 + 9420409 GCCAGGATTGCTTTTATAGCCAGTCTTCAGGTGCCCACTGTAGGAACAATGTCATTTAACCCTCGGGATTATTCTGTGCCAAATATGGATAATGACTAATATTCAACACAGATATTCTCAGCTCAGAAGAGCAATTAGCAAATTCATAAATTAAGTGCTTGCTTCCTTTTTATTCAAATACAAACGTTTGTTAAAAGATATTATTTTGCTTTACACTTTTTCTCTCAGAAATAAACAGATGCTTGAATTCCCACAGTGCTGCTTGAGCCTCACACCATGTCATCCTGCCAGGCACCCAGATCCAGTTCTAGAGTTTCACATGATCATGAgtgttggttaataagtcaatgtgaactgggaggggagatttttcaggagggacacagggctctccctttaatcACATACACTCCCTGCTTTCATTGGAAAGTGTATAATGATGTCAGAGTGCCCCAGAATGGAGCTAGTTGGAAGACTGCCATCATAGGGATGCCTTAGTGAATTAATAAGGTTTTAATTTCTGGCTCTCAACTTTGTAGATGTAAAAGTTGATTTATCAATATGTGAGAAAGGATGAATCTTTCTGAAGGTTATGTCATCACACTCACTAAGCACACAGAGAATAATGTCTAGAATCTGAGTGCCATGTTATCAAATTATACTGAGACTCTTGCAGTCACACGGGCTGACATGTAAGCATCGCCATGCCTAGTACAGACTCTCCCTGCAGATGAAATTATATGGGATGCTAAATTATAATCCGAACAATGTTTGGTGAGCCAAAACTACAACAAGGGAAGCTAATTGGATGAATTTATAAAAATATGCCTCAGCCAAAATAGCTTAATTCAGTCTCCCTTATCATAAGGATAATCTTGCCTAAAGGGACAGTAATATTAAAGACACTAGGAATAACCTCTGTACTTTGGACAGTAGACCTGC ATAGCCCATTAGGCCTCAATGAAGTCTTATGCAAGACCAGAAGCCAATTTGCCATTTTAAGGTGATTCTCCATGTTTCTGCTCTAACTGTGCTTCACAATACTCAAGACACTGAATCAGGATGTTTCCTGGAGTGCAGGGAGCTGTCCGTGTTACTGAGCAGTTCTCAGCAACACAAAGATCCTACTGACTCCTCATCAGACTTCTTTCTCACTGGAATTTTACACCTGGGCTGTTAACACCAGGCCAGGTCAAATTCAAAGGAGAGAAAAAAGCTCATTATGAAGGGTAAAATCCAAAACACTGTGCATAAAGATATGTGTGCACAATTTTTATACATAAAGATTTCATAAAGCCAAAGCATCAGGAAATGAAAAGAGATACAGAAAGAAAAATGATGGTAAATGAGACATTAATTTACCCTTCTAATCTCTATCACAGCAAAAAGATAATTAAAAAATCTATATGAGGACCACAAAATACACAAAAATTATGTAGAAAAGCCTATAGCCTGAAAAAGTATACATTGAAATTTGTGTGTCCATAAAATGTTTACAAAATTCAGTACATATTACACACCCCACCCTAAAAACATCTAAGCAAGGTAGAGAATGTAGAAATGCTACAGATTATATTCTCTGATTATGACACAACAAAACTAGAAATTACAGCATGGAAATTTAAAAGCTTTCTCTTAAATAATTCTATGTCAAAAAGAAATCCAggccgggtacagtggctcatgcctgtaattccagtactttgggaggccaaggtgggcaggtcacttgaggtcaggagttcaagaccagcctcatcaacatggcgacaccctgtctctactaaaaatacaaaaattagctgtgcctagtggcgcatgcctgtaatcccagctacttaggaggctgaggcaggagaattccttgaacccagaaggtggaggttgcagtgagctgagattgcaccactgcactccagcctacgtgacac agcaagactctgtcaaaaaaaaaaagaaagaaaTCCAAATAAAATTTCCAGAATATGTGGAAAATAGTGACAATAAAAATATTACACATGtgtaatcccagcattttgagatgccaaggtggcaggatcacttgagaccaggagttcgcaaccagcctggacaacatagggagactccatctccacacacgccaaaaaaaaattttaaatagccaggtatagtggtacttcttgtaatcccatctacttgggaggctaaggtgggagaatcacccaacctcaggagttcagggcttcagcaagccatgatcatatcactgcactccagcctCAGCA + +a score=160884 +s hg18.chr1 91517 1775 + 247249719 acagagcaagatcctatctcaaaaaaaaaaaaaaaaTCACATGTGGGAAATAGCTATAGCACAAtaaaaataaatgtattaagtatgaacaacaaaaaagctagtaaaggttgaacaacaactatccttaggaaagtggaaataatgtattaataaatatgaaagcaggctagccacggtgactcacatctgtaatcccagcactttgggaggctgaggcaggcagatcacctgaggtcaggagttccagaccagcctggccaacatggtgaaatcttgtctctcctacaaatacaaaaactagccaggcttggttgtgcactcctgtaattcgagctacttgggaggctgaggcaggagaatctcttgaacctgagaggcagaggttgcagtgagccaagatcatgccactgcactccagctggggcaacagagtgacactccatctcaaaataaataaataagaaagcagaaactaataaactagaaaacagaaacatagaactaatttataaatcaaagcactatgccttgaaaagaGGGAGAAAAATTGTGAATTAAGGAAGGGAAGAGATGGTTGGAGAGGAGGTGGGAGAAGGCAGAGATAATTGAAGGAGCAAAAGCATCTGGAGAAGCAAAGCCACTGAAAGATGAACAGGGCTCTGAAAGAGATGCTTGACTGCTATCTTTTCAAATGACTGCAGTTCCCAGTGACATCATTTTTCTCCTCCCTGGAAGTCTGAGGGGCAGTTCACTTATCTCCTCCCCTCCCCTACTCCTCACCCCACACTCAAAACCTGTCTATGCTCCTTTCATTCTCATATGACAGATTTCAGATGGCATTCTTATTTCCCTGATTTCTTTTTGAGATAGCTTGCATTTCCCTCCTCTATataaagccaccgtttatcaaatgcctacatggaccaagcagtccacaagggctt cacagacagttttactaaactcatgccaaaactttcaggttttatacctaccttatagataaagaaattgaagcttatagagtttaagtaatgttcccaaagcctcgtggctagtaattcaaacctaatttctgcctactccaaagtctatttttccttatgatactctactgcctctcCAtggataaagacagagatcacatattaataaaatttgcacaaagtcggcaaattgttgaaagggaaggctaagatgattaataaaatcaagagccagatgatctcaacaacctgaaataactggctgacaaccaatttgaataactccctgcgggtgaagttcaaagtactatttgggtttttttttaaagtttggctgggtgcagcggctcacgcctgtaatccaagcacttagggaagccaaggtgggcagatcatgaagtcaggagttgaagaccagcccggtcaacatggtgaaaccccatctctactaaaaataaaaaattagccgggcctgctggtggatgcctgtagtcccagctactcgggaggctaaggcaggagaatcgcttgaacccaggaggtggaggttgcagggagccgagatcgcaccactgcactccagcctgggcgacagagcgagattccgtctcaaaaagtaaaataaaataaaataaaaAATAAAAgtttgatatattcagaatcagggaggtctgttgggtgcagttcatttgaaaaattcctcagcattttagtGATCTGTATGGTCCCTCtatctgtcagggtcctagcaggaaattgttgcactctcaaaggattaagcagaaa +s panTro2.chr1 223998133 1767 + 229974691 acagagcaagatcctatctc---aaaaaaaaaaaaaTCACATGTGGGAAATAGCTATAGCACAAtaaaaataaatgtattaagtatgaacaacaaaaaaactagtaaaggttgaacaacaactatccttaggaaagtggaaataatgtattaataaatatgaaagaaggctaggcacggtgactcacatctgtaatcccagcactttgggaggctgaggcaggcagatcacctgaggtcaggagttccagaccagcctggccaacatggtgaaatcttgtctctcctacaaatacaaaaactagccaggcttggttgcacactcctgtaattccagctacttgggaggctgaggcaggagaatctcttgaacctgggaggcagaggttacagtgagccgagatcatgccactgcactccaactggggcaacagagtgacactccatctcaaaataaataaataagaaagcagaaactaataaattagaaaacagaaacatagaactaattcat-----aaagcactatgccttgaaaagaGGGAGAAAAATTGTGAATTAAGGAAGGGAAGAGATGGTTGGACAGGAGGTGGGAGAAGGCAGAGATAATTGAAGGAGCAAAAGCATCTGGAGAAGCAAAGCCACTGAAAGATGAACAGGGCTCTGAAAGAAATGCTTGATTGCTATCTTTTCAAATGACTGCAGTTCCCAGTGACATCATTTTTCTCCTCCCTGGAAGTCTGAGGGGCAGTTCACTTATCTCCTCCCCTCCCCTACTCCTCACCCCACACTCAAAACCTGTCTATGCTCCTTTCATTCTCATATGACAGATTTCAGATGGCATTCTTATTTCCCTGATTTCTTTTTGAGATAGCTTGCATTTCCCTCCTCTATataaagccaccgtttatcaaatgcctacatggaccaagcagtccaaaagggctt cacagacagttttactaaactcatgccaaaactttcaggttttatacctaccttataggtaaagaaattgaagcttatagagtttaagtaatgtttccaaagcctcgtggctagtaattcaaacctaatttctgcctactccaaagtctatttttcctcatgatactatactgcctctcCAtggataaagacagagatcacatattaataaaatttgcacaaagtcagcaaattgttgaaagggaaggctaagatgattaataagatcaagagccagatgatctcaacaacctgaaataactggctgacaaccaatttgaataattccctgcgggtgaagttcaaagtactatttggggtttttcttaaagtttggctgggtgcagcggctcacgcctgtaatccaagcacttagggaagccaacgtaggcggatcatgaagtcaagagttgaagaccagcctggtcaacatggtgaaaccccgtctctactaaaaataaaaaattagccgggcgtgctggtggatgcctgtagtcccagctactcgggaggctaaggcaggagaatcgcttgaacccaggaggtggaggttgcagggagccaagatcgcaccactgcactccagcctgggcgacagagcgagattccgtctcaaaaaattaaataaaataaaataaaaaataaaagtttgatatattcagaatcagggaggtctgttgggtgcagttcatttgaaaaattcctcagcattttagtGATCTGTATGGTCCCTCtatctgtcacggtcctagcaggaaattgttgcactctcaaaggattaagcagaaa + +a score=258242 +s hg18.chr1 93292 2826 + 247249719 gagtttaatgaagggtctctttccagggttaagggaactgctagggtttggatatttgaccactccaaactcatgttgaaatgtgatccccattgttggaggtggggcctaatgggaggtgttttggtcctgagtgtggacctctcacgaatgtcttggtgccatccaagtgagttcttgctcgctcttttttttctttttgagatgtagtttcactcttgctgcccaggttggaatgtagtggtgcgatcttggctcactgcaacatccacctcacgggttcaacccattctcctgtgtcagcctccagagtagctaggattacaggtgcccaccactatgcccagctaatttttggtatttttagtagagacggggtttcaccatgttggccaggctggtctcaaactcctgacctcaggtgatacacctgcctcggcctcccaaagtgctgggattacaggtgtgagccaccatgcctacctagttctagctctcttaattcccacaagagctggttgttaacaagagcctggcacaaacccctctctctc--gccacgtgatctctgcacatgccagcttcccttccccttctgccatgagtggaaacagcctaacgccctcaccagaagcaaatggtggcaccatgcttcttgcacaccttcagaactgtgagccaaataaacctctcttctttaaaattattcagcctctggtattcctttataacaacacacacacacacacacacacacatacacacacacgcaaaagcagactaaaacaggaactaattagaaatggtgatgcaccgagggattggcaCCGAGGCTCCCCAACAGGAACTGAGGTCATGGATAGAAGGACACATTCATGTTATTTTTTTCTAATGGTTAAGTAATTATTTGctcttactctcaaaatttctgccaaggcctcc catggaccaaactcaactagaatctaggaagcagagaacctgagtgttgcattcagcagaagtcagcttcctagggaatcttgcaggaagggtgaaggtagagaatctggtggggaagcaagcaaatgcccatcacaTGCACTTTCCTccaacagagcgactcagatgctataaaacttgctaacacagtctcagggtctgatcacagtaacatacaatccaggttttaatcatcagaaatcacagtcctattgtcttctgcacagacccaaacacacttggaggtcatgttcaatatgaatacctcacagagaaggaaatttacacgcgagaagtacatctgcagaaagccagctggcatgtcaaccattcaaaaactcagggtgttctggataaagaagactcaggaagacaagtatgaagcataatctgtgacattccatgcggcagacattagacacatacaagagagttgttggaaagcggaatttatcttcatataaacaacactgagctaaatctcaatatttcagatctctagaactatccatcagtgaaatggattgcaaatacaaagagtaataccatgtcacttaagaatagaatcatggacgaggctgccacctgctgttgggggccactgcagaagaaattccagaacactggactggagagcacctcactttccttacagctctaagtttctgACTCAGTGACCTGATTCACTACCATATACACAAAGACCCACTTACACAAATGACTGTTCTTCACACTAGGCCCATGGAGACAGGGATAAAATTCTGAATTTGCTCAGATACCTTCTCCGCTACTGACATCTAGGCATTACACAATTCATCTCTTCATATTTAACCTTTGAAGTTTGCTACTTCTCAGAGAGACTAATGAGTAGTGAGCAAATATCCTGAAGCTGAGAATGCTTCTACCTCCTCTCAAAACAACGGAATATTCATCAAAACACAGCAGTTCTG CACTTAACTTTAGGCCTTTTCTAACACCTTGTTTCTTGGCAGTAACTGTGGCCAGAATAGCTCTTTCCACAGATAAAGGACCTTTTGAAAGGATAGGGTCTCTAGATAGAAAAGCAAATGCCTCATTCCAGAAGGTCTTCAAGAAGAAAATGTTGTGGTGATAACAAACATAACTGATTATAATCTATTCTGTGAAAAAAGCTTATGAAACAGTAGATGTGTGTATCTAGTACATAAGAGCTGAATGTCAATATATATATA--GATATATACacacactcaaataaataatagttatctctaactagagaaattctagttgccttatattttcttctttttccttactatattttctacaataaacatgtgtttttaacaagaaaaGTCTTTTCTGGTGTGCTTTTTAATTTTCTTTGTTTAAGTGAGAGTGAGGCTACATAACTACATGGCTAGGTAGACTTTTAGAAAACTTGGCTGCTCTAGAAAATTGACATATCCTGATTTCTTCCATAGCTTGGATCTTGACCTAGAGGGAAATATAAAAGTGTTGACTTGAACCTGAGGGGTGCCATTTTCACTGCTGAAGTAGTTTCATGGATCATGAATTGGAGAAATGACTTCAGCAACATGGGTGTTAAAATCAGAAAGCACAAGTGACCCACAACAGATGATGGAGAACAAAGAGCAAGCTGGGAAA-GCAGTGGCCTTTAATACAGAAAAGAAGAAGTATAGCCACAATAAATATTAGGCAGACAGCAGTTCAGCAGTTTATACTATTAAGCTGTTGTTTAGGGGAATAGTAAACTGACATGACCCTTGAGGTAGGTATATATAGGTAAATTCTATGTGTCCCTTGAAATAGGTGTATGACACAACTTCTGGCATCTACATGGATTT +s panTro2.chr1_random 7090211 2818 + 9420409 gagtttaatgaagggtctctttccagggttaagggaactgctagggtttggatatttgaccactccaaactcatgttgaaatgtgatccccattgttggaggtggggcctaatgggaggtgttttggtcctgagtgtggacctctcacgaatgtcttggtgccatccaagtgaattcttgctcgctcttttttttctttttgagatgtagtttcactcttgctgcccaggttggaatgtagtggtgcgatcttggctcactgcaacatccacctcatgggttcaacccattctcctgtgtcagcctccagagtagctaggattacaggtgcccaccactatgcccagctaatttttggtatttttagtagagatggggtttcaccatgttggccaggctggtctcaaactcctgacctcaggtgatccacctgcctcggcctcccaaagtgctgggattacaggcgtgagccaccgtgcctacctagttctagctctcttaattcccacaagagctggttgttaacaagagcctggcacaaacccctctctctctcgccaagtgatctctgcacatgccagcttcccttccccttctgccatgagtggaaacagcctaaagccctcaccagaagcaaatggtggcaccatgcttcttgcacaccttcagaactgtgaaccaaataaacctctcttctttaaaattattcagcctctggtattcctttataacaacacacacacacacacacacacacat----------gcaaaagcagactaaaacaggaactaattagaaatggtgatgcaccgagggattggcaCCGAGGCTCCCCAACAGGAACTGAGGCCATGGATAGAAGGACACATTCATGTTATTTTTTTCTAATGGTTAAGTAATTATTTGctcttactctcaaaatttctgccaaggcctcc catggaccaaactcaactagaatctaggaagcagagaacctgagtgttgcattcagcagaagtcagcttcctagggaatcttgcaggaagggtgaaggtagagaatctggtggggaagcaagcaaatgcccatcacaTGCACTTTCCTccaacagagcgactcagatgctataaaacttgctaatgcagtctcagggcctgatcacagtaacatacaatccaggttttaatcatcagaaatcacagtcctattgtcttctgcacagacccaaacacacttggaggtcatgttcaatatgaatacctcacagagaaggaaatttacacacgagaagtacatctgcagaaAGCCAGCTGGCATGTCAACCATTCAAAAATTCAGGGTGTTCGGGATAAAGAAGACTCAGGAAGACAAGTATGAAGCATAATCTGTGACATTCCATGCGGCAGACGTTAGACACATACAAGAGAGTTGTTGGAAAGCGGAATTTATCTTCATATAAACAACACTGAGCTAAATCTCAATATTTCAGATCTCTAGAACTATCCATCAGTGAAATGGATTGCAAATAGAAAGAGTAATACCATGTAACTTAAGAATACAATCATGGACAAGGCTGCCACCTGCTGTTGGGGGCCACTGCAGAAGAAATTCCAGAACACTGGACTGGAGAGCACCTCACTTTCCTTACAGCTCTAAGTTTCTGACTCAGTGACCTGATTCAGTACCATATACACAAAGACCCACTTACACAAATGACTGTTCTTCACACTAGGCCCATGGAGACAGGGATAAAATTCTGAATTTGCTCAGATACCTTCTCCGCTACTGACATCTAGGCATTACACAATTCATCTCTTCATATTTAACCTTTGAAGTTTGCTACTTCTCAGAGAGACTAATGAGTAGTGAGCAAATATCCTGAAGCTGAGAATGCTTCTACCTCCTCTCAAAACAACGGAATATTCATCAAAACACAGCAGTTCTG CACTTAACTTTAGGCCTTTTCTTACACCTTGTTTCTTGGCAGTAACTGTGGCCAGAATAGCTCTTTCCACAGATAAATGACCTTTTGAAAAGATAGGGTCTCTAGATAGAACAGCAAATGCCTCATTCCAGAAGGTCTTCAAGAAGAAAATGTTGTGGTGATAACAAACATAACTGATTATAATCTATTCTGTGAAAAAAGCTTATGAAACAGTAGATGTGTGTATCTAGTACATAAGAGCTGAATGTCAATATATATATATAGATATATACACACACTCAAATAAATAATAGTTATCTCTAACTAGAGAAATTCTAGTTGCCTTATATTTTCTTCTTTTTCCTTACTATATTTTCTACAATAAACATGTGTTTTTAACAAGAAAAGTCTTTTCTGGTGTGCTTTTTAATTTTCTTTGTTTAAGTGAGAGTGAGGCTACATAACTACATGGCTAGGTAGACTTTTAGAAAACTTGGCTGCTCTAGAAAATTGACATATCCTGATTTCTTCCATAGCTTGGATCTTGACCTAGAGGGAAATATAAAAATGTTGACTTGAACCTGAGGGGTGCCATTTTCACTGCTGAAGTAGTTACATGGATCACGAATTGGAGAAATGACTTCAGCAACACGGGTGTTAAAAACGGAAAGCACAAGTGACCCACAACAGATGATGGAGAACAAAGAGCAAGCTGGAAAAAGCAGTGGCCGTTAATACAGAAAAGAAG---TATAGCCACAATAAATATTAGGCAGACAGCAGTTCAGCAGTTTATACTATTAAGCTGTTGTTTAGGGGAATGGTAAACTGACATGACCCTTGAGGTAGGTATATATAGGTAAATTCTATGTGTCCCTTGAAATAGGTGTATGACACAACTTCTGGCGTCTACATGGATTT + +a score=207872 +s hg18.chr1 96118 2256 + 247249719 GGTCACTCTAAAGTAGCCATGAGGCTTAAGATAGTTCAGCTGTTTGGGGATAAGTTAAATCATTTGCCATTGTCTTTCTGCAATTTGCATATCCTACAGTTATCATTGCCATTACTGAATGGCACAGAGAAAAATTCTGGTCTAAAGTGGTTCTCAAACCTGGTtgctggagggccaccctcagtgatgatgatttaatctgtagaagaatagaacattgatagtttttatatatctccaggtaattttaatatataactggggtgagaatcattgACATAATTGTAACAGGATAATATTCAGGAAATATGGAGATAAATAATTTTCTTCTCGACATTAAAAAAATCTAATAAAAAGTTTTATGTTTTCCCCTAACTCAGGGTCATCAGCCTTCAAGCTTCAGTCTCTGTGTGTTCACAGGTGCTGTAAACACACGCATCACTACTAATATCCCACTTCAGTGCTATTGCTGCTCCCAAAACTCCAGGTATTTTTAACCTTATAAACCTCCAGAATAATGAGACCACTGGGTTCAGTAAATTGCTTTGTTTTGAAGCACTATTAGACAAAGTGGGAGACTAGAAGATAAATCTGTCAATGACATGTCCTTTAAGACTACTTAGATTTTGTTGAATTTGTGGATCATTCCTTACTTGAGCAAATGGTAAATTAACTCTCTCTTTTCTCTCTCTCTCTAGCTGGCACACTTTTTCCAGTAGCCATTCTACTTGGTATGCTTACTTATCAGCTGTCCTCCAGGGGCCTCACATTAGATGTTTCTC-TGACTAACCAAACATGACACACAGCTGAAGTCAGAAAAACCAGATTGATAATTTCACTCAAACTATTTTCCTTCATTCTAACAATTTACTGGAGTACACAATTGTGACTATTTTTAGCCATAGGAACTCATAGAAAGACCAACTTCATTAGACCTACAAAATCGAAT TGTGTAACAGTATATGCAGTATGTGTAGGAATAAAAAGCATTTCTCAAATATGCAGTACTGGATTTTGCAAAAGCACCTTACACTTAGCTATAAAGGAGTGGAAAACACAAAGATGAGTAACTGCACTTTTCAAAAGACTAGAGCTATACCAATAATACAAAGGTGTAAACAAATAATGATGAGATGACAAAGGCTGAGTGTTTTCTATTTGGAAGCTATGTTGTTGAGTTATTTATGTATATAATTTCATGCAATCTTCATGTTATGGGGATGTTctaatccactgtgactctgtccttaaataaaagggagatttggacatagagagaggcacacggggaggatgccatatgagaattgacactgtgctgtcacaagccaaggaactactggaaggagagaaagaggactggaacagttccttccttagcaccttttcaggcagcctagccctgccagcttcttgatctggacttctcacctctagaattgtgaggcaataaatctctgttgcttaagttacccagtttgtggtaccttattacaggagccctaggaaaataattcaTTATataatctgctaaggtagatatgatcattgtctccaatttccatatgaagaaactatgcctcaggcattgtgtcagttgtccaaaatcatacattcctgactcacttcaatgaattcttcattcagcaaaatttttaaggtaccttaaaaaaattatgttaactcttagggccttgctttaaagcttcaatgggcttttcctttgcaaagaataaaatcctaatacttaagcatagctctctttcctggctatgtttctgacatcctcttgtaccatgctcctccttaatcattctgaggttacatcttaagtcctttccccttgccattcccacttcttggaatactttcccatcaactcttcaaagaactgccttctttaagtatttggtctcagttccaatgtcacttccctgt aaaagcttcctggccatcaagccttctttacacactctattttattttttcatggttcctataacaacctaatatattctcaattgattaactgttttgctgaatactgccttccataagaatggaaagaaaacatggccaggtgcagtggctcacacctgtaatcccaccacttcaggaggctgaggcaacatggcaaaaccttctcttcaaaaaattttttaaaagttagctggatgttgtggaggcaagaggatcacttgaggatcacttgagtccatgaggtcaaggctgcagtgagtcatgtttgcaccactg +s panTro2.chr1 243304 2257 + 229974691 GGTCACTCTAAAGTAGCCATGAGGCTTAAGATAGTTCAGCTGTTTGGGGATAAGTTAAACCATTTGTCGTTGTCTTTCTGCAATTTGCATATCCTACAGTTATCATTGCCATTACTGAATGGCACAGAGAAAAATTCTGGTCTAAAGTGGTTCTCAAACCTGGTtgctggagggccaccctcagtgatgatgatttaatctgtagaagagtagaacattgatagtttttatatatctccaggtaattttaatatataactggggtgagaatcattgACGTAATTGTGAGAGGATAATATTCAAGAAATGTGGAGATAAATAATTTTCTTCTCGACATTAAAAAAATCTAATAAAAAGTTTTATCTTTTCCCCTAACTCAGGGTCATCAGCCTTCAAGCTTCAGTCTCTGTGTGTTCACAGGTGCTGTAAACACACACATCATTACTAATATCCCACTTCAGTGCTATTGCTGCTCCCAAAACTCCAGGTATTTTTAACCTTATAAACCTCCAGAATAATGAGACCACTGGGTTCAGTAAATTGCTTTGTTTTGAAGCAGTATTAGACAAAGTGGGAGACTAGAAGATAAATCTGTCAATGACATGTCCTTTAAGACTACTTAGATTTTGTTGAATTTGTGGATCATTCCTTACTTGAGCAAATGGTAAATTAACTCTCTCTTTTCTCTCTCTCTCTAGCTGGCACACTTTTTCCAGTAGCCATTCTACTTGGTATGCTTACTTATCAGCTGTCCTCCACGGGCCTCACATTAGATGTTTCTCTTGACTAACCAAACATGACACACAGCTGAAGTCAGAAAAACCAGATTGATAATTTCACTCAAACTATTTTCCTTCATTCTAACAATTTACTGGAGTACACAATTGTGACTATTTTTAGCCATAGGAACTCATAGAAAGACCTACTTCATTAGACCTACAAAATCGAAT TGTGTAACAGTATATGCAGTATGTGTAGGAATAAAAAGCATTTCTCAAATATGCAGTACTGGATTTTGCAAAAGCACCTTACACTTAGCTATAAAGGAGTGGAAAACACAAAGATGAGTAACTGCACCTTTCAAAAGACTAGAGCTATACCAATAATACAAAGATGTAAACAAATAATGATGAGATGACAAAGGCTGAGTGTTTTCTATTTGGAAGTTATGTTGTTGAATTATTTATGTATATAATTTCATGCAATCTTCATGTTATGGgggtgttctaatccactgtgactctgtccttaaataaaagggagatttggacatagagagaggcacacggggaggatgccatatgagaattgacactgtgctgtcacaagccaaggaactactggaaggagagaaagaggactggaacagttccttccttagcaccttttcaggcagcctagccctgccagcttcttgatctggacttctcacctctagaattgtgaggcaataaatctctgttgcttaagttacccagtttgtggtactctattacaggagccctaggaaaataattcaTTATataatctgctaaggtagatatgatcattgtctccaatttccatatgaagaaactatgcctcaggcattgtgtcggttgtccaaaatcatacattcctgactcacttcaatgaattcttcattcagcaaaatttttaaggtaccttaaaaaaattatgttaactcttaggtccttgctttaaagcttcaatgggcttttcctttgcaaagaataaaatcctaatactcaagcatagctctctttcctggctatgtttctgacatcctcttgtaccatgctcctccttaatcattctgaggttacatcttaagtcctttccccttgccattcccacttcttggaatactttcccatcaactcttcaaagaactggcatctttaagtatttggtctcagttcaaatgtcacttccctgt aaaagcttcctggccatcaagccttctttacacactctattttattttttcatggttcctataacaacctaatatattctcaattgattaactgttttgctgactactgccttccataagaatggaaAGAAAACATggccagatgcagtggctcacacctgtaatcccaccacttcaggaggctgaggcaacatggcaaaaccttctcttcaaaaaattttttaaaagttagctggatgttgtggaggcaagaggatcacttgaggatcacttgagtccatgaggtcaaggctgcagtgagtcatgtttgcaccactg + +a score=94883 +s hg18.chr1 98374 1036 + 247249719 cactctagcctaggtgacagagctagtcactatcaaaaaaaaaaaaaaaa---gaatggagagaatgctacatgagagaaaggatcttatctatcatgttcacctcccaagaggtgaacatatcccccaaagcctgatagagagaagatgctcattaatatttaatgcatgaCCATGTGCAGACTTGGGAGGAAAAATATGCCTCAGCCTATCAATATTGGATCCTTAATAAACAAGGATGTTTCTGCATCATTTCCCCACAACACCGAACAAGTGTGGCTCACTGTGGATGTTTAAGCAAATGCATTGTTTTTCCAGTTATATATCTGGTAGAGATGAGGCCATTGATAGGAATGGGAAGACGATCTCCTTTTATTTTGATGACCCAGCATGGCTGAACACTCAGTGACTACCACTGCACTTTGTTGTACTTTCAGCATTAGAGATGCCAGCCCTGTAGGATATAAAACAGGAACATCTAGTCCTCAATTATATTCAGAATTACTCAAGTCTTAGAAGCACCACTTGTCTTTTTTCAAGGGAGAGAAATGCTCAAGTGATGGGCTGAAGTGAAGGGAGGGAGTCACTCACTTGAACGGTTCCCTTAGGCTGTGTGGATGCAAACAGCATTAGACAATGACACTGACAGTGGGAAATGCACTGGAGACGATGACTGGCAAAGCCCTCCTTTTCTCCCCATCCACTATAGATACTGACAGCAAAGGGTTTGTCACAATGACAACTATACACTCCCAATATCACAGAAGAAGGAGGAATAAAAGGGTATATTATGAGTGACTGAAGTTTAGAATAAATTAATAAATATTATGTCCCTCATCCATAGAAACCACAAAGGTCTAGTAAGGCTAAGGATATAACAAGAAAATAATATGAATATTTGCTTCCCCTTCCTAGTGTAATAGAGTAAGTTACAAATGGCTT CAGGAAGGGGAGAGAGGAAGAAGAGTGGATGAGATACGTAAGAGTGCTTGAGGGCTAATTTTATGAAAGCTTTGGGAAGTTTTAAGAAAAAGAAAAG +s panTro2.chr1_random 7095288 1039 + 9420409 cactctagcctaggtgacagagctagtccctatcaaaaaaaaaaaaaaaaaaagaatggagagaatgctacatgagagaaaggatcttatttatcatgttcacctcccaagaggtgaacatatcccccaaagcctgatagagagaagatgctcattaatatttaatgcatgaCCATGTGCAGACTTGGGAGGAAAAATATGCCTCAGCCTATCAAAATTGGATCCTTAATAAACAAGGATGCTTCTGTATCATTTCCCCACAACACCGAACAAGTGTGGCTCACTGTGGATGTTTAAGCAAATGCACTGTTTTTCCAGTTATATATCTGGTAGAGATGAGGCCATTGATAGGAATGGGAAGACGATCTCCTTTTATTTTGATGACCCAGCATGGCTGAACACTCAGTGACTACCACTGCACTTTGTTGTACTTTCAGCATTAGAGATGCCAGCCCTGTAGGATATAAAACAGGAACATCTAGTCCTCAATTATATTCAGAATTACTCAAGTCTTAGAAGCACCACCTGTCTTTTTTCAAGGGAGAGAAATGCTCAAGTGATGGGCTGAAGTGAAGGGAGGGAGTCACTCACTTAAACGGTTCCCTTAGGCTGTGTGGATGCAAACAGCATTAGACAATGACGCTGACAGTGGGAAATGCACTGCAGACGATGATTAGCAAAGCCCTCCTTTTCTCCCCATCCACTATAGATACTGACAGCAAAGGGTTTGTCACAATGACAACTATACACTCCCAATATCACAGAAGAAGGAGGAATAAAAGGGTATATTATGAGTGACTGAAGTTTAGAATAAATTAATAAATATCATGTCCCTCATCCATAGAAACCACGAAGGTCTAGTAATGCTAAGGATATAACAAGAAAATAATATGAATATTTGCTTCCCCTTCCTAGTGTAATAGAGTAAGTTACAAATGGCTT CAGAAAGGGGAGAGAGGAAGAAGAGTGGATGAGATACATAAGAGTGCCTGAGGGCTAATTTTATGAAAGCTTTGGGAAGTTTTAAGAAAAAGAAAAG + +a score=182569 +s hg18.chr1 99410 2041 + 247249719 CTATTTTTCAAGGTACAtgtgtgtatgcgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgAAAGACAGAAGAAAGAGGGAGACCTTAGAAGACTATGAGACACTAAGAGAAAAATTAAGGTAAAAAAGACACACACTTAGAAAAACACACATAGGGAGGAGGGAGGAGGTTAAGACATTTTACTATGTGCTGTGAATGGAAACTACAAACCATTTTTGATatatgcaatatatatacatatatacacacatatacatatGTATTTAAATATTTAAATTACAttttctctttttttagagatatggtttcactatgtcactctgcccaggctgcagtacagtggttgttcacagtcatgatcatagcacattatagccttgaactcctgggctcaagcaaccctcctgtattagtctccccagtagttgggattactagcatatgccaccatgtccACCTTTATGCTTTTTAAAGTGAAAAACCATACTAAGAATGAGGCAGCTCAACTTAATAATAAAAACATTTCAAATGtaaagaaatttacaaaagaaaaacaatcaaccccattaaaattgggcaaagggaatgaacagacacttttcaaaagaatacatgcatgcagccaacaaacatacaaaaaaaaagttcaacatcactgatcattagagaaatgcaaatcaaaaccataatgagataccatctcacaccagtcagaatagctatcattaaaaagtcaaaaaataacagatgctagtgaggctatggagaaaagggaatgcttatacactgttgttgggtgtgcaaatcagttcaatcattgtgcaaggaa-agtgattcctcaaagagctaaaagcagagctaccattcgacccagtaatcccactactgggtatatacccagatgaatataaaccattctaccataaagacacatgcatacaa atgttcattgcagcactgttcacaatagcaaaagtatgggatcaacctaaatgcccatcaatgacagattggataaagaaaatgtggtacatatacaccatggaatactatgccgccattaaaaaatgatatcatgtcttttgctggaatatggatggaccttctattatccttagcaaactaatgcaggaacagaaaaccaaatacagcatactctcagttataagtgggagctaaatgatgagaactcatgaacacaaagaataaaacagacactggggtctacttgagggtggagggtgagaaaaggaagagaaacagaaaagataactattgggtactaggtttaatacctgggtgatgaaatgatctgtacaataaccccctgtgacaccagtctacctatgtaacaaatgcccctaaacttaaaataaaagtt-aaaaaaaaaAGAAAATTAAAATCTCCTTATCATCTACCTGGTAATATGAAAAACACATATCTTTCATTCATTCCTTTCAACTGATGAGGAAACTGAGGCATTGGGAGTTAGTAAAAGTCCACATTGAGATATGAGACCCACCACTggctggacacagtggctcacacctgtaatcccagcactttgggaggccgatgctggtggatcacctaaggtcaggagttcgggaccaggctggccaacatggtgaaacccccatctctactaaaaatacaaaaattagctgggtgtggtggcaggcacctgtaataccagctactagggaggctgaggcaggagaatcgcttgaacccaggaggtggagtttacagtgagccaaaatcatgccattgcactccagcctgggcaacaagagcaagactctgtcggggaaaaaaaaaaacaaaaaaaaCCACCACCATCATTTTGCAAGTGTTACCACTATTGTGTGTTAATATTGTAGAAGTATTCCTAATTATGATTTCTTTGTATTCCTAATTGTAATAGCTT TGTATTTGAAAAATTATTGATTCATACTC--TATGTTATTATTTTGTATGCGATGACAACAGAATATATTATCATGCTCCTTTTGTGAATCTCATTCATAATATAA +s panTro2.chr1 246632 2037 + 229974691 CTATTTTTCAAGGTACAtgtgtgtacgcgtgtgtgtgtgcgtgtgtgtgtgtgtgtgtgtgtg----AAAGACAGAAGAAAGAGGGAGACCTAGGAAGACTATGAGACACTAAGAGAAAAATTAAGGTAAAAAAGACGCACACTTAGAAAAACACACATAGGGAGGAGGGAGGAGGTTAAGACATTTTACTATGTGCTGTGAATGGAAACTACAAACCATTTTTGATatatgcaatatatatacatatatacacacatatacatatGTATTTAAAGATTTAAATTACAttttctctttttttagagatgtggtttcactatgtcactctgcccaggctgcagtacagtggttgttcacagtcatgatcatagcacattatagtcttgaactcctgggctcaagcaatcctcctgtattggtctccccagtagttgggattactagcatatgccaccatgtccACCCTTATGCTTTTTAAAGTGAAAAACCATACTAAGAATGAGGCAGCTCAACTTAGTAATAAAAACATTTCgaatgtaaagaaatttacaaaagaaaaacaatcaaccccattaaaattgggcaaagggaatgaacagacagttttcaaaagaatacatgcatgcagccaacaaacatac-aaaaaaaagttcaacatcactgatcattagagaaatgcaaatcaaaaccataatgagataccatctcacaccagtcagaatagctatcattaaaaagtcaaaaaataacagacgctagtgagtctatggagaaaagggaatgcttatacactgttggtgggtgtgcaaatcagttcaatcattgtgcaaagaatagtgattcctcaaagagctaaaagcagagctaccattagacccagtaatcccactactgggtatatacccagatgaatataaaccattctaccataaagacacatgcatacaa atgttcattgcagcactgttcacaatagcaaaagtataggatcaacctaaatgcccatcaatgacagattggataaagaaaatgtggtacatatacaccatggaatactatgccgccattaaaaaatgatatcatgtcttttgctggaatatggatggaccttctattatccttagcaaactaatgcaggaacagaaaaccaactacagcatactctcagttataagtgggagctaaatgatgagaactaatgaacacaaagaataaaacagacactgggttctacttgagggtggagggtgagaaaaggaagagaagcagaaaagataactattgggtacaaggtttaatacctggttgatgaaataatctgtacaataaccccctgtgacaccagtttacctatgtaacaaatgcccctaaacttaaaataaaagttaaaaaaaaaAAGAAAATTAAAATCTCCTTATCATCTACCTGGTAATATGAAAAAAACATATCTTTCATTCATTCCTTTCAACTGATGAGGAAACTGAAGCATCGGGAGTTAGTAAAAGTCCACACTGAGATATGAGACCCACCACTggctggacgcagtggctcacccctgtaatcccagcactttgggaggccgatgctggtggatcacctaaggtcaggagttcgggaccaggctggccaacatggtgaaacccccatctcttctaaaaatacaaaaattagctgggtgtggtggcaggcacctgtaataccagctactagggaggctgaggcaggagaatcgcttgaacccaggaggtggagtttacagtgagcgaaaatcacgccattgcactccagcctgggcaacaagagcaagactctgtcgggaaaagaaaaa---aaaaaaaaaCACCACCATCATTTTGCAAGTGTTACCACTATTGTGTGTTAATATTGTAGAAGTATTCCTAATTATGATTTCTTTGTATTCCTAATTGTAATAGCTT TGTATTTGAAAAATTATTGATTCATACTCTATATGTTATTATTTTATATGCGATGACAACAGAATATATTATCATGCTCCTTTTGTGAATCTCATTCATAATATAA + +a score=51978 +s hg18.chr1 101451 561 + 247249719 AGTATAAATTTGTGATTTTGCTTTAATTTGAAATATTAATTTCAAATATGTTATCACAATTTGATACAAACTATTGACAGTAAATCTGTGGATTAAGTAATGTCTTAGTAGGTATTGGGAAAATTTGAAACTAGTAACATGGAGGACTATTGTCATTGTTTATTTCAAAGCCAGTTAAAATTCTGCAAAGCAGTGTACATAAAAATAATTTCAAGAAATTTATAAAATACCGAGATTACGGTGTATAAACAACTTTAGATTCTTTGTTTAAGAAATTCTGCCAGTTTGTAATATATGCTTCATTCAAAGTAGCTAAGGGCTGTACCTGGCTAATAGTAGGCACCTAATATTTGTTGAAAAGGAATACTGAGTAGCTGGGACCTCCTGAGTAGCTGGGACCACACACATTTAACCTGTATTTATAAAATTACTGTTTAGAGAATAACATTTGATGGAATCATGCTTTTACTTTCTGCTTACGACTCAATTGTTTGTactgacattaacatcccaaatccttagcatggcctacaaggccctgagcaatgtggcacctgctga +s panTro2.chr1_random 7109461 561 + 9420409 AGTATAAATTTGTGATTTTGCTTTAATTTGAAATATTAATTTCAAATATGTTATCACAATTTGATACAAACTATTGACAGTAAATCTGTGGATTAAGTAATGTCTTAGTAGGTATTGGGAAAATTTGAAACTAGTAACATGGAGGACTATTGTCATTGTTTATTTCAAAGCCAGTTAAAATTCTGCAAAGCAGTGTAAATAAAAATAATTTCAAGAAATTTATAAAATACCGAGATTATGGTGTATAAACAACTTTAGATTCTTTGTTTAAGAAATTCTGCCAGTTTGTAATATAtgcttcattcaaagtagctaagggctgtacctggctaatagtaggcacctaatatttgttgaaaaggaatACTGAGTAGCTGGGACCTCCTGAATAGCTGGGACCACACACATTTAACCTGTATTTATAAAATTGCTGTTTAGAGAATAACATTTGATGGAatcatgcttttactttctgcttatgactcaattgtttgtactgacattaacatcccaaatccttagcatggcctacaaggccctgagcaatgtggcacctgctga + +a score=669341 +s hg18.chr1 102012 7363 + 247249719 agcctgctgcctcatttaataactctttgtctctttcccagatccagccactctaacattttttagctcctggaccaagacaagctcttcccagaacctgacctttgtacctgttctttattcctggagtatttttcccctgacaaattacttatcatctatcataattcaggttaaatggcactaactcagggaaggcttccctaactgcctcccttctccaaccaaattaggaacaattatatggccacatagtatcgaatcaagtttataattttaaaataattgggagattttgttgtttaacacttgttttcactataagactgtaattacatgcaagtaagaaccatgcctgtttgttcactcctgccacagtcagaatagtgcctggaatatgcagtaagggctgaacaaacactaaataaatgaaCAAGTGAATAAATGGATATTGTCTCATTTTTAGAACAGAGTACTAAATGGATCATGAACACTATCTGGTATGTCACGTAGGTAATTTACAAGGGCTACAATTTCAGCTCAGATTTACCTTTTCCTGGATACAGGTCTTGATAGGTCTCTTGATGTCATTTCACTTCAGATTCTTCTTTAGAAAACTTGGACAATAGCATTTGCTGTCTTGTCCAAATTGTTACTAAGAATCAAGAGAGATATCTGACATGAAATGACATTGGAAAACATTAAACACGATTGAAATAATGCTAGCCAATATGGTTATTATTAGAAACCAATTACATTTTCAACTTAAAAATAGTAATACTTATTGCAGACTCAAATGTGCTTATTCTAAAACAAGTAAATGTTTGCCTATGGTCTGAGATTCTAATCCACGGAGTTCATTCTAATCCACATTCAACACTATCATGTACCAGTGGGCCTCATAACCCACCTAGCCCTGTGATTTTTCAGGTTCACTTTTCTAAACTTGT GAATTAAATATTTATTTTCTTAGTTCAGAAGAGGAAAAAAACTCTTGTAATTGTTGCCCATTTCAGGAGAAATCTTGCATATGAAAACAAGAGATAAATATACACAACTGAGGGCTGTGGTTTAAACAAAATCTTGAGAATGTTTTTTGACCTTATACATTTGTGCTTTAGTATAACAAAATGATATAGACAAAGGTAACTTTTAATAGAACCAGTCACTACATTAAAAAAA-TGACAAATTCTTCTGCTTAGCTAAGCAACAGAGAAGGTAAAATACTAATTCAATTCATCAATTTAAGCAATACTCATTAAGAGCCAAGTATGTGCTCACTGAATAAGCTGCTAAGGTTTGGTGGTTACAGAGTGTGCGGTGAAATGATGTCTACATCACAGTCCAACATTCACAGAGTTTAAAAGCCTACCAAGAATCAAGACAGACACAAATACCTAACATAGACGTTTGTATATGATAAGAGAGCCAGAGTACAATTTAGGAGAAGAAATTGTATGGAAGGAAGGTTCATTTCCATTAGACCAGAAAAGACAGCACATTTGAAGGCCTGAATAAGAAATATTCTGGATAAGATATTGTggctgctaccagaatggctcttgatgatctctacctcttggtatttatacccttatataatctctttcctatagtgtaagctggtcccaggtacttgtttctattgaatagaatagaacaaaagaaatgagatgccacttctgagattagtttataagatactgtgaatttcatcttgtgccctctccctctctctctttctcttgccctctcatttgaatgaagccaactggcatgctgtcagtggcacagtgtaagtcctgttacaagaaattgacgattacctgtagccaaccctaagtgaagaactgaggtcctcagtcctacaaatggagagaaactgaatctagctaagaaccatgtgagtgagctgggaagaagatccaccctcagttg aaatttaagatgaCATATTGAGCAGACATACTGAGACACACTGAAAGTAAGAGAGCAGGAGGAAACAAAACCAGGGTCATACAAAGAACACAACTGATTTTGAGATTCTCACATaagtattacaccttcagtgagcacgtgtactagaaatttaaaaaataaataaaataaaccttcaaagtgagctagcaaataaatttccctatggtctcagctctgagtggagagagaaaatgttccctgtggagtttatagccagaatccagctctcaaacaggtttcagcctgaactcacacaatctgtgtggcttccaaatttgcaagctgagaatttaattcaaagtggtctcaggttgatagcagtccaaaatgctaggtaggaaaaaaaatcctctctggacaaataaatcatcaaagcaagctcataagagcaggtttcaaaggtcatgagcttctaacacacacacacaaaaatcacacacacaaaatgggggtagcagcaacatgggtagcgtattcaaacttgaaaagactttaaatatttgtattattagatgtagattatgaaacacatattttAATGTGGTTAATTTTTTTAAGGAATCACAACTATGAGTAAAGACCAAGAAAATTGTGCTGGATGGCCACTTCCACCATGGCTCCCCTCCTATTTAAGTCTGGGTACTGTGTCACCCGAAGTCTTCAGGCACATTGTTCCAGGTCTGGGTTTGCCTATGAAAGAAACTCATGAGAGCTGGAAATGAGGAGTGAAGAGGAGGTCTTCACATAAAGCAGGCTTAAGGATTAGACATAGCAGGTTTGACAGATGTGATGGCTTGCAGAATCCTTTATGAGCTCCCACTGTCCATCTGGATAAGATTTACAGACCTTTCAGAAATTCCTATAAGCTTGGGTTCTGTGCCCACACTCTAGACTGTCAGGCTAAGATCTCTGATATAAAACAGACCTCTTCTGATTTTGTCTAGCTG CTTTTCTAATATCTATTCACCAAGCTCTTCCAATAATAGCATAAGGCCCTAATTAATATTAAACTTTTATCATTATAATACATAGGATGTCTTCTGTTTTCCTGATCAAATTCTGACTACTATTAAAATATAAAGAATTGTCCAGAAATATATAAAAAAAGAATCACACATTGATCTTCTTTAAATGAAAATATAACAATTGTATGGACTAGGATGATTACAGTTGTTCAGTTCTGACTGTTATTTGAAGAAAAAAGCAATAAGAAgcctcagcaacttaacagaaggagctgccatttactaggagaaaagattgtggatgagagtgtagcaaaggtcagaattctgtgaagcttgagatgtttattaTAATGAATTATCTTTTATACTCACTACAATTTCCTAACAATTTTGGGGTTTATATTTTTGAAAGAGATATACCTTTAATTTTCTTTCTTTGTACTATTGTTAGGTAACTTTAATGTGCAGATTATACTACAgtgaaagttgccaatgacaaggcaaagtcacttacatcagacccaaagcaaagtggagccgggtcatgaaaaaggggatcttgtgtgtctgtccacgataagcactatcacaaggactttctataaactcacaagaaaTTTCTGCCCACCCAGCACACA--GTTTGTCCAGCTCATCCTGTAGGTGTCTCTATAATAGGACCTATCATAAAAAAttcctcaagactgcagcatttcagataagccaccctcacaagaacacttgcctagcaatggctgtttctgccagtaagttaacaccagctcctgcatcagaccctgtgaccaatgatgtttgtttcaaaacagcttgcatggacttctttttgtctttacatattttccttacctcaacctcttgggatgcacctatgattgatcatagcacaaatatctcagattataatccttgtttatttccaaataaatttatttctttggagatccactt tttctgTTATTATACATTGACATTGTTAttatgaaattggttgggtgatgtgtcttattttcttgtctccagaagaatttctgtaacagtgcaattaaacgttctttgcatgtttgctagaactcacctgtaaaattgtctgagcAACCAAAGCCTGGTTTTTGTGTTTAGTTTTTCTTTTGTGATTGGGGAGGGGGGTTTATCGTACTGATTCAAGGTGTGAAGGTAACATCATTTTGATTTTATACATCTTCTTCAGTCCATTTAAGCATGTTACATAGCGTTGTTTGTTCTTTTCATGATATTCTTtacagtagtctcctaaatgttccctctgattctg-----------------------------ccatgagcccctacaatctatttcaactcagaagctatagagtttgtttaaaacatgtaacatattatgccacctttcttactgtaaaacatcccatggtttctcatagtatttatagtaaaagtgaaatttttatgatggcctgagaaacttttcccattagatgcccaagtgctggtctggtctgatcttctcatcttcccttgggtgattctgtggcagtcacactagcctccttgctgctccacaaaaactccagcatgatcctacttcaggatatttgccattgttactgcatctgcctggaaccttttctcccatataaacatagagattgctcttgcctgtccttcaagtctattcttaaatgtcccattctctgtgaagctttcctgcccaccctatttaaattacagacttcactcccaattccccatctactttaagagtcttcatttatcattccttgacaaactgtaaatatacatgttcacttttttatcgtctgtctccaaatactggaatgttaagttctgtaatgtcagatatttctgtttggttcactggtgtattcttaaagcatgttacatactaggtatactcaatgaatatttgtt gaataaatatcacattgggcttattccagaaattcaagcttgtttcaatagttagagcaatctacaaatgtaattcattacattaactaattaaaggagctaaatcacatcaccaccacaataatgcagaaaaccacatttgatacaactcaatattcatgtctgcctaacaaacatctcatgatactaggaaaagaggaagggatatattattttcatgtataaagcactaaccattgtagcatgccaatatactcaaaattcaatgaaattcctatcaaaatcttagcattcctcttagtcctcaacaaagcatttctaaaatgtgtatagaagaccaaagggccaaaagagtcaacttctgaagaagcgcaaaaagaaagttgaggaaatcttaaaacatgttattgagcttaaagttgcaaaaataaactcatgtaccataattcatgagtagaaaaatagactagtggaataacataaaaataaaaacaatgcttacataaaatgttgtaactgatttggatgtcattagaaatcagtaagtaaatagatggacaatgtaatgaaagatgctaggcaaatAAtgtggtagggagaataatggccctcaaagatgcccatgcctaaccctggaacctgtgaatatgttacactgaatgcaataaaggcttatcagatgtgattaaggatgcaaaccgagatggagagatcttcctgggttacccagatgggcccagtctaatcacatgagttcttaaaaatggagaacctttcttagctgagtccagagagagatgtgacaatgaaagaatggtcagagaaatgtgacattgccagctttaaaaagagagaggagaggcaatgagaaaaggaatgctgatgttctctagaagatagaaaaggccaggatatggattctaccctagccaccataaagaaacatgcctgtcgacaacttgattttagttcactaaaattcatgcctg atttctgacttgtgtacactgtaagatgacaagtttgtgttattttaggtcacttagtttgtagaaatttgttacagcagtaatagaacaagtggttatccatatgaggcaaattagattggatacctatctccaatagaaatcaattcaaggtgaattccaggaaaatacttaaaacatttagattaaaaataaatgagaatttttgttacttttggtaggtcatagaaccaagaaaaacaaacattaaggaggaaaaatgaacatatgactacatcaaaatataaagcttctctatttggaagatatcataaggtgacaaatcataaactgtaatatttacaacatatatataagtgaataaatatacatttagaatatatatgaactcccaaaaatcaacaggaaaaataagacatagaacaagcaaaatgcataaacaaaagaaggcaaaacaaaaataatgactcataattatatgaaaagaagctcatcttcatagatgagcagataaatgcaaattaaaaccaccctgagatgctttttacatccatgagcctgataaaagttagagtctaaaagtaataa----caaagatgggaagtaatagaaaatcttgtccattactggttaaagtataaactgatacagctactttatagaatattacattatagaataaagttgtgagtatgtatatgcagtgactcagcatattcattgctagtatgtactcaagagaaacttacaggagtggactaggaagtaaatacaaaatgattacaacattgtttgttatatcaaaaaataaaaaagacacccaattttccagcaaaaaaaataagtaaaaataaatcctggtgtattctaacaatggaataatatatagccattaaaataaatcaactattactgtacatatgaatgtaaatatcagcaaaacatattgtttagtgaaaaactaagaagctgaagaagaatatataca atatggttacatttatatgaagtccaaaaacttgcaaaataaagaaatgtatttagaaatagattcacatgtgagaaaactagaagaaaattaatgaaaggataagagggatagcagtaattctgagtagttgagggaaTTTCAATTGGAAAAAAATAATATCATATTCTTTAAGTCAGGTAGTGGGTATTAGCATTTGTTTTACCATCGTTCTTTATTCTTATAGCTACACTATATATTTTCAATGTATTTAATGTATTTTTTGCATAATTAAATATTATGCAATAAAAATGAGAAAACAAAAAAGTAGAAAATGATAAATTACAATAAAGAAATGGAGAAAAAATTATAATCTAGTTGAGTAATGGTATATTACATAGCTATTTTCTTAAGTAGATGTATGTACATGATGTATGCACGATTGTACATACATGTTCttaattatatataaatatatatgtacatatttttaatataaaataCTAAACAAAGTACACCAAAATATTAGCTCCTAT +s panTro2.chr1 248901 7392 + 229974691 AGCCTGctgcctcatttaataactctttgtctctttcccagatccagccactctaacattttttagttcctggaccaagacaagctcttcccagaacctgacctttgtacctgttctttattcctggagtatttttcccctgacaaatgacttatcatctatcataaatcaggttaaatggcactaactcagggaaggcttccctaactgcctcccttctctaaccaaattaggaacaattatatggccacatagtatcgaatcaagtttataattttaaaataattgggagattttgttgtttaacacttgttttcactataagactgtaattacatgcaagtaagaaccatgcctgtttgtttactcctgacacagtcagaatagtgcctggaatatgcagtaagggctgaacaaacactaaataaataaaCAAGTGAATAAATGGATATTGTCTCGTTTTTAGAACAGAGTACTAAATGGATCATGAACACTATCTGGTATGTCACGTAGGTAATTTACAAGGGCTACAATTTCAGCTCAGATTTACCTTTTCCTGGATACAGGTcttgataggtctcttgatgtcatttcacttcagattcttctttagaaaacttggacaatagcatttgctgtcttgtccaaattgttactaagaatcaaaagagatatctgacatgaaatgacattggaaaacattaaacacgactgaaataatgctagccaatatggttatTATTAGAAACCAATTACATTTTCAACTTAAAAATAGTAATACTTATTGCAGACTCAAATGTGCTCATTCTAAAACAAGTAAATGTTTGCATATGGTCTGAGATTCTAATCCACGGCGTTCATTCTAATCCACATTCAACACTATCATGTACCAGTGGGCCTCATAACCCACCTAGCCCTGTGATTTTTCAGGTTCACTTTTCTAAACTTGT GAATTAAATATTTATTTTCTTAGTTCAGAAGAGGAAAAAAACTCTTGTAATTGTTGCCCATTTCAGGAGAAATCTTGCATATGAAAACAAGAGATAAATATACACAACTGAGGGCTGTGGTTTAAACAAAATCTTGAGAATGTTTTTTGACCTTATACATTTGTGCTTTAGTATAACAAAATGATATAGACAAAGGTAACTTTTAATAGAACCAGTCACTAAATTAAAAAAAATGACAAATTCTTCTGCTTAGCTAAGCAACAGAGAAGGTAAAATACTAATTCAATTCATCAATTTAAGCAATACTCATTAAGAGCCAAGTATGTGCTTACTGAATAAGCTGCTAAGGTTTGGTGGTTACAGAGTGTGCAGTGAAATGATGTCTACATCACAGTCCAACATTCACAGAGTTTAAAAGCCTACCAAGAATCAAGACAGACACAAATACCTAACATAGACGTTTGTATGTGATAAGAGAGCCAGAGTACAATTTAGGAGAAGAAATTGTATGGAAGGAAGGTTCATTTCCATTAGACCAGAAAAGACAGCACATTTGAAGGCCTGAATAAGAAATATTCTGGATAAGATATTGTGACTGCCAccagaatggctcttgatgatctctacctcttggtatttatacccttatataatctctttcctatagtataagctggtcccaggtacttgtttctattgaatagaatagaacaaaagtaatgagatgccacttctgagattagattataagatactgtgaatttcatcttgtgccctctccctctctctctttctcttgccctctcatttgaatgaagccaactggcatgctgtcagtggcccagtgtaagtcctgttacaagaaattgatgattacctgtagccaaccctaagtgaagaactgaggtcctcagtcctacaaatggagagaaactgaatctagctaagaaccatgtgagtgagctgggaagaagatccaccctcagttg aaatttaagatgGCATATTGAGCAGACATACTGAGACACACTGAAAGTAAGAGAGCAGGaggaaacaaaaccagggtcatacaaagaacagaactgattttgagattctcacataagtattacaccttcagtgagcacgtgtactagaaattaaaaaaataaattaaataaacctacaaagagagctagcaaataaatttccctatggtctcagatctgagtggagagagaaaatgttccctgtggagtttacagccagaatccagctctcaaacaggtttcagcctgaactcacacaatctgtgcggcttccaaatttgaaagctgagaatttaattcaaaatggtctcaggttgatagcagtccaaaatgctaggtaggaaaaaaaatcctctctggacaaataaatcatcaaagtaagctcataagagcaggtttcaaaggtcatgagcttctaacacacac-caaaaaaatcgcacacacaaaatgggggtagcagcaacatgggtagcatattcaaacttgaaaagactttaaatatttgtattattagatgtagattatgaaacacatattttaaTGTGGTTAATTTTTTTAAGGAATCAAAACTATGAGTAAAGACCAAGAAAATTGTGCTGGATGGCCACTTCCACCATGGCTCCCCTCCTATTTAAGTCTGGGTACTGTGTCACCCGGAGTCTTCAGGCACATTGTTCCAGGTTTGGGTTTGCCTATGAAAGAAACTCATGAGAGCTGGAAGTGAGGAGTGAAGAGGAGGTCTTCACATAAAGCAGGCTTAAGGATTAGACATAGCAGGTTTGACAGATGTGATGGCTTGCAGAATTCTTTATGAGCTCCCACTGTCCATCTGGATAAGATTTACAGACCTTTCAGAAATTCCTATAAGCTTGGGTTCTGTGCCCACACTCTAGACTGTCAGGCTAAGATCTCTGATATAAAACAgacctcttctgattttgtctagctg cttttctaatatctattcaccaagctcttccaataacagcatgaggccctaattaatattaaacttttatcattataatacttaggatgtcttctgttttcctgatcaaattctgactACTATTAAAATATAAAGAATTGTCCAGAAATATATTTTAAAA--ATCACACATTGATCTTCTTTAAATGAAAATATAACAATTGTATGGACTAGGATGATTACAGTTGTCCAGTTCTGACTGTTATTTGAAGAAAAAAGCAATAAGAAgcctcagcaacttaacagaaggagctgccatttactaggagaaaacattgtgggtgagagtgtagcaaaggtcagaattctgtgaagcttgagatgtctattaTAATGAATTATCTTTTATACTCATTACAATTTCCTAACAATTTTGGGGTTTATATTTTTGAAAGAGATATACCTTTAATTTTCTTTCTTTGTACTATTGTTAGGTAACTTTAATGTGCAGATTATACTACAgtgaaagttgccaatgacaaggcaaagtcacttacatcagacccaaagcaaagtggagccgggtcatgaaaaaggggatcttgtgtgtgtgtccacgataagcactatcacaaggactttctataaactcacaagaaaTTTCTGCCCACCCAGCACACTCTGTTTGTCCAGCTCATCCTGTAGGTGTCTCTATAATAGGACCTATCATAAAAAAttcctcaagactgcagcatttcagataagccaccctcacaagaacacttgcctagcaatggctgtttctgccagtaagttaacaccagctcctgcatcaggccctgtgaccaatgatgtttgtttcaaaacagcttgcatagacttctttttgtctttaaatattttccttacctcaacctcttgggatgcatctatgattgatcatagcacaaatatctcagattatagtccttgtttatttccaaataaatttatttctttggagatccactt tttctgTTATTATACATTGACATTGTTAtcatgaaattggttgggtgatgtgtcttattttcttgtctccagaagaatttctgtaacagtgcaattaaacgttctttgcatgtttgctagaactcacctgtaaaattgtcagagcAACCAAAGCCTGGTTTTTGTGTTTAGTTTTTCTTTTGTGATTGGGGAGGGGGGTTTATCGTACGGATTCAAGGTGTGAAGGTAACATCATTTTGATTTTATACATCTTCTTCAGTCCATTTAAGGATGTTACATAGCGTTGTTTGTTCTTTTCATGATATTCTTTACAGTAGTCTCCTAAATGTTCCCTCTGCTTCTGTTgtctcctaaatgttccctctgcttctgccatgagcccctacaatctatttcaactcagaagctatagagtttgtttaaaacatgtagcatattatgacacctttcttactgtaaaacatcccatggtttcttgtagtatttatagtaaaagtgaaatttttatgatggcttgagaaacttttcccattagatgcccaagtgctggtctggtctgatcttctcatcttcccttgggtgattctgtggcagtcacactagcctccttgctgctccacaaaaactccagcgtgatcctacttcaggatatttgccattgttactgcatctgcctggaaccttttctcccatataaacatagagattgctcttgcctgtccttcaagtctattcttcaatgtcccattctctgtgaagctttcctgcccaccctatttaaattacagacttcactcccaattccccatctactttaagagtcttcatttatcattccttgacaaattgtaaatatacatgttcacttttttatcatctgtctccaaatactggaatgttaagttctgtaatgtcagatatttctgtttggttcactggtgtattcttaaagcatgttatatactaggtatactcaatgaatatttgtt gaataaatatcacattgggcttattccagaaattcaagcttgtttcaatagttagagcaatctacaaatgtaattcattacattaacaaattaaaggagctaaatcacatcaccaccacaataatgcagaaaaacacatttgatacaactcaatattcatgtctgcctaacaaacatctcatgatactaggaaaagaggaagggatatattattttcatgtataaaacactaaccattgtagcatgccaatatactcaaaattcaatgaaattcctaccaacatcttagcattcctcttagtcctcaacgaagcatttctaaaatgtgtatagaagaccaaagggccaaaagagtcaacgtctgaagaagtggaaaaagaaagttgaggaaatcttaaaacatgttattgagcttaaatttgcaaaaataaactcatgtaccataattcatgagtagaaaaatagactagtggaataacataaaaataaaaacaatgcttacataaaatgttgtaactgatttggatgtcattagaaatcagtaagtaaatagatggacaatataatgaaagatgctaggcaaatAAtgtggtagggagaataatggccctcaaagatgcccatgcctaaccctggaacctgtgaatatgttacactgaatgcaataaaggcttatcagatgtgattaaggatgcaaaccaagatggagagatcttcctgggttatccagatgggcccagtctaatcacatgagttcttaaaaatggagaacctttcttagctgagtccagagagagatgtgacaatgaaagaatggtcagagaaatgtgacattgccggctttaaaaagagagaggagaggcaatgagaaaaggaatgctgatgttctctagaagatagaaaaggccaggatatggattctaccctagccgccataaagaaacatgcctgtcgacaacttgattttagttcactaaaattcatgcctg atttctgacttgtgtacactgtaagatgacaagtttgtgtgattttaggtcacttagtttgtagaaatttgttacagcagtaatagaacaagtggttatccatatgaggcaaattagattggatagctatctccaatagaaatcaattcaaggtgaattccaggaaaatacttaaaacatttagattaaaaataaatgagaatttttgttacttttggtaggtcatagaaccaagaaaaacaaacattaaggaggaaaaatgaacatatgagtacatcaaaatataaagcttctctatttgaatgatatcataaggtgacaaatcataaactgtaatatttgcaacatatatatgagtgaataaatatacatttagaatatatatgaacttccaaaaatcaacaggaaaaataagacatagaacaagcaaaatgcataaacaaaagaaggcaaaacaaaaataatgactcataattatatgaaaagaagctcatcttcatagatgagcagataaatgcaaattaaaaccaccctgagatgctttttacatccgtgagcctgataaaagttagagtctaaaagtaataattaacaaagatggcaagtaacagaaaatcttgtccattactggttaaagtataaactgatacagctactttatagaatattacattatagaataaagttgtgagtatgtatatgcagtgactcagcatcttcattgctagtatgtactcaagagaaacttacaggagtggactaggaagtaaatacaaaatgatgacaacattgtttgttatatcaaaaaataaaaaagacacccaattttccagcaaaaaaaataagtaaaaataaatcctggtgtattctaacaatggaataatatatagccattaaaataaatcaactattactgtacatatgaatgtaagtatcagcaaaacatattgtttagtgaaaaa----gaagctgaagaagaatatataca atatggttacatttatatgaagtccaaaaacttgcaaaataaagaaatgtatttagaaatagattcacatgtgagaaaactagaagaaaattaatgaaaggataaaagggatagcagtaattctgagtagttgaggggaTTTCAATTGGAAAAAAATAGTATCATATTCTTTAAGTCAGGTAGTGGGTATTAGCATTTGTTTTACCATCATTCTTTATTCTTATAGCTACACTATATATTTTCAATGTATTTAATGTATTTTTTGCATAATTAAATATTATGCAATAAAAATGAGGAAACAAAAAAGTAGAAAATGATAAATTACAATTAAAAAATGGAGAAAAAATTATAATATAGTTGAGTAATGGTATATTACATAGCTATTTTCTTAAGTAGACGTATGTACATGATGTATGCACGATTGTACATACATGTTCttaattatatataaatatatgtgtacatatttttaatataaaataCTAAACAAAGTACACCAAAATATTAGCTCCTAT + +a score=132031 +s hg18.chr1 109375 1459 + 247249719 GTTAGTGAGATAATGTTTTGTTTTTTTGTATTTTAAGTTTTACATAGTAGGtgtatttttctgttttcatactgctataaagaactgcccaagactgggtaatttataaaggaaagaagtttaattggctcaccgttcagcacagcttgggaggcctcaggaaatctacaatcatggcggaagacaaagaggaagcaagccagcttcttcgcaaggcagcatgaagaagtgccgagcaaaggggaaagaatcccttataaaaccatcaaatctcgtgagaactcactatcacaagaacagcacaggggaaactgcccccatgattcaattacctccacctggtctctcccttgacctgtggggattatggggactatggggattacaattcaagatgagattcaggtggggatacaaagcctaaccatatcaGTAGGCATGTATTGAATTTTAAACTCAGAGAAAAATACTAGTGTTTTT-ATAGGATTCTTACTAAAGAAAAACCAGAAAGTAATAAACCATCTACGCTAAGACATAAAATTCAGTTGTTTAGTTACAAGATAGAATGTGGCCTTGTAAGAAAGCAAATTAACTTCTAACATACAAAGCCTTAGAGAAGATTCAAGTGACTGACGGATCTTAAACAGAGCTATTATTACAACTCGAACTGCAGTAAAATATCCTCAGCAACATAGATGTGTGTGTTTCACTAGTCAGAGCAATACAAATTTAATGAAACTCCACTGGTGGTGTTTTTAATCAGACAATTTCTGAAGATGTCCTGGCTTATTCACAGATGCAAGCCAAATCTCTAGAAGAGTACCATAATAAGAAAAAAAAGAATACAGGCAATTGAGAGCTGTTCCAAAGTTTAGGGAGTTTTTGTAAGGAATTAATAAATAAAAATGTTCTTGAAAGACAGAAATTAATATGCAGTTCATACTGTCAG AATTGCAGGCAATTTATCAAAGTCCCCTAATCCTCCAAAATCGCTATTTTTTTTTTGACACACACTTTACAGTACAGAAGAAAATGTCTCCGGCAATAAATCACAAAGTTAAAATTACCTAGTCTACAATTAACTACACAGTGATGGTAAATCATTTTCTACCAAAAGAAAGAAATGTCTTGTCTATTCAGGTTCTGCTCTACTTAAAAGTTTTCCTTGTTGGCGAGCAAGTGGTTAGAAAATTATATTTTATACGTACATTCAGCTTAACTATCATTCAGCTCAGGAAGATGACTCAGGGCCTTATCCATACCTTCAAGTTTGCTCTTAGCAAGTAATTGTTTCAGTATCTATATCAAAAATGGCTTAAGCCTGCAACATGTTTCTGAATGATTAACAAGGTGATAGTCAGTTCTTCATTGAATCCTGGATGCTTTATTTTTCTTAATAAGAGGAATTCATATGGATCAGCTAGAAAAAAATTAAGAGGAAAATCACATGGAAAGttat +s panTro2.chr1 258082 1456 + 229974691 GTTAGTGAGATAATGTTT-GTTTTTTTGTATTT-AAGTTTTACATAGTAGGtgtatttgtctgttttcatactgctataaagaactgcccaagactgggtaatttataaaggaaagaagtttaattggctcacagttcagcacagcttggaaggcctcaggaaatctacaatcatggcggaagacaaagaggaagcaagccagcttcttcgcaaggcagcatgaagaagtgccgagcaaaggggaaagaatcccttataaaaccatcaaatctcgtgagaactcactatcacaagaacagcacaggggaaactgcccccatgattcaattacctccacctggtctctcccttgacctgtggggattatgggggctatggggattacaattcaagatgagattcaggtggggatacaaagcctaaccatatcaGTAGGCATGTGTTGAATTTTAAACTCAGAGAAAAATACTAGTGTTTTTTATAGGATTCTTACTAAAGAAAAACCAGAAACTAATAAACCATCTACGCTAAGACATAAAATTCAGTTGTTTAGTTACAAGATAGAATGTGGCCTTGTAAGAAAGCAAATTAACTTCTAACATACAAAGCCTTAGAGAAGAATCAAGTGACTGACGGATCTTAAACAGAGCTATTATTACAACTCAAACTGCAGTAAAATATCCTCAGCAACATAGATGTGTGTGTTTCACTAGTCAGAGCAATACAAATTTAATGAAACTCCATTGGTGGTGTTTTTAATCAGACAATTTCTGAAGATGTCCTGGCTTATTCATAGATGCAAGCCAAATCTCTAGAAGAGTACCATAATAAGAAAAAAAAGAATACAGGCAATTGAGAGCTGTTCCAAAGTTTAGGGAGTTTTTGTAAGGAATTAATAAATAAAAATGTTCTTGAAAGAGAGAAATTAATATGCAGTTCATACTGCCAG AATTGCAGGCAATTTATCAAACTCTCCTAATCCTCCAAAATTGCTA--TTTTTTTTGACACACACTTTACAGTACAGAAGAAAATGTCTCCGGCAATAAATCACAAAGTTAAAATTACCTAGTCTACAATTAACTAGACAGTGATGGTAAATCATTTTCTACCAAAAGAAAGAAATGTCTTGTCTATTCAGGTTCTGCTCCACTTAAAAGTTTTCCTTGTTGGCGAGCAAGTGGTTAGAAAATCATATTTTATACGTACATTCAGCTTAACTATCATTCAGCTCAGGAAGATGACTCAGGGCCTTATCTATACCTTCAAGTTTGCTCTTAGCAAGTAATTGTTTCAGTATCTATATCAAAAATGGCTTAAGTCTGCAACATGTTTCTGAATGATTAACAAGGTGACAGTCAGTTCTTCATTGAATCCTGGATGCTTTATTTTTCTTAATAAGAGGAATTCATATGGATCAGCTAGAAAAAAATTAAGAGGAAAATCACATGGAAAGTtat + +a score=195249 +s hg18.chr1 110834 2199 + 247249719 atattatatatctattatatataatatatatctattacatat--tatatattgtatatctattacatatatattatatatgtattatatatattatatattatatatgtattatatatattatatattatatatctattatatatataatattatatattatatatCATTTCCAAATTCCCCAGCGTTCATATTTGTCAGTGCAAGTAAAGAGCCTTACTGCTGATGAGGTTTGAGGTATGACCATTTGGCCAGAATTTATGAACTCTACATGTCGCTTGATGTGTGCCTCAGGGTATACttttttttttttttt---gagacggagtcttgctctgtcgcccaggctggagtgcagcggtgcgatctcagctcaccgcaagctccgtctcccgggttcacgccattctcctgcctgagcctcctgagtagctgggactacaggcgcccgccactatgccctgctaattttttgtatttttagtacagacggggtttcaccgtgttagccaggatggtctcgatctcctgacctcgtgatccacccgcctcggcctcccaaagtgctggaattacaggtgtgagccaccacgcccggccAGGGTACACTTTTAAGCAGAGACACTACTTTGAAGGTCATAAAAAATATAATAAGAGATAAGGCTAATTTCCtttaataataataa------aatcctttaataaaaatataaaggaataatataataattttctttaataaaatataataaGAGATAAGGCTAATTTCCTTTAATAAAATATAGTAACTACATACCAACAGAATTCCAAAAAAAGAAATGGAGAGGAAGGGAGCATGGGTCATTAATCTTGTCAAAAATATAAAATTATATACGAGGAATTCCTAGAAACTGTTTTCCTTGTCTGCGGCCATTGTGCTGCTGCTACACAACTACCGCAAGCAGCCCTTCA CGCCCTCCTCCCAGTACAAAGCTAATTGACTTGTGAGAAATGTTAAGCTTGGAAGAGTCAGCATCACTGCACTTATTTTTTATTCTACTCTGACATTAGAATAATCCTTGAGTGGGGGAAAGGTTAAAAACCCCCCTGGATAAGTGTTACTAATTAATGATGATTGTTTTAAACAATGTTTGGATAATTTTTCCTTGTCCCTTGACATAAACTTGATAAATAACTGAGAAGTGAGAAGGAGATTAGTGGGTTGATTAAATTCCATTCAGGTACTTAAAGTTAGCTCCAAAAATTTAGCTATTTGTAAATTGTCATGCATTGTTAATGTATAAGAGATGTAGATTTCATTTATCTTTGGTGGAGCGAGATGAAGCAGTGAATCATTGAAGACTGAAAGAAAGAAAAAGGTCTTTTCCCTTTTCTTTAAGAAGCATCATTAGTTAAAAACATGTTAGTTGATACCAGAGAACTATATTTAAAGGGACAGCAATAAGCAAATTGATTACTCTGGTGATTATTGGAGTGACATTGCCTTTTAGTTGTACTTTCACAAAAATTCACAATATTTGCCAAAGTCAAGTTATCCATTACACTATTAATTTGTCATTCTTTTGTTTATATAGTCAATATCTCTATCTCAATTGGATCTATCTCAACTGCTTCTAAACAAGCCACCATAGTCTCTCCCATTTCAACAATCTCTTCCAAGTACCACTTCATTTCTTCTTTTCATATTTTTGAAAACTTTTGAAAAACTACCTATTTTCCTCCTCCATTTCTTGTTCATTCCATTCTAGTGGACATGGAATCTGTTCCTCCTCCAAAACGGAATTTGGTAACCCTTAAATTACTAAACCCAAAACAATATGTTGTCTTTATCTTTACCTCTCTGTGGCATTTAATGATAAGACCACTACTTTCTTCTCTTTTACCCTTCTTTCTTGAATTCAGTCAGACAACGTACTTACATTTTTCGTCTTATTCTCCAT CTTAGAAACCACCTCAGCTTTCTCCATTCAGCTATAAAATTGTGCTTTTCCTCAAAGATTAATCTGCCTCTCCTCTCACTCTATACTATCTCTGTTAGCTAATTTTATTTGTGCACATTGCTTATACTGGGCATTATATACACATATGCATGTGTGTACATGTGCACACACACACTGTATGTGGACatgtatatatatatatgtgtgtgtgtatatatatagtatatatataAATTACAATAACATAAAGGTGGCATTTTAAATTAGTGGA +s panTro2.chr1 260178 2182 + 229974691 atattatatatctattatatataatagatatctattatatatattatatattgtatatctattacatatata------------------------atattatatatctattatatatattatatattatatatctattatatatataatattatatattatatatcATTTCCAAATTCCCCAGCGTTCATATTTGTCAGTGCAAGTAAAGAGCCTTAGTGCTGATGAGGTTTGAGGTATGACCATTTGGCCAGAATTTATGAACTCTACATGTCGCTTGATGTGTGCTTCGGGGTACACttttttttttttttttttgagacggagtcttgctctgtcgcccaggctggagtgcagcgatgcgatctcagctcaccgcaagctccgtctccctggttcacgccattctcctgcctgagcctcctgagtagctgggactacaggcgcccgccactatgccctgctaattttttgtatttttagtacagacggggtttcaccgtgttagccaggatggtctcgatctcctgacctcgtgatccacccgcctcggcctcccaaagtgctggaattacaggcgtgagccaccacgctcggccAGGGTACACTTTTAAGCAGAGACACTACTTTGAAGGTCATAAAAAATATAATAAGAGATAAGGCTAATTTCGtttaataataataataataaaatcctttaataaaaatataaaggaataatataataattttctttaataaaatataataaGAGATAAGGCTAATTTCCTTTAATAAAATATAGTAACTACATACCAACAGAATTCCAAAAAAAGAAATGGAGAGGAAGGGAGCATGGGTCATTAATCTTGTCAAAAATATAAAATTATATACGAGGAATTCCTAGAAACTGTTTTCCTTGTCTGTGGCCATTGTGCTGCTGCTACACAACTACCGCAAGCAGCCCTTCA CGCCCTGCTCCCAGTACAAAGCTAATTGACTTGTGAGAAATGTTAAGCTTGGAAGAGTCAGCATCGCTGCACTTATTTTTTATTCTACTCTGACATTAGAATAATCCTTGAGTGGGGGAAAGGTTAAAAACCCCC-TGGATAAGTGTTACTAATTAATGATGATTGTTTTAAACAATGTTTGGATAATTTTTCCTTGTCCCTTGACATAAACTTGATAAATAACTGAGAAGTAAGAAGGAGATTAGTGGGTTGCTTAAATTCCATTCAGGTACTTAAAGTTAGCTCCAAAAATTTAGCTATTTATAAATTGTCATGCATTGTTAATGTATAAGAGATGTAGATTTCATTTATCTTTGGTGGAGTGAGATGAAGCAGTGAATCATTGAAGACTGAAAGAAAGAAAAAGGTCTTTTCCCCTTTCTTTAAGAAGCATCATTAGTTAAAAACATGTTAGTTGATACCAGAGAACTATATTTAAAGGGACAGCAATAAGTAAATTGATTACTCTGGTGATT-TTGGAGTGACATTGCCTTTTAGTTGTACTTGCACAAAAATTCACAATATTTGCCAAAGTCAAGTTATCCATTACACTATTAATTTGTCATTCTTTTGTTTATATAGTCAATATCTCTATCTCAATTGGATCTATCTCAACTGCTTCTAAACAAGCCACCATAGTCTCTCCCATTTCAACAATCTCTTCCAAGTACCATTTCATTTCTTCTTTTCATATTTTTGAAAACTTTTGAAAAACTACCTATTTTCCTCCTCCATTTCTTGTTCATTCCATTCTAGTGGACATGGAATCTGTTCCTCCTCCAAAACGGAATTTGGTAACCCTTAAATTACCAAACCCAAAACAATATGTTGCTTTTATCTTTACCTCTCTGTGGCATTTAATGATAAGACCACTACTTTCTTCTCTTTTACCCTTCTTTCTTGAATTCAGTCAAACAACGTACTTACATTTTTCGTCTTATTCTCCAT CTTAGAAACCACCTCAGCTTTCTCCATTCAGCCATAAAATTGTGCTTTTCCTCAAAGATTAATCTGCCTCTCCTCTCACTCTATACTATCTCTGTTAGCTAATTTTATTTGTGCACATTGCTTATACTGAGCATTACATACACATATGCATGTGTGTACATGTACACACACACACtgtatgtggacatg--tatatatacatgtgtgtgtatatatatatagtatatataAAAATTACAATAACATAAAGGTGGCATTTTAAATTAGTGGA + +a score=17777 +s hg18.chr1 113033 202 + 247249719 aattaccctgatttgatcactacacattctatacatgtaaagaaaatatcactctgtatcccaagaatatgtacaattatggtttgtcaaatgaaaaAGTTCATACATTGAAAAATTTTAGATAAATATCAAACTTTCTCTGAAACTGTAACTGTAAAATGTAAAAAACAGTAATTGCTATATTGCTTATTTCTGAGTAGAA +s panTro2.chr1 224022798 201 + 229974691 aattaccctgatttgatcactacacattctatacatgtaaag-aaatatcactctgtatcccaagaatatgtacaattatggtttgccaaatgaaaaAGTTCATACTTTGAAAAATTTTACATAAATATCAAACTTTCTCTGAAACTGTAACTGTAAAATGTAAAAAACAGTAATTGCTATATTGCTTATTTCTGAGTAGAA + +a score=3621 +s hg18.chr1 113251 39 + 247249719 CCTAATCATTATGTGTAATTACAATTACATATATATATG +s panTro2.chr1_random 1172673 39 - 9420409 CCTAATCATTATGTGTAATTACAATTACATATATATATG + +a score=4427 +s hg18.chr1 113290 49 + 247249719 TAATTGTAATTACACATAATGATTAGGGAAATGTCTCATATTCTATATA +s panTro2.chr10 95659061 49 - 135001995 taATTGTAATTACACATAATAATTAGGGAAATGTCTCATATTCTATATA + +a score=46693 +s hg18.chr1 113339 531 + 247249719 TATAGACAGAAAGAGAGAAAATATATGAGGGAGAGAAGGAATCTTTCCATCTCCTTTGAGTTCCACGGTGTTGAGAGTCAGGACAACTGCAATTGCTTCATCATGCCTGCTTGCAATTATAGGGCTTTTGAACCATTTGTTCCCTCCTTAGATATCCTCATTTTTTTCAGATTCTTGCTTAGAAGTCACTCCTCCGTGGACCTCCTCTGACATATTAAACATTGCAGTCCATtataagctgcaagaggacagggatttttgcctgttttattccctactgtatcaccaggggctagagcaatatctgacaaacagtgggcatgtaatgaatatttgttaagtgaaGTAATAAATTCaatcaaatcacatcacctgtttaaagcacttcattggcttcacattgcacttagaataaagagaaattctttttatacaatatacaatatattttatacaatataagttcctgcagaatgcagacactttctacttctccagcctcttttcgactcctctcctactagcttctgt +s panTro2.chr1_random 1172712 510 - 9420409 TATAGACAGAAAGAGAGAAAATATATGAGGGAGAGAAGGAATCTTTCCATCTCCTTTGAGTTCCACGGTGTTGAGAGTCAGGACAACTGCAATTGCTTCATCATGCCTGCTTGCAATTATAGGGCTTTTGAACCATTTGTTCCCTCCTTAGATATCCTCATTTTTTTCAGATTCTTGCTTAGAAGTCACTCCTCCGTGGACCTCCTCTGACATATTAAACATTGCAGTCCATtataagctgcaagaggacagggatttttgcctgttttattccctactgtatcaccaggggctacagcaatatctgacaaacagtgggcatgtaatgaatatttgttaagtgaaGTAATAAATTCaatcaaatcacatcacctgtttaaagcacttcactggcttcacattgcacttagaataaagagaaattct---------------------ttttatacaatataagttcctgcagaatgcagacactttctacttctccagcctcttttcaactcctctcctactagcttctgt + +a score=20908 +s hg18.chr1 113870 240 + 247249719 atttaagccatattagacctttcttcagttttttatatagactttgtcgcatcacacctcagagattctgtacatgttcttcctcctgcctagaaaggatcgtccctccacttttgccaactaatccctgctcaacttttcatctcagcaggaggcccattctctttggcaatcctctggcctccagcccatttattatatgctcacatgtcaacatgtacttcgtacagcatgtaacac +s panTro2.chr1 224023740 240 + 229974691 ATTTAagccacattagaccattcttcagttttttctatagacttcgttgcatcacacctcagagattctgtacatgttcttcttcctgcctagaaaggatagtccctccactttcgccaaataatccttgctcaacttttcatctcagcaggaggcccattctctttggcaatcctctggcctccagcccatttattatatactcacacgtcaacatgtacttcgtacagcatgtaacac + +a score=390882 +s hg18.chr1 114110 4346 + 247249719 aattgcacttttatattttaacaaattatatttcccatattgaactgtaagtctcctgaaagcaggaattttgttcttgctcatcatcaactttttcaacatccagtgcaccatttagaacttagatgtagtcaatacaggtttgtggaatgaaagaGGAAAAGAAAGAATTAATATTCCTTTAAATTAGGATGGCAAAGATCGTATATAGAAAATTGGCTAAGTTGTGGTCCATTCATGTTTGCTCCCAATTAAGGAGCACAGCTATGAAAAGGAAGGCTTCAAATTAATAACCAATAGATTTTTTTAAAAAGAAAACTggccaggtactgtggcttatgtctgtaatatcagcatgttgggaggccaaggcaggattacttgagcccagaaattccagaccagcctgagaatttggcaaaactctgtctctacaaaaaatacaaaaattagccaagtttggtggcatgtgcctgtagtaccagctacttgggaggctgaggtggaagaatagcttgagtctgggaggtcaaggctgcaatgagctgtgattgcaccactgcactcaagcctgggtggtagagtaagaccctgtctcaaaaaaaaaaaaaaaaaaagaaaaaTCACTAAGCAAAATAAGACATGTGAAGGATCATGTCAAAGGAAAGAAAAATTAGGGGAACATTAAAAGCTTTCTTCCCAAGCCACTAAATCAACTTGACTAACAAAATTACCACTTGATTTAGTATTAGAAAATTACATTACATATCAAACATAAACCCATTAATCAAATACTAAAGAAATTTCTGAGTTAAATGGTATAATGTTAGCTTATGCCAGAGCTGACCTTGAAAGATTGTTCAAATATGGCTCAGTGTGATTGAAAGTTCTGTGTGAATATGTTTTTGGAAAGATCCAACAGCAACACCTTAGTGTATGTTTTTGAAATA AAATATATCTGAGTAGCAGCAAAGTTATTCTCAAATTTCCATTTTATAGCTGGAGATGTTATACCGTGACGTACATGATAGGACCCAATATGGATCAATCCCTTTTAGAAGTCAATCAGGAAGAGGGGAGCAGTTAAAACAGTTGCTTGGTTTACAAACATTAGAACAATTTTCTTATTCACACCATCTGATTATTGTATGTTATTTTTTCCCCAACGTTTAGACTACACAATGAGTTAAGAATGATAAAAATAAGCTCACCAATATACTATGTACATATTTACCAAAATCTGTGCATGCTTATACATATAAACACAGCTGATAATTTATTAGTTAGGCTCATTTGTAATTTTTGTCACTATAGACCAGTTTTTTATTTAAATTGAAGATTAGTATACATTTTAAATGATTAGTCAAAATAAAAAATCTAAAATGTGCTCTAAATACCTCTTAGGTCAG-AAAAAAAAAGTCAAAAGCTAGAGTATAGAGAAATTAAGAAACGCCCTAAATTTCTAATCTGACAAAAATTCATACAAGATTTAAATATTTTAATGGAAAATAGAACAGAACTAATTATTGAAGAAATTATAGAAAGGAAACAAAATAAACAGATTATATGGAGGATTTTTAGAAGATAAGTAAATAAATTAATATACTAGGAAAAAACAAGGGAAATATACTTGATAAATAAATACAGGTAAGAGTTCTTTTGAAATAATGATAAAATAGAAAATCTCTGTCAAAACTAAAAGGAAAGATGCATAAATATATAAATAAACGATAAAA-AATGTTGCATACATATATGACTTTTTCAGAATCAAAAAATTTAAATTTCTGtaataaaatttaaatgtttataaatttaaaaaactagaagaaagaatgttgactgttcacaatacaaataaatgacaactatttgaggtgatggatacgctaattatccttatttgatcactgggcattgtatacatgtatcaaaatatc actctgtatcccatgaatatgtacaattatttgtctcaaaaacaaacaaaaAaaagataatgggagaatgttgaaaactcagagagaagagcaactctcacagatagggatccagataacattagcagctgatttctcagcagaaaccttgaaggccagtaggcagtggattatatatttaaaataatgaagaaacctgtcaattgagaaatatatagctggaaaacttatccttcaaaaatgaaggagaaattaagacatttccggatttttttttaaaactg-aaaaaaatccatttatccctgaatttgacattcaggaagtgttaagtccttcaggttgaaataaatgaactctaggcaataactatataagtaaataagcaagctgtatgaatatacaaagctctctggtaaaggtaaatacataaacaaacataaaaacagtcctattgtaattttggtttgtaactctgctttttattttctacataatttaaaaggcaaatgcataaaatgtaattgtaaatctgttagctggtatacaatgaataaagatataatttgtcacatcaataacataaaaagagtagagctatatatatagcagtagaattttggtatgtgattgaacttaagttgaaataaattcaaattaaaatgttataactctaggatgttatatgtaattctcatagtaaccaaaaatgaaatatacatagaatataaacaaaaggaaatgagactagaaacaaaatgtgtcactacaaaaaaatcaactaaagataaaaaagaaataattgagaaaatgattggcaaaaaTCAGTAACTCTGACGTATTAAAACTTTCCATGCTACATAAATCTGAAAACTCTATTTCACATAAAACTGGAGCTGAAAGAAACAAATATTTACCTATAAAGTTAAAAGTTATATAGGGAACAAACACtaattttttttagaaaaaattataaaaaGAGTAAAAATAT GCCTTATACTACCGTAATTTCATGTTTTACAGCTCTGGGAAAATAGAAAATAAAATGTTCTGTTAGCATGAATCCCTCTGTGCCCCCAAAAAACCCTATGGATTGCATCATTATTACCTAAAAAGTCTATTCTCAAATGCAGCAGAGTGATATTTTTTACAAGGTAGATATTAATTTTAGATATGGAATAATATTGGTGATTTCAATTTTATAACACTGGGTTAAGATGAAAGAATGAGAAGATAAAGGTCCCTCAGCAATATAACTCACAAACATGTTCAGAAGCAGTAAGAAGTTACATTAATTATCTTTTGAAAGTCGATAATCTACATCTTTAATGTATGCATATAGCATAGCTAATGTACTATCCCTGGGtccatttattcaatgaataattgccgctatgtgtcagacatttttctaggcctaggaatggatacataagtgaacaaagcaaagattctggttcttgtagagtttccattaaaagacaatTTAGTAAAACTTTTCTTCCCCCAAATTATAAAATCTGTAAGATGATTTAACAACATGTGTAAAAGTCATTGTGGGCCAGGCACGGTGGCTCATACCAGGTGTGGTGACTCATAGcactctgtcacccaggatggagtgcagtggcacaatctctgctcactgcaacctctgcctcctgggtacaagcgattctcctgcctcagctttctgagtagcaaggactacaggtgcacaccatcacgcctggctaatttttgtactattagtacagacggagtttcaccatgttggccaggctggtctcgaactcctgacctcaaatgatccatctacctcggcctcccaaagtgctggaattacagatgtgagccacaatgcccggccTTATTTTCTACAACTTTGGTAACTTTAGCATATACCCCAAATCTGTAAGACATAATATTATAATTCAAATGCAACTCATGGCTTCTCTTTGTACTCTTTCTCTAGCTTTT GAATTATTTATTCTAATACCAGTTTTAATTCTGACACAAAATCATGGGAGTTCTAATCAAAATCCAACCTTTTATCATAAAAACTATGAAGAAATTATGAGTAGAATTTAAAAAGGAAAATAGGCCTATTAATTAGATTTGTCTTTGTAGCATTTAACTCTATAATAA-----ATAATATTTTATGCCTATGAGTCCCCAACAAAGCCTCCAGCTTCTATTTAGATATAAACTGTAAAAGTCACTACTGGATCCACAAGCAAGACTATGGTAAATAAATTTCTCCACCTAACCAGCTTCTTTTACATGATGTTACATGTTTCTTTTGTTTTttcattttggcaaatattgattgtcatcttcgtgtttgtctatgtcctaagtgctgggatacagaatctgaaaagatggacacaggacctgccttcaagttcaccc +s panTro2.chr1 262360 4344 + 229974691 AATTGCACTTttatattttaacaaattgtatttcccatattgaactgtaagtctcctgaaaggaggaattttgttcttgctcatcatcaactttttcaacatccagtgcaccatttagaacttagatgtagtcaatacaggtttgtggaatgaaagaGGAAAAGAAAGAATTAATATTCCTTTAAATTAGGATG-CAAAGATCGTATATAGAAAATTGGCTAAGTTGTGGTCCATTCATATTTGCTCCCAATTAAGGAGCACAGCTATGAAAAGGAAGGCTTCAAATTAATAACCAATAGATTTTTTAAAAAAGAAAACTggccaggtactgtggcttatgtctgtaatatcagcatgttgggaggccaaggcaggattacttgagcccagaaattccagaccagcctgagaatttggcaaaactctgtctctacaaaaaatacaaaaattagccaagtttggtggcatgtgcatgtagtaccagctacttgggaggctgaggtggaagaatagcttgaatctgggaggtcaaggctgcaatgagctgtgatcgcaccactgcactcaagcctgggtggtagagtaagaccctgtctcaaaaaaaaaaaaaaa----gaaaaaTCACTAAGCAAAATAAGACATGTGAAGGATCATGTCAAAGGTAAGAAAAATTAGGGAAACATTAAAAGCTTTCTTCCCAAGCCACTAAATCAACTTGACTAACAAAATTACCACTTGATTTAGCATTAGAAAATTACATTACATATCAAACATAAACCCATTAATCAAATACTAAAGAAATTTCTGAGTTAAATGGTATAATGTTAGCTTATGCCAGAGCTGACCTTGAAAGATTGTTCAAATATGGCTCAGTGTGATTGAAACTTCTGTGTGAATATGTTTTTGGAAAGATAAAACAGCAACACCTTAGTGTATGTTTTTGAAATA AAATGTATCTGAGTAGCAGCAAAGTTATTCTCAAATTTCCATTTTATAGCTGGAGATGTTATACCGTGACATATATGATAGGACCCAATATGGATTAATCCCTTTTAGAAGTCAATCAGGAAGAGGGGAGCAGTTAAAACAGTTGCTTGGTTTACAAACATTAGAACAATTTTCTTATTCACACCATCTGATTATTGTATTTTATTTTTTCCCCAACGTTTAGACTACACAATGAGTTAAGAATGATAAAAATAAGCTCACCAATATACTATGTGCATATTTACCAAAATCTGTGCATGCTTATACATATAAACACAGCTGATAATTTATTAGTTAGGCTCATTTGTAATTTTTGTCACTATAGACCAGTTTTTTATTTAAATTGAAGATTAGTATACATTTTAAATGATTAGTCAAAATAAAAAATCTAAAATGTGCTCTAAATACCTCTTAGGTCAGAAAAAAAAAAGTCAAAA-CTAGAATATAGAGAAATTAAGAAATGCCCTAAATTTCTAATCTGACAAAAATTCATACGAGATTGAAATATTTTAATGGAAAATAGAACAGAACTAATCATTGaagaaattatagaaaggaaacaaaataaacagattatatggaggatttttagaagataagtaaataaattaatatactaggaaaaaacaagggaaatataattgataaataaatacaggtaagagttcttttgaaataatgataaaatagaaaatctctgtcaaaacttaaaggaaagatgcataaatatataaatAAATGATAAAACGATGTTGCATACATATATGACTTTTTCAGAATCaaaaaatttaaatttctgtaataaaatttaaatgtttataaatttaaaaaactagaagaaagaatgttgactgttcacaatacaaataaatgacaaatatttgaggtgatggatatgctaattatccttatttgatcattggacattgtatacatgtatcaaaatatc actctgtatcccatgaatatgtacaattatttgtctcaaaaacaaaCaaacaaaagataatgggagaatgttgaaaactcagagagaagagcaactctcacagatagggatccaggtaacattagcagctgatttctcggcagaaaccttgaaggccagtaggcagtggattatatatttaaaataatgaagaaacctgtcaattgagaaatctatagctggaaaacttatccttcaaaaatgagagagaaattaagacatttccggattttttttttaaactgaaaaaaaatccatttatccctgaatttgccattcaagaagtgttaagtccttcaggttgaaataaatgaactctaggcaataactatataagtaaataagcaagctgtatgaatatacaaagctctctggtaaaggtaaatacataaacaaacataaaaacagtcctattgtaattttggtttgtaactctgctttttattttctacataatttaaaaggcaaatgcataaaatgtaattgtaaatctgttagctggtatacaatgaataaagatataatttgttacatcaataacataaaaagagtagagctatatgtatagcagtagaattttggtatgtgattgaacttaagttgaaataaattcaaattaaaatgttataactctaggatgttatatgtaattctcatagtaaccaaaaacaaaatatacatagaatataaacaaaaggaaatgagactagaaacaaaatgtgtcactacaaaaaaatcaactaaagataaaaaagaaataattgagaaaa----tgGCAAAAATCAGTAACTCTGACGTATTAAAACTTTCCATGCTACATAAATCTGAAAACTCTATTTCACATAAAACTGGAGCTGAAAGAGACAAATATTTACCTATAAAGTTAAAAGTTATATAGGGAACAAACACTAATTTTTTTTAGACAAAATTCTAAGAAGAGTAAAAATAT GCCTTATACTACCCCAATTTCATGTTTTACAGCTCTGGGAAAATAGAAAATAAAATGTTCTATTAGCATGAATCCCTCTGTGCCCCCAAAAAACCCTATGGATTGCATCATTATTACCTAAAAAGTCTATTGTCAAATGCAGCAGAGTGATATTTTTTACAAGGTAGATATTAATTTTAGATATGGAATAATATTGGTGATTTCCATTTTATAACACTGGGTTAAGATGAAAGAATGAGAAGATAAAGGTCCCTCAGCAATATAACTCACAAACATGTTCAGAAGCAGTAAGAAGTTACATTAATTATCTTTTGAAAGTCAATAATCTACATCTTTAATGTATGCATATAGCATAGCTAATGTACTATCGCTGGGtccatttattcaatgaataattgccgctatgtgtcagacatttttctaggcctaggaatggatacataagtgaacaaagcaaagattctggttcttgtagagtttccattAAAAGACCATTTAGTGAAACTTTTCTTCCCCCAAATTATAAAATCTGTAAGATGATTTAACAACATGTGTAAAAGTCATTGTGGGCCAGGCATGGTGGCTCATACCAGGTGTGGTGACTCATAGcactctgtcacccaggctggagtgcagtggcacaatctcggctcactgcaacctctgcctcctggatacaagcgatgctcctgccccagctttctgagtagcaaggactacaggtgcacaccaccacgcctggctaatttttgtactattagtacagacggagtttcaccatgttggccaggctggtctcgaactcctgacctcaaatgatccgtctacctcggcctcccgaagtgctggaattacagatgtgagccacaatgcccggccTTATTTTCTACAACTTTGGTAACTTTAGCATATACCCCAAATCTGTAAGACATAATATTATAATTCAAATGCAACTCATGGCTTCTCATTGTACTCTTTCTCTAGCTTTT GAATTATTTATTCTAATACCAGTTTTAATTCTGACACAAAAGCATGGGAGTTCTAATCAAAATCCAACCTTTTATCATAAAAACTATGAAGAAATTATGAGTAGAACTTAAAAAGGAAAATAGGCCTATTAATTACATTTGTCTTTGTAGCATTTAACTCTATAATAAATAACATAATATTTTATGCCTATGAGTACCCAACAAAGCCTCCAGCTTCTATTTAGATATAAAATGTAAAAGTCACTACTGGATCCACAAGCAAGACTATGGTAGAGAAATTTCTCCACCTAACCAGCTTCTTTTACATGATGTTACATGTTTCTTTTGTTTTTTCATTTTGGCAACtattgattgtcatcttcgtgtttgtctatgtcctaagtgctgggatacagaatctgaaaagatggacacaggacctgccttcaagttcacCC + +a score=572998 +s hg18.chr1 118459 6270 + 247249719 tttttttttttttttgagatgcagttttgctcttgtcacccaggctggagtgtactggtgagatctctgctcactgcaacctccaccttcagggttcaagtgattctcctgcctcagcctcccaagtagctgtgattacaggtcccagccaccacgcctagctaatttttgtatttttagtagagacagcgtttcatcatgctggtcaggctggtctcgaactcctaacctcaggtagtcgacccacctcggcctcccacagtgctgagattacaggcatgagccaccacgccctgctaggagttcacgctttagttggggaaaatatacaataagcaagccagtttttaaaatgagaactgcaattagagttaaatgctacaaagacaaaCTCACAGGAAGATGGGATGTAGAATGATAAGGCTCTCAGAATAGTAAGAGAAACTATTGCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTTTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTCGAACTTGTCCTGCAGCTGTGAAACCAATGTGCAGTTGTGACACCAAAGCAGTGTGGCTGAACACCTAAAAGAATACGCTTTTTTTCTGATTATCAAACAAACCCAAATCATCACAGTAGACCACGATCTTAATAACAATCTCAAAAACTCAGGAGTAAACACTCAGATATGGAAtttttcttttctttcttttttccttttataagatggagtctcactctgttgcccaggctggagtgcactggtgcgatctcagctcactgcaacctccatctcccagttcaagtgattctcctgcctcagcctcttgagtagctgggactataggcatgcaccac cactacaggcgtgtgccaccacacctggctaatttttgtatttttagtagagatggggttttgccatgatggccaggctggtctcgaactcctgacctcaggtgatcctcccgctttggcctcccaaagACtttttttttttttttaatatagagacaagttctcagtacgttgcccaggctggtctcaaactcctgagctcaagtgatcctcccacctcagcttcccaaagtgctgggactGActggatgcagtggctcatgcttgtaaactcagcactttgggaggccaaggtgggaggatcgcttgagcccaggagttcaagaccagactgggtgatataacACAATAGTCAACTTCaacaggagagagaatctgtaaacttgaatatagatcttccgaaattatccagtcagtggacagagaaaaaaagaataaaagagagaaaagaaggctgggtgtggtggctcaagcctgtaatcccaacactttgggaggccgaggcaggcagattaagaggtcaggagttcaagaccagcctgtccaacatgacaaagccccatctctactaaaaatacaaaaattagccgggtgtggtggcacacacctgtagtcccagctacttgggaggctgaggcaggagaatcgcttgaacccaggaagcggaggttggagtgcaatgtgagccgagaccacacattacactccagcctgggtgacagagcatgactctgtctcaaaaagaaaaaaa--------------aaagagacagagaaaagaaagccaacaagacaccattaagcaaaccattgtcaggttatgggagtttgagaaggaaagtagagaaaggagaataaagcttatttaaagaatggctgacaactgcctaaatcatgggaaagatttagacatctaaatccatgaagcttaaagattcctaaagaggttcaaaccaaatagatactcaccaagtcacaatataatca aatagtcaaaagttaaagaaactttgcaggtcaggacagaatcgaataatacattcaaagtgctgaaagaaaaaaactgccagcaactaatactatgtctgacaaagctgtccttcagaaaggaaaaagaaataatgtgtttcctcgacaaacaaagctgagggcattcaggaccactaggtctaccttaaaaaaatgcttaacggagtttttcaagtaaaaatgaaTGAAGTTgggagcggtggctcatgcctgtaatcccattttgggaggctgaggtgggtggatcacctgaggtcgggaggtcaagaccagcctggccaacatggcaaaaccccacctccagtaaaaatacaaaaaattagccaggtatgaaggccactgagatcgtgccactgcactccagcctgggtgacaagagtcaaactacatttcaaaaacaaaaaacaaaacaaACAAAAAAAACAAAACTTGAGGCCTGGCCTTCTGCTCCTCTCCAACCTCCCCTTCTCTGGGCCCAAGCCACCTTGGCTGAGGAGGGGGCGAGGAGGTGTGAGCCCCTGCCAGGAACCCCCTGCCCGGACCAAGTGCTCGGCCCCCAGGCCTGCGTTCAGTGAGGCCTCCCGTGGCGTCAGCATGTTCGTGTGGAGGAATGTGGAAGGTCACTCTGCGGCCGTGTTCTCCTGGTACTCCATCCCCTTCCTGACCCCTCCCTGCAGCCACACGAGGCCCAGCAACCTGCCAGTCACTCAGTGGCCTCCAACCAGAGAAAACAACCTGCCAAGTTGGCAGCTGTTGCTCATGAGCGTCCACCAGGTGGGACAGGGAGTGTTGACCCTGGGCGGCCCCCTGGAGCCACCTGCCCTGAAAGCCCAGGGCCCGCAACCCCACACACTTTGGGGTTGGTGGAACCTGGTAAAAGCTCACCTCCCACCATGGAGGAGGAGCCCTGGGCCCCTCAGGGGAGTCCCTGCTGGACAGTGAGACAG AGAATGACCATGATGATGCTTTCCTCTCCATCATGTCTCCTGACACCCAGTTGCCTCTACCACTCAGATGATGTCAGGCCCAGTCCCTCAGTGCCCTGCGCAAGGAACAGGACTCATCTTCTGAGAAGGATGGACGCAGCCCCAACAAATCAGACAAGGACCACATCCGGTGGCCCATGAGTGGCGCTCATGATCTTCAGCAGGCGGCACCAGGCCCTGGCGGGGCGCACCAGGGTCACCCCAACCAGGATAACCGGACCGTCAGCCAGATGCTGAGCGAGCGGTGGTACACCCTGGGGCCCAATGAGATGCAGAAATAC---AACCTGGCCTTCCAGGTGAAGGTGGCCCACTTGCAACAAGGACCGAAAGAAGTCCAGCTCAGAGGCCAAGCCCACAAGCCAGGGGCTAGCAGGAGTGTAACAAGGGCTCGTGGGAGCGGAGCATATCAGAGACGGGCACTGCCACTGCCCCTGGGGTGTCCTCTGAACTCCTGTCAGTTGCAGCCCAAACACTCCAGAGCTCGGATACCAAGGAGCAGCTTCTGTGGGGCAGAACGGCTGCACACAGTCAGGGAACCTGGCTCAGCCTGGCCCAAGCCTTCTCCCACAGCGGGGTACACAGCCTGGACGGCAGGGAAATAGACCGTCAGGCACTACGGGAACTGACACAGGTGGTGTCTGGCACTGCATCATACTCTGGCCCAAAGCCTTCTACTCAGCATGGAGCTCCAGGCCACTTTGCAGCCCCTGGTGAGGGAGGTGACCCGTGGGCAGCCCTGCTGCCGCCCACGTGAGCTGCTCATTCCCAGCACATGGCCAGCGAGGTCATAGCGAGTGACGAAGAGCACACGGTCATCCATGAGGAGGAGGGGGTGATGATGTCATTGCTGATGATGGCTTTAGCACCACCGACACCGATCTCAAGTTCAAGGAGTGGGTGACCGACTGAGAGTGGGGACAACTCTGGGGAGGAGCCAGAGGGCAACA AGGGCTTTGGTGGGAAGGTATTTGCACCTGTCATTCCTTCCTCCTTTACTCCTGCCGCCCCTTGCTGGATCCTGAGCCCCCAGGGTCCCCCGATCCACCTGCAGCTTTTGGCA--GTCTATGGTCACACCCTGTCCTCCTCCTACACATACTCGGATGCTTCCTCCTCAACCTTGGCACCCACCTCCTTCTTACTGGGCCCAGGAGCCTTCAAAGCCCAGGAGTCTGGTCAACGCAGCAGAGCGGGCCCCCTACGGCCCCAACCCCTGGGGATGGGGGCCCAGGGACGCCTTCCAAGGTGGCCTGTTTCCTCCCAATGGATCCTGCCACCTTCTG-------GTGCAAGAGACCTGAAAGTGTGGGCGACCTGGAGCTACCAGGCTCCTCAGTCATCAGGGTCCCTCCCAACACTAAGGCTTTCCTAGGCAGGAGCTGGGCTGAGCCACCCGGGGGGCAGAGCCTGAAGAGAAACTGACTGGGCTTTCGGGGTCGGGGCAGAGGGAACCCCACGGACATGGACCCCACACTGGAGGACCCCACCGCGCCCAAATGCAAGATGAGAAGATGCTCCAGCTGCAGTCCAAAGCCCAACACCCCCAAGTGTGCCATGTGTGATGGGGACAGCTTCCCCTTTGCCTGTACAGGTGGAGAAGCCGAGGACAGGCTCAGGGAACCGGAGACCAAGAAGGCGCTGTCCTCTTCACTGCATGTACCCTGGACCAGTGCCGGCCCTGATCATGCAGCTCTTCCAGGCCCACTGCTTCTTCCTGTCCACTAGGCCACAGCCGCCCTCCAGGCCCACTATGCACACATCTTCCCCTCCAAGGTTTGTTCTGCCCCTGCCCTGACTCCCAGCCCTGTGGGGGTCCTGACCGCACCTCACCTGGCTCAGACTCTTGACGCTGCCCTGGCTGCCCCACCAGTGCTTCTGCCCGAGAGTCACGTGAGGCTGAGAGTAGGGGCAGGGGCAGCAGTGGTGCCAGTTG GGGGGCGGTCCAGTGGGAGGAGCCTCAGCCTCGCAGGCTGCTCCGTGGGACTGATGACTGCATGATCTTCTGGGCACCTCACGGATCTTCAACTGCAGGTGAAACGGATGCTGGTGGTGGGTGCAGGGCCGCTGGGAGCTGCTGCATGGTTCCCAGAGGCTGGACTGAGGCAGGTGCCAACTGAAGCTGCTGGGGCAGCATGGGCAGGATGTTCTGCACACAAACCTTGGAGAAGAAGATGTGTGCATAGCAGGTCCACTGCTGCTGCCCCTGCCCTGACTCCCAGCCCTGCCTGACCCCACCTCAACCTGCTCAGGCTCTGGCACAACCCTGGCTGCCCTGCCACTGCCTCTGCCCCAGAGTTGGTGCCTTGACAGCCTGGTTGGAAGGGGACACCCCAGCCCTGCCTCAACACCTGGGGGTCTCCATAACTAGCACAGGCAGGTGGGCAACCCCAAAGATCCCAGGACTCACAGTACCCCCTGAGAACATGGACAGTATGTGGGGGTAGCAATGGAGGGCAGGATGGTTATCTTCTCCCAGGTGAAGCCATTTAATCCTTTCAGTTTGGGACGGAGTAAGGCC--------TTCCtttttttttttttttttttttttttttttgagaccgagtcttgctctgtcgcccaggctggagtgcagtggtgcgatcttggctcactgcaacctcttcccgctgggttcacgccattctcctgcctcagccttccgggtagctaggattacaggtggacgctaccacgtccggctaatttttgtatttttagtacagacggggcttcatcatcttggccaggctgatttcgatctcctgacatcgtgatctgcctgcctccccctcccaaagtgctgggattacaggcgtgagccaccacgcctggccAAGGCCTGCTCCTCTTATCTATACCCCCTACCCCTGCAGCTGTGCC-GGGGGAAAGCTGGGCAGTTTCCCTCCTCCGAGCCCC TGTACATACCATGAATTGTGGGACCTTCAGAGCTTTTCACTTTTCGGAAAATAGCTCCTGCTGGGGCTACAAGATGGAGTGTGAAGAGGGCCTTGGGCCACAGGGAGGCGCCTGTGGACTAGGGGGAGTTCATGCACCCCTTCTTTCCCCAGAGGGGCTGGACTCAGGTGAGTATGGGGGTGGGGGCTCCTGCACTTCGACACAGGCAGCAGGAGGGTTTTCTCCCCATTCCCTCTGCACTCCCAACTTGAGCTATACTTTTTAAGAAAGTGATTCACCCTGCCTTTGCCCCCTTCCCCAGAACAGAACACGTTGATCGTGGGCGATATTTTTCATTGTGCCAAAAAGTTGCCATGACCGTCATTAAACCTGTTTAACACCAAATAATAAGGAAAATAAAATAAAAAATT +s panTro2.chr1 267601 6301 + 229974691 tttttttttttttttgagatggagttttgctcttgtcgcccaggctggagtgtaatggtgagatctcggctcactgcaacctccacctccagggttcaagtgattctcctgcctcagcctcccaagtagctgggattacaggtcccagccaccacgcctagctaatttttgtatttttagtagagacagcgtttcatcatgttggtcaggctggtctcgaactcctgacctcaggtagtcgacccacctcggccttccacagtgctgagattacaggcatgagccaccacgccctgctAGGAGTTCATGCTTTAGTTCGGGAAAATATACAATAAGCAAGCCAGTTTTTAAAATGAGAACTGCAATTACAGTTAAATGCTACAAAGACAAACTCACAGGAAGATGGGATGTAGAATGATAAGGCTCTCAGAATAGTAAGAGAAACTATTGCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTCGAACTTGTCCTGCAGCTGTGAAACCAATGTGCAGTTGTGACACCAAAGCAGTGTGGCTGAACACCCAAAAGAATATGCTTTTTT-CTGATTATCAAACAAACCCAAATCATCACAGTAGAGCACGATCTTAATAACAATCTCAAAAACTCAGGAGTTAACACTCACATATGGAAttttttttttctttctcttttccttttataagatggagtctcactctgttgcccaggctggagtgcactggtgcgatctcagctcactgcaacctccatctcccagttcaagtgattctcctgcctcagcctcttgagtagctgggactacaggcatgcaccac cactacaggcgtgtgccaccacacctggctaatttttgtatttttagtagagatgaggttttgccatgttggccaggctggtctcgaactcctgacctcaggtgatcctcctgctttggcctcccaaagACttttttttttttt--aatatagagacaagttctcagtatgttgcccaggctggtctcaaactcctgagctcaagtgatcctcccacctcagcttcccaaagtgctgggactGActggatgcagtggctcatgcttgtaaactcagcactttgggaggccaaggtgggagggtcgcttgagcccaggagttcaagaccagactgggtgatataacAcaatagtaaacttcaacaggagagagaatctgtaaacttgaatatagatcttctgaaattatccagtcagaggacaaagaaaaaaagaataaaaaagagaaaagaaggctgggcgtggtggctcaagcctgtaatcccaacactttgggaggctgaggcaggcagattaagaggtcaggagttcaagaccagcctggccaacatgacaaaaccccatctctactaaaaatacaaaaattagccgggtgtggtggcacacacctgtagtcccagctacttgggaggctgaggcaggagaatcgctttaacccaggaggcggaggttggagtgcaatgtgagccgagaccacacattgcactccagcctgggtgacagagcatgagtctgtctcaaaaaaaaaaaaagaaagaaagaaaaaaaagagacagagaaaagaaagccaacaagacaccattaggcaaaccattgtcaggttatgggagtttgagaaggaaagtagagaaaggagaagaaagcttatttaaggaatggctgaaaactgcctaaatcatgggaaagatttagacatctaaatccatgaagcttaaagattcctaaagaggttcaaaccaaatagatattcaccaagtcacaatataatca aatattcaaaagttaaagaaactttgcaggtcaggacagaatcgaataatacattcaaagtgctgaaagaaaaaaactgccagcaactaatattatgtctgacaaagctgtccttcagaaagaaaaaagaaataacgtgtttcctcgacaaacaaagctgagggcattcaggactactaggtctaccttaaaaaaatgcttaacggagtttttcaagtaaaaatgaaTGATGTTgggagcggtggctcatgcctgtaatcccattttgggaggctgaggtgggtggatcacctgaggtcgggaggtcaagaccagcctggccaacatggcaaaaccccacctccagtaaaaatacaaaaaattagccaggtatgaaggccactgacatcgtgccactgcactccagcctgggtgacaagagtcaaactacatttcaaaaacaaaaaataaaacaaaccaaaaaaacaaaacttgagGCCTGGTCTTCTGCTCCTCTCCAACCCCCCCTTCTCTGGGCCCAAGCCACCTTGGCTGAGGAGGGGGCGAGGAGGTGTGAGCCCCTGCCAGGAACCCCCTGCCCGGACCAAGTACTCGGCCCCCAGGCCTGCATTCAGTGAGGCCTCCCGTGGCATCAGCATGTTCGTGTGGAGGAATGTGGAAGGTCACTCTGCGGCCGTGTTCCCCTGGTACTCCATCCCCTTCCTCACCCCTCCCTGCAGCCACACGAGGCC-AGCAACCTGCCAGTCACTCAGTGGCCTCCAACCAGAGAAAGCAACCTGCCAAGTTGGCAGCTGTTGCTCATGAGCATCCACCAGGTGGGACAGGGAGTGTTGACCCTGGGCGGCCCCCTGGAGCCACCTGCCTTGAAAGCCCAGGGCCCGCAACCCCACACACTTTGGGGGTGGTGGAACCTGGTAAAAGCTCACCTCCCACCATGGAGGAGGAGCCCTGAGCCCCTCAGGGGAGTCCCTGCTGGACAGTGAGACAG AGAATGACCATGATGATGCTTTCCTCTCCATCATATCTCCTGACACCCAGTTGCCTCTACCACTCAGATGATGTCAGGCCCAGTCCCTCAGTGCCCTGCGCAAGGAACAGGACTCATCTTCTGAGAAGGATGGATGCAGCCCCAACAAATGGGACAAGGACCACATCCGGTGGCCCATGAGTGGCGGTCATGATCTTCAGCAAGCGGCACCAGGCCCTGGCGGGGCGCACCAGGGTCACCCCAACCAGGATAACTGGACCATCAGCCAGATGCTGAGTGAGCGGTGGTACACCCTGGGGCCCAATGAGATGCAGAAATACCACGACCTGGCCTTCCAGGTGAAGGTGGCCCACTTGCAACAAGGACCGAAAGAAGTCCAGCTCAGAGGCCAAGCCCACAAGCCAGGGGCTAGCACGAGTGTAACAAGGGCTCATGGGAGCAGAGCATATCAGAGACGGGCACTGCCACTGCCCCTAGGGTGTCCTCTGAACTCCTGTCAGTTGCAGCCCAAACACTCCAGAGCTCGGATACCAAGGAGCAGCTTCTGTGGGGCAGAACGGCTGCACACAGTCAGGGAACCTGGCTCAGCCTGGCCCAAGCCTTCTCCCACAGCGGGGTACACAGCCTGGATGGCATGGAAATAGACCATCAGGCACTACGGGAACTGACACAGGTGGTGTCTGGCACTGCATCATACTCTGGCCCAAAGCCTTCTACTCAGTATGGAGCTCCAGGCCACTTTGCAGCCCCTGGTGAGGGAGGTGATCAGTGGGCAGCCCTGCTGCTGCCCACCTGAGCTGCTCATTCCCAGCACATGGCCAGTGAGGACATAGCGAGTGACCAGGAGCACACGGTCATCCATGAGGAGGAGGGGGTGATGATGTCATTGCTGATGATGGCTTTAGCACCACTGACACCGATCTCAAGTTCAAGGAGTGGGTGACCGACTGAGAGTGGGAACAACTCTGCGGAGGAGCCAGAGGGCAACA AGGGCTTTGGTGGGAAGGTATTTGCACCTGTCATTCCTTCCTCCTTTACTCCTGCCACCCCTTGCTGGATCCTGAGTCCCCAGGGTCCCCCGATCCACCTGCAGCTTTTGGCAAAGTCTATGGTCCCACTCTGTCCTCCTCCTACACATACTCGGATGCTTCCTCCTCAACCTTGGCACCCACCTCCTTCTTACTGGGCCCAGGAGCCTTCAAAGCCCAGGAGTCTGGTCAAGGCAGCAGAGCGGGCCCCCTACGGCCCCTACCCCTGGGGATGGGGGCCCAGGGACGCCTTCCAAGGTGACCTGTTTCCTCCCAATGGATCCTGCCACCTTCTGAAAGAAGGTGCAAGAGACCTGAAAGTGTGGGCGACCTGGAGCTACCAGGCTCCTCAGTCATCAGGGTCCCTCCCAACACTAAGGCTTTCCTAGGCAGGAGCTGAGCTGAGCCACCCGGGGGGCAGAGCCTGAAGAGAAACTGACTGGGCTTTCGGGGTCGGGGCAGAGGGAACCCCACGGGCATGGATCCCACACTGAAGGACCCCACCATGCCCAAATGCAAGATGAGAAGATGCTCCAGCTGCAGTCCAAAGCCCGACACCCCCAACTGTGCCATGTGTGATGGGGACAGCTTCCCCTTTGCCTGTACAGGTGGAGAAGCCGAGGACAGGCTCAGGGAACCGGAGACCGAGAAGGCGCTGTACTCTTCACTGCACGTGCCCTGGACCAGTGCCAGCCCTGATCAAGCAGCTCTTCCAGGCCCACTTCTTCTTCCTGTCCACTAGGCCACAGCCGCCCTCCAGGCCCACTATGCACACATCTTCCCCTCCAAGGTTTGTTGTGCCCCTGCCCTGACTCCCAGCCCTGTGGGGGTCCTGACCGCACCTCACCTGGCTCAGACTCTTGACGCTGCCCTGGCTGCCCCACCACTGCCTCTGCCCGAGAGTCACGTGAGGCTGAGAGTAGGGGCAGGGGCAGCAGTAGTGCCAGTTG GGGGGCGGTCCAGTGGGAGGAGCCTCAGCCTCGTGGGCTGCTCCGTGGGACTGATGACTGCATGATCTTCTGGGCACCTGACGGATCTTCAACTGCAGGTGAAACGGATGCTGGTGGTGGGTGCAGGGCCGCTGGGAGCTGCTGCATGGTTCCCAGAGGCTGGACTGGGGCAGGTGCCAACTGAAGCTGCTGGGGCAGCATGGGCAGGATGTTCTGCACACAAACCTTGGAGAAGAAGATGTGTGCATAGCGGGTCCACTGCTGCTGCCCCTGCCCTGACTCCAAGCCCTGCCTGACCCCACCTCAACCTGCTCAGGCTCTGGCGCAACCCTGGCTGCCCTGCCACTGCCTCTGCCCCAGAGTTGGGGCCTTGACAGCCTGGTTGGAAGGGGACACCCCAGCCCTGCCTCAACACCTGGGGGTCTCCATAACTACCACAGGCAGGTGGGCAACCCCAAAGATCCCAGGACTCACAGTACCCCCTGAGAACATGGACAGTATGTGGGGGTAGCAATGGAGGGCAGGATGGTTATCTTCTCCCAGGTAAAGCCATTTAATCCTTTCAGTTTGGGATGGAGTAAGGCCTGCTTCtttttttttttttttttttttttttttttttttttgagaccgagtcttgctctgtcgcccaggctggagtgcagtggtgcgatcttggctcactgcaacctcttcccgccgggttcacgccattctcctgcctcagccttccgagtagctaggattacaggtgcacgctaccacgtccggctaatttttgtatttttagtacagacggggcttcatcatcttggccaggctgatttcgatctcctgacatcgtgatctgcctgcctccccctcccaaagtgctgggattacaggtgtgagccaccacgcctggccAAGGCCTGCTCCTCTTATCTATACCCCCTACCCCTGCAGCTGTGCCGGGGGGAAAGCTGGGCAGTTTCCCTCCTCCAAGCCCC TGTACATACCATGAATTGTGGGACCTTCAGAGCTTTTCACTTTTCGGAAAATAGCTCCTGCTGGGGCTACAAGATGGAGTGTGAAGAGGGCCTTGGGCCACAGGGAGGCGCCTGTGGACTAGGGGGAGTTCATGCACCCCTTCTTTCCCCAGAGGGGCTGGACTCAGGTGAGTATGGGGGTGGGGGCTCCTGCACTTCGACACAGGCAGTGGGAGGGTTTTCTCCCCATTCCCTCTGCACTCCCAACTTGAGCTATACTTTTTAAGAAAGTGATTCACCCTGCCTTTGCCCCCTTCCCCAGAACAGAACACGTTGATCATGGGCGATATTTTTCATTGTGCCAAAAATTTGCCATGACCGTCATTAAACCTGTTTAACACCAAATAATAAGGAAAATAAAATAAAAAATT + +a score=55912 +s hg18.chr1 124729 624 + 247249719 CGGGCTTGGCGCAGAAACTCACTCCAAATAAATTACCTACCAAAACATTTACATAATGGTGGAAATATTCCAAAATTCAATATTTTGGGATTTATACACAAAAGATAAACAAATTAGAGGCCAAGAGGCTGCCGGAAGGGAAAAACAGGGCCTGGAATGGCCGACGTGAGGAATGAGCTGGGCCTAAAGAGGCCACTGGCAGGCAGGAGCTGGACCTGCCGAAGTGGCCGAAAGGCAGGAGCTTTGGACTGGGGAGGCCGCAGTGAGGCGAGAGCTAGCTGGGCGTGGAGAGTCCGCTGTGAGGCCGAGGCCGAGGCTGGGCCCGTGCAGGCCTTCGAGACGCAGGAGGCCGGGCCTGCAAAGGCCGACTGGAGATCAAGTTCTGCGCCTGAAGAGGCTGCCAAAAGTCAAAAGCGGGGCCTGGGAAGGCCGCCGAGAGCCATGAGCTGGGCTGGGCCGAAAGAGGCCACTGGGAGGCAGGAGGAGCTGGGCCTGGAGAGGCTGACTCGAGGAAGTTTTGCACCTGGAGAGGCCGTCGAGAGGACGGAGCTGGGCCCAGGGAGGCCGACTTGCTGCTCTTCCAGGCCCACTTCCAGGCCGACTTGAGGACGACTTGGGCCTGCA +s panTro2.chr1_random 7175462 620 + 9420409 CGGGCATGGTGCAGAAACTCACTCCAAATAAATTACCTACCAAAA----TATATAATGGTGGAAATATTCCAAAATTCAATATTTTGGGATTTATACACAAAAGATAAACAAATTAGAGGTCAAGAGGCTGCCAGAAGGGGAAAACGGGGCCTGGAAAGGCCGTTGTGAGGAATGAGCTGGGCCTAAAGAGGCCACTGGCAGGCAGTAGCTGGACCTGCCGAAGTGGCCGAAAGGCAGGAGCTTTGGACTGGGGAGGCCGCAGTGAGGCGAGAGCTAGCTGGGCCTGGAGAGTCCACTGTGAGGCCGAGGCCGAGGCCGGGCCCGTGCAGGCCTTCGAGAGGCAGGAGGCCGGGCCTGCAAAGGCCGACTGGAGATCAAGTTCTGCGCCTGAAGAGGCTGCCAAAAGTCAAAAGAGGGGCCTGGGAAGGCCGCCAAGAGCCATGAGCTGGGCTGGGCCAAAAGAGGCCACTGGGAGGCAGGAGGAGCTGGGCCTGGAGAGGCTGACTCGAGGAAGTTTTGCACCTGGAGAGGCCGCCAAGAGGACGGAGCTGGGCCCGGGGAGGCCGACTTGCTGCTCTTCCAGGCCCACTTCCAGGCCGACTTGAGGACGACTTGGGCCTGCA + +a score=3198 +s hg18.chr1 125369 47 + 247249719 TGGAGCTAAGCCTGGAGAGACTGACTTCGGGACGATTTGGGCCTGCG +s panTro2.chr1 203149100 47 + 229974691 TGGAGCTGGGCCTCGAGAGGCCAACTTCAGGAGGATTTGGGCCTGCA + +a score=10475 +s hg18.chr1 125416 119 + 247249719 GAGGCCGCCGGGAGGCCCAAGCTGGGCCTAGAGGAGCCCACCGACCGGAGGCCATTTGGGGCCTGCAGATGTCATCGGAGGGCCAGGAGCTGAGCCTGGAGAGGCCACCGCGAGGCCTG +s panTro2.chr1_random 7176082 118 + 9420409 GAGGCCGCCGGGAGGCCCAAGCTGGGCCTAGAGGAGCCCACCTACCGGAGGCCGTTTGGGGCCTGCAGATGCCATCGGAGGG-CAGGAGCTGAGCCTGGAGAGGCCACCGTGAGGCCTG + +a score=7657 +s hg18.chr1 125535 79 + 247249719 AGCTGGGCCTGGGGAGCTTGGCTTAGGGAAGTTGTGGGCCTACCAGGGCCGCTGGGAGCTGGGCAGGAGCTGAGTCCAA +s panTro2.chr1 224035422 79 + 229974691 AGCTGGGCCTGGGGAGCTTGGCTTAGGGAAGTTGTGGGCCTACCAGGGCCGCTGGGAGCTGGGCAGGAGCTGAGTCCAA + +a score=51195 +s hg18.chr1 125614 592 + 247249719 AGACGTTGTTGGGACCTGGAGTCGGGCCAGAGTCCGGCCTGGAGATGCAGCCGGGAGGAAGAGCTGGGCCCGGAGGGGGCGCCGGGAGGCTGCAAGTGGGTCTGAGAGGCCAACTTGAGGAGGCCTGGCCTCTGCCTCCCGCATTGCCCAGCTGTTCCTCCTGGCTGCATCTCCCACCTCCCAGCAAACAAGCTCTTTTGGCTCAGCTCCCGCCTGCGTTTGTAGACCCCAAAGTTTCTGCAACCAAGCTCTTCAGACCCACATCCCTTCTCCCAGTGACTGAACAGTCCCAGCTCCGGCTGGAGAAGGGTGTCTGCAGA-CCCCGCTGTTGCCTCCCAGGGGAGTCTCCAGGCCCAGCTCTCGCCCCACCGCGACCTCCCAGGCCCAAGTCCCTGCCTACCTCCCAGCAGCCCGAGTGCGATCCTGTTCCTCCCTCACGGTGGCCTGTTGAGGCAGGGGGTCACGCTGACCTCTGTCCGCGTGGGAGGGGCCGGTGTGAGGCAAGGGCTCACACTGACCTCTCTCAGCGTGGGAGGGGCCGGTGTGAGGCAAGGGGCTCACGCTGACCTCTGTCCGCGTGGGAGGGGCCGGT +s panTro2.chr1_random 7176200 591 + 9420409 AGACGTTGTTGGGACCTGGAGTCAGCCCAGAGTCAGGCCTGGAGATGCAGCCGGGAGGAAGAGCTGGGCCCGGAGAGGACGCCGGGAGGCTGCAAGTGGGTCTGAGAGGCCAACTTGAGGAGGCCTGCCCTCCGCCTCCCGCATGGCCCAGCTGTTCCTCCTGGCTGCATCTCCCGCCTCCCAGCAAACAAGCTCTTTTGGCTCAGCTCCCGCCTGCGTTTGTAGACCCCGAAGTTTCTGCAACCAAGCTCTTCAGACCCACATCCCTTCTCCCAGTGACTGAACAGTCCCAGCTCCGGCGGGAGAAGGGCGTCTGCAGACCCCCACTGTTGCCTCCCAGGGGAGTCTCCAGGCCCAGCTCTCGCCCCATCGCGACCTCCCGGGCCCAAGTCCCTGCCTACCTCCCAGCAGCCCGCGTGCGACCCTGCCCCTCCCTCACGGTGGCCTGTTGAGGCAGGGGCTCAGGCTGACCTCTGTCAGCATGGGAGGGGCCGGTGTGAGGCAAGGGCTCCCGCGGAC--CTGTCAGCGTGGGAGGGGCCGGTGTGAGGCAAGGGGCTCACGCTGTCCTCTCTCAGCGTGGGAGGGGCCGGT + +a score=16633 +s hg18.chr1 126206 202 + 247249719 GTGAGGCAAGGGCTCACACTGACCTCTCTCAGCGTGGGAGGGGCCGGTGTGAGGCAAGGGGCTCACGCTGACCTCTGTCCGCGTGGGAGGGGCTGGTGTGAGGCAAGGGCTCAGGCTGACCTCTCTCAGCGTGGGAGGGGCCGGTGTGAGGCAAGGGGCTCACGCTGACCTCTGTCCGCGTGGGAGGGGCCGGTGTGAGACA +s panTro2.chr1 203152230 202 + 229974691 GTGAGGCAAGAGCTCACACTGAACTCTCTCTCCGTGGGAGGGGCCGGTGTGAGGCAAGAGGCTCACGCTGTCCTCTCTCGGCGTGGGAGGGGCCGGTGTGAAGCAAGGGCTCACACTGACCTCTCTCGGCGTGGGAGGGGCCGGTGTGAGGCAAGGGGCTCACGCTGACCTCTGTCAGTGTGGTAGGGGCCGGTGTGAGGCA + +a score=11076 +s hg18.chr1 126408 188 + 247249719 AGGGGCTCACACTGACCTCTCTCAGCGTGGGAGGGGCCGGTGTGAGGCAAGGGGCTCAGG-------------------------------------------------------------------------------------------------CTGACCTCTGTCCGCGTGGGAGGGGCCGGTGTGAGGCAAGGGGCTCAGGCTGACCTCTGT-----------------------------------------------CCGCGTGGGAGGGGCCGGTGTGAGGCAAGGGGCTCAGGCTGACCTCTGTCCGCGTGGGAGGGGCCGGG +s panTro2.chr1 203155717 332 + 229974691 AGGGGCTCACGCTGACCTCTCTCAGCGTGGGAGGGGCCGGTGTGAGGCAAGGGGCTCAGGCTGACCTCCCTCAGTGTGGGAGGGGCCGGTGTGAGTCAGGGCCTCAGGCTGACCTCTCTCAGTGTGGGAGGGGCCGGTGTGAGTCTATGGGCTCAGCCTGACCTCTGTCAGCCTGGGAGGGGCCGGTGTGAGGCTAGGGGCTCAGGCTAACCTCTGTCAGCCTGTGAGGGGCCTGTGTGAGGCAAGGGGCTCAGGCTGTCCTCTCAGCATGGGAGGGTCCGGTGTGAGGCAAGGGGCTCAGGCTGACCTCTCTCAGCGTGGGAGGGGCCGGT + +a score=5436 +s hg18.chr1 126596 60 + 247249719 GTGAGGCAAGGGCTCACACTGACCTCTCTCAGCGTGGGAGGGGCCGGTGTGAGGCAAGGG +s panTro2.chr1_random 7176791 60 + 9420409 GTGAGGCAAGGGCTCACACTGACCTCTCTCAGCGTGGGAGGAGCCAGTGTGAGGCAGGGG + +a score=18226 +s hg18.chr1 126656 239 + 247249719 GCTCGGGCTGACCTCTCTCAGCGTGGGAGGGGCCGGTGTGAGGCAAGGGGCTCGGGCTGACCTCTCTCAGCGTGGGAGGGGCCGGTGTGAGGCAAGGGGCTCGGGCTGACCTCTGTCCGCGTGGGAGGGGCCGGTGTGAGGCAAGGGGCTCGGGCTGACCTCTCTCAGCGTGGGAGGGGCCGGTGTGAGGCAAGGGGCTCACGCTGACCTCTGTCCGCGTGGGAGGGGCCGGTGTGAGG +s panTro2.chr1 203156110 239 + 229974691 GCTCAGGCTGACCTATGTCAGCATGGGAGGGGCCTGTGTGAGGCAAGGGGCTCAGGCTGAACTCTGTCAGCGTGGAAGGGGCCGATGTGAGGCAAGGGGCTCAGGCTGACCTCTGTCAGCGAGCGAGGGGCCTGTGTGAGTCTATGGGCTCCCGCTGACCTCTGTCAGCCTGGGAGGGGCCGGTGTGAGGCTAGGGGCTCAGGCTGACCTTTGTCAGCGTGGGAGGGGCCGGTGTGAGG + +a score=12466 +s hg18.chr1 126895 150 + 247249719 CAAGGGCTCACACTGACCTCTCTCAGCGTGGGAGGGGCCGGTGTGAGACAAGGGGCTCACGCTGACCTCTGTCCACGTGGGAGGGGCCGGTGTGAGGCAAGGGGCTCACACTGACCTCTCTCAGCGTGGGAGGGGCCGGTGTGAGGCAAG +s panTro2.chr1 203157314 149 + 229974691 CAAGGGCTCACACTGATCTCTCTCAGCGTGGGAGGGGCCGGTGTGAGGCAAGGGGCTCACGCTGATCTCTCTCGGAGTGGGAGGGGCCGGTGTGAGGCAAGGG-CTCACGCTGACCTCTCTCAGCGTGGGAGGGGCTAGTGTGAGGCAAG + +a score=2383 +s hg18.chr1 127045 28 + 247249719 GGGCTCACGCTGACCTCTGTCCGCGTGG +s panTro2.chr1 229694308 28 - 229974691 GGGCTTACGCTGACCTCTGTCAGCGTGG + +a score=78315 +s hg18.chr1 127073 855 + 247249719 GAGGGGCCGGTGTGAGGCAAGGGCTCACACTGACCTCTCTCAGCGTGGGAGGAGCCAGTGTGAGGCAGGGGCTCACGCCTCTGGGCAGGGTGCCAGAGGCATGAGTTGGGCATCAACAGGCCACCGTGAGGGAGGAGCTGGGCCGCACGCGGGCTGCTGGGAGGCAGGCAGGGACTTGGCCCCGGGAGGCCGCCGTGGGGGCAAGAGCTGGGCCTGGAGAGGCCCCTGGGAGGCAAGGGCGGGGCCTGCAGAGGCTGTTCTCCAACCAGTGCTAGAACTGTACAGGCCACCAGGAGGCAGGAGGTGGGCCCTCAGAGCTTGGCTGGAGAAAGTTCGGGGCCTACAAAGGCGGTTGGGAGCTGGGCAGGAGTTGAGCCAAAAGAGCTTGCTTACTTGCTGGGAGGCAGGGCCGGGAGAGCCCGACTTCAGGACAACTTGGGCCTGCGGCGGTCGCCGGGAGGCCCAACCTTGGCGTGGAGGAGCCCACCGACCGGAGACCATTTGGGGCCTGGAGATGCCATCGGAGGGCAGGAGCTCATCCTGGAGAGGCCACCGTGAGGCCTGACCTGGGCCTGGGGAGCTTGGCTTGAGGAAGCTGTGGACCGACCAAGGCCGCCAGGAGATGGGTAGGCACTGAGTCCAAAGAGGTTGTTGAGAGGCAGGAATCGGGCCTGGAGACCCAACCAGGAAGAAGAGCTGGGCCCGGAGAGAACGCCCGGAGGGTGCAAGTGGGTCTGGAGAGGCCGACTTGAGGAGGTTCTGGGCCCGGAGAGGCCGCTGGAAGGGAAAAACTGGGCCTGGAAAGGCCGTTGTCAGGAATGAGCCCCATGGGCCTGAAGAGGCCACTGGCAGGCG +s panTro2.chr1 274511 855 + 229974691 GAGGGGCCGGTGTGAGCTAAGAGCTCACACTGACCTCTCTCAGCGTGGGAGGATCCAGTGTGAGGCAGGGGCTCACGCCTCTGGGCAGGGTGCCTGAGGCATGAGTTGGGCATCAACAGGCCACCGTGAGGGAGGAGCTGGGCCACACGCGGGCTGCTGGGAGGCAGGCAGAGACTTGGCCCCGGGAGGCCGCCGTGGGGGCAAGAGCTGGGCCTGGAGAGGCCCCTGGGAGGCAAGGGTGGGGCCTGCAGAGGCTGTTCTCCAACCAGTGCTAGGCCTGTACAGGCCACCAGGAAGCAGGAAGTGGGCCCTCAGAGCTTGGCTGGAGAAAGTTCGGGGCCTACAAAGGCGGTTGGGAGGTGGGCAGGAGTTGAGCCAAAAGAGCTTGCTTACTTGCTGGGAGGCAGGGCCGGGAGAGGCCGACTTCAGGACAACTTGGGCCTGCGGCGGTCGCCGGGAGGCCCAAGCTTGGCGTGGAGGAGCCCACCGACCAGAGACCATTTGGGGCCTGGAGATGCCATCGGAGGACAGGAGCTCATCCTGGAGAGGCCACTGTGAGGCCTGACCTGGGCCTGGGGAGCTTGGCTTGAGGAAGCTGTGGGCCGACCAAGGCCGCCAGGAGATGGGTAGGCACTGAGTCCAAAGAGGTTGTTGAGAGGCAGGAGTCGGGCCTGGAGACGCAACCAGGAAGAAGAGCTGGGCCCAGAGAGGACGCCCGGAGGGGGCAAGTGGGTCTGGAGAGGCCGACTTGAGGAGGTTCTGGGCCCGGAGAGGACGCCGGAAGGGAAAAACTGGGCCTGGAAAGGCCGTTGTGAGGAATGAGCCCCATGGGCCTGAAGAGGCCACTGGCAGGTG + +a score=65540 +s hg18.chr1 127928 702 + 247249719 GGAGCTGGGCCTGCCGAAGCGGCCGAGAGGCAGGAGCTTTGGACTCGGGAGGCCGCAGTGAAGCAACAGCTAGCTGGGCGTGGAGAGTCCGCTGTGAGGCAGAGGCTGGGCCTGTGCAGGCCTTCGGGAGGCAGGAGGCTGGGCCTTGTCGAGGCCTGCAGAGGCCACCGAAAGTCAAAAGCGGGGCTTGGGAAGGCCGCCGGGAGGCATGAGCTGGGCTGGGCCGAAAGAGGCCACTGGGAGGCAGGAGGAGCTGGGCCTGGAGAGGCTGCCGAAAGGCAGGAGCTTCACCTGAGGATGCCACAGTGAGACACCATCTGGGTCTGGAGGGTCCACTGTGAGGCAGAGGCTGACCTGTAGAGTCCGACAGTAGACAGAAGTTGGGCAAAAGCCTGATTTGAGGAAGTTTTGGGCTTCAAGAGTCAGCCACGAGGCAGGCACTAGGCCTGGAAATGGCCTCACAGTCATAAGTTGGGCCTAAATGGGCCACTGTGAGGGAGGAGCTGTGCCTGTTGAGGCTGCTGGCAGGCAGGCAGAAATTTGGCCTGGGGCAGCTGCCATGAGGCAAGAGCTGGGCCTGGAAAAAGCCCCTGGGAGGCAAGAGCAGGGCCTGCAGAGGCTGTTCTCAAGTCAAAGCTGGGCCTGTTGATGCCACCGGGAAGCAGAAGGTGGGCCTGGAGAGTTTGACTTGAGGAAGTTTTG +s panTro2.chr1 224036698 702 + 229974691 GGAGCTGGGCCTGCCGAAGCGGCCGAGAGGCAGGAGCTTTGGACTTGGGAGGCCGCAGTGAGGCGACAGCTAGCTGGGCGTGGAGAGTCCGCTGTGAGGCAGAGGCTGGGCCTGTGCAGGCCTTCGGGAGGCAGGAGGCTGGGCCTTGTCGAGGCCTGCAGAGGCCACCGAAAGTCAAAAGCGGGGCTTGGGAAGGCCGCCGGGAGGCATGAGCTGGGCTGGGCCGAAAGAGGCCACTGGGAGGCAGGAGGAGCTGGGCCTGGAGAGGCTGCCGAAAGGCAGGAGCTTCGCCTGAGGATGCCACAGTGAGACACCATCTGGGTCTGGAGGCTCCACTGTGAGGCAGAGGCTGGCCTGTAGAGTCCGACAGTAGACAAAAGTTGGGCAAAAGGCTGATTTGAGGAAGTTTTGGGCTTCAAGAGTCAGCCACAAGGCAGGCACTAGGCCTGGAAATGGCCTCACAGTCATGAGTTGGGCCTAAATGGGCCAGTGTGAGGGAGGAGCTGTGCCTGTTGAGGCTGCTGGCAGGCAGGCAGAAATTTGGCCTGGGGCAGCTGCCATGAGGCAAGAGCTGGGCCTGGAAAAAGCCCCTGGGAGGCAAGAGCAGGGCCTGCAGAGGCTGTTCTCAAGTCAAAGCTGGGCCTGTTGATGCCACCGGGAAGCAGAAGGTGGGCCTGGAGAGTTTGAATCCAGGAAGTTTTG + +a score=42031 +s hg18.chr1 128630 478 + 247249719 GGCCTACATTGGCCGCCATTAGCTGGACAGGAACTGGGCCAAAAAAGGCTGTTGTGAGGCAGCAGTTGTGCCTGTAGACCCAGCCAAGAGGAAGAGGTGGGCCTGGAGAAGCCCCCATGAGGCAGAGGTTGGGCCTGTAGACGCTGACAGGAGGCAGGAGCTGGGCCTGGACAGGTCAACTTGAGGAGATTTTGGGCCTTCATAGGCCACCAGGAGGCAGCAGTTGGGACTAGAGAGTCTGACTTGAGTAAGTTTTGGGCCCGGAGATGATGTCCTGGGACAGGAGTTGGCCGTGGAGAGGCCACCGTGAGGCATAAGCTGGATGTAGAGAGGCCAGTGTGAGGCAAGACCTGGGCCTGTCTAGGCTGCTGGGAGACAGGCAGGAATCTGGCCAGGGAAGGTTGCCATGAGACAAAAGTTGGGCCTGGAAAGGCCCTTGTGAAGCATGAGCTTGGCCTAAAGAGGCCACTGGGTGGCA +s panTro2.chr1_random 7178181 477 + 9420409 GGCNTACATTGGC-GCCATGAGCTGGACAGGANCTGGGCCAAAAAAGGCTGTTGTGAGGCAGCAGTTGTGCCTGTAGACCCAGCCAGAGANNAGAGTNGGGCCTGGAGAAGCCCCCATGAGGCAGAGGTTGAGCCTGTAGACGCTAAAAGGAGGCAGGAGGTGGGCCTGGAGAGGTCAACTTGAGGAGATTTTGGGCCTTCATAGGCCACCAGGAGGCAGCAGTTGGGACTAGAGAGTCTGACGTGAGTAAGTTTTGGGCCCGGAGATGACGTCCTGGGACAGGAGTTGGGCCTGGAGAGGCCACCGTGAGGCATAAGCTGGATGTGGAGAGGCCAGTGTGAGGCAAGACCTGGGCCTGTCTAGGCTGCTGGGAGACAGGCAGGAATCTGGCCAGGGAAGGTTGCCATGAGAGAAAAGTTGGGCCTGGAAAGGCCCTTGTGAAGCATGAGCTTGGCCTAAAGAGGCCACTGGGTGGCA + +a score=105363 +s hg18.chr1 129108 1151 + 247249719 GGAGCTGGGTGTGTAGAAGCTGCTGAAAGGTTGGGAGCTTGGCTTGGGGGGTCCACAGTGAGGTAGAAGCTGGGCGTGAAGAATCTGCTGTGAGGCAGACGTTGGGACTGTAGAGGCTGACGGGAGGCAGAGGCTGGGCCTGGAGGGGCCACCAAGATGCAGGAGCTGGGCCTGGAGAGGCTGCAAAGAAGCATGAGCTGGGCCTGGTGAGGTCAACTTGAGAAAGTTCAGGGCCTGGAGAGAAGGCTGGGAGGCAGGAGCTGGGTCTAAAGAGGCCATTGTAACGATGGAGCTGTGCCTGTGGAGGCTGTTGTGAGGCAGTAGCCTCATCTGCGGAGGCTGCCGTGACGTAGGGTATGGGCCTAAATAGGCCATTGAGAGTCATGAGCTTGGTCTGTAGAGGCTGACTGGAGAAAGTTCTGGGCCTGGAGAGGCTGCCGGGAGGTAGGAGCTGGGCCAAAAgatgtaagcacatttgcatttattaggcactttatttccattattacactgtaatatataataaaataattatggaactcaccataatgtagaatcagtgggcgtgttaagcttgttttcctgcaactggatgttcccacctgagcgtgatgggagaaagtaacagatcaataggtattagattctcataaggacagcgcaacctcgatccctcacatgcacggttcacaacagggtgcgttctcctatgagaatctaatgctgctgctcatctgagaaggtggagctcaggcgggaatgtgagcaaaggggagtggctgtaaatacagacgaagcttccctcactccctcactcgacaccgctcacctcctgctgtgtggctccttgcggctccatggctcaggggttggggacccctgCTCAAGTGCATCCAAAACGACCCTTCCCACACCAGTCTTCACAGTGGTCAAGGGCAGCAACCACTTAG CTCCCAAGGCATGTGCCTCAGCTGGCATTTCGTCACAATCAACAGTAAGTGGTAGCTTGAGTCACTGTGAGGTCACCTACTGGAAATCACCAGCATCCCATTTCCCACTGGCAAAGAGCTCAGCACTGCCCCCTGGGAAACCAAACCTATGCCCAAATCCCATCTGTGTGGGTTTACCTCCTGGGACCCTTCCTAACATAT +s panTro2.chr1 275366 1150 + 229974691 GGAGCTGCGTGTGTAGAAGCTGCTGAAAGGTTGGGAGCTTGGCTTGGGGGGTCCACAGTGAGGCAGATGCTGGGCGTGAAGAATCTGCTGTGAGGCAGATGTTGGGACTGTAGAGGCCGACGGGAGGCAGAGGCTGGGCCTGGAGGGGCCACCAAGATGCAGGAGCTGGGCCTGGAGAGGCTGCAAAGGAGCATGAACTGGGCCTGGTGAGGTCGACTTGAGAAAGTTCAGGGCCTGGAGAGAAGGCTGGGAGGCAGGAGCTGGGTCTAAGGAGGCCATTGTAACGATGGAGCTGTGCCTGTGGAGGCTGTTGTGAGGCAGTAGCCTCATCTGCAGAGACTGCAGTGACGTAGGGTATGGGCCTAAATAGGCCATTGTGAGTCATGAGTTTGGTCTGTAGAGGCTGACTGGAGAAAGTTCTGGGCCTGGAGAGGCTGCCGGGAGGTAGGAGCTGGGCCAAAAgatgtaagcacatttgcatttattaggcactttatttccattattacactgtaatatataataaaataattatagaactcaccataatgtagaatcagtgggcgtgttaagcttgttttcctgcaactggttgttcccacctgagcgtgatgggagaaagtgacagatcaataggtattagattctcataaggacagcgcaacctagatccctcacatgcacggttcacaacagggtgcgttctcctataagaatctaatgctgctgctcatctgagaaggtggagctcaggcaggaatgtgagcaaaggggaatggctgtaaatacagacgaagcttccctcactccctcactcgacaccgctcacctcctgctgtgtggctccttgcggctccatggctcaggggttggggacccc-GCTCAAGTGCATCCAAAATGACCCTTCCCACACCAGTCTCCACAGTGGTCAAGGGCAGCAACCACTTAG CTCCCTAGGCATGTGCCTCAGCTGGCATTTCGTCACAATCAACAGTAAGTGGTAGCTTGAGTCACTGTGAGGTCACCTACTGGAAATCACCAGCATCCCATTTCCCACTGGCAAAGAGCTCAGCGCTGCACCCTGGGAAACCAAACCTATGGCCAAATCCCATCTGTGTGGGTTTATCTCCTGGGACCCTTCCTAACATAT + +a score=1144609 +s hg18.chr1 130272 12488 + 247249719 tacttgagaggctgaggtgagacaatcgatttagcccaggagtttgagatcagcctggacgacataactaaatctcatctctaCAaggacgaggtgggaggatcacttgagcccaggaatttgtggccagcctgggcaacaaaagaagaccccatctggccaacatggccaacctggccaccacggtgaaactctgactctacaaaaatgatctgggcatgggtgacatgcgtgtgtagtcctagctacttgggaggttgagatgggaggattgcttgatctcagaaggccaaagctatagtgagctatgatcacatcactgcactccagcctggatggcacaggaagattctgtctcaaaaaaaagaaaagaaatatatatttaatctctgtccctggttcctggcacagagcttctaaagctcttacaaagacctcagtgatagatgtgacaggagcatcttttgttttaatatttggtcttggtcccaggtttctaacacaagagcctctaagaactttgggatctccagcatggtaagaatgcatttggggatgttgttgagatgactgggtgactgcaagctcctaaatttcttcaagaggagggctgattaccatgcaaccacatggtaagaggcttggaactttcagcctcatgcactgaactccagggggaagaggggctggagactgacttaatcaccaacagccaaaggttttatcaatcatgcttgcataataaagcctccataaacaccctgaaaggggtttgcagagctttcagggttgctggacacaggagatgctgggagggtcgcatgttcaacagagggcatgggagctctgtgcccctccgaacttaacttgccctgggtatctttctttttttt-gagacaggatcaggctcttttgtccaagctggagtgcagtggcacaa tctcagcttactgtaacctaagcctccccagtccccagctcaaggtatcctctcatctcagcttccctagtagttggaactctaggtgcacaacaccacaccagttattattattattttttaattttttatagagacaggttttcaccatgttgcccaggctggtctcaaactcctgagtttaagcgatcctcccaccttggcctcccaaagtgctgagattacaggcatgagccactgcatccagcatgcacgtctctttcattgactgtttctgagatgtatccttcacaatgaaccagtaataggaaatgaactggccagatgtggtggctcacatctgtaatcccagcactttcagaggctgaggtgggaggatcacttgagaccaggaatttgtggccagcctggccaacacaacaagaccccatctatacaaaaaataaaagaaactagccagatgtggtggtgcaggcatgtagtctcagctactagggaggctgaggtgggagaaccactggaacccagacaatcaaggctgcaatgagctatgactgcaccattgcacaccagcctgggcaacaaaataagaccctctctctcagaaaaaaagaaaataaactgtttttctgagttccgtaaactgttctagcaaattattaaacccaagaagacagttacgggaacccccgattggtaacaggttggtcaaaagtatggtgacaacttaggacttgccattgtcatctgaagtgaggatggcctcgtgggactgagcccctaacttgtggggtctgtgctaactccaggtagtgtcagaataaagtcatgggatacccagttaatatccagagcactgaagaatctggtgtagaaactccatacgtacattcagtcggaagtgtgtgagtagagacaaacaTGGGCTTTTCTGTCACCTACCTGCTTAACTGCATAGgagaggcaatatgtggtgctcatgaacaaag caaacattaaagtcagaccagacccaacatttgactcagtcttaatatccaggtgagcctgcgcaaatcattcattattcctaaggttttcatcactccattcataaaatggggataactgtggcacctacatgtgattctgtgagaattaacgaaatattatgcttgGGGTTATTGTGATCATTATACCTGTTCCAAACTATTTGACAAGGACAGTGATGGATGAAGACATCAAAAAATCAGAAACTGCAATGAGGTCTCTCAGGCAAAATTCCATACAAGCAAATTACTGTGTCTACAAAGCATTCCTGCCACACTTAATTCACCATTCCCTGAACAGAATATGCCATCTTCGTTGTTCAGGTCTGTACAGTGCTGGTTTCCCTTCCCGGACAGTTTGCGCTATCCCATCCCGGCCCATTCCCCATCCCTCCACCTCCCCCTTCCCTCCCCACTCTCATACAACTCTTCCTCATCTTTCAGGACTTGGCTTCAATGTCACCTTAACTGGAAGCTTCTCTCACTCTCCAGAAGAGCTTCCCATTGCACCTGATGCATGGGAAACATAATTTGATCATTTTTAAGTTACAGTCCAAATCTTTTTGTACCTGAATAACATGTTGCCCAGTCAGTCTCTCTTCCTGGATTCACAAGTCTTTCATGGTAGATCCAGCTGGAAGTGACAAAAAGACATCTTTTGACATAAAGGGATGACACAGACAGACATAAGTTCTTAAATGTCTTAAATGTTATGTGAGAATTAAACAGAATTCAAAGACTTGTGGGGAGCACTTAGGAAGTTACTGGGAATGTCATGAAGGGTTAAtttgtattttattttattttttgagacagtctcattctgtcacctaggctggagtgcagtggtgcaatcaggctcactgcagccttgaccacctgggctcaagtaatcTCACTTAATTTTTATTTGGTTTAAGAAAGTCTTGGTTGAGGgtggtggcttatgc ctgtaatctcagcactttgggaggctgagagaggtatattacttgaggccaggagtttgagatcagactgggcaatatattaagaccctgcctctaccaaaaaACAGAGTGAATGTgtggaagacaatttttccacagactgggaatgagggaataatttcaggatgattcaagtgcattacatatattgtgcactttatttctattattactacatagtaatatataatgaaatgattctacaactcactataacgtagactcagtgggatctctgagcttgttttcctgcaactagactgtccatctggggtgatgggagacagtaacagaatatcaggcattagattctcataaggagtacacaacctagatccctcgcatgcacacttcacaacagagtttgtgctcctgtgagaatctaatgctgctgctgatctgacaggacatggagctcaggtggtcatgcaagcgatgggaggggctagaaatacagatgaagtttcccttcactcgcctgctgctcacctccagctctgtggccctgtGGTTGGAGACCGCTGCTCAAGTGCATTTGAAAGGAACCAACCCACGCCATTCTTCAGAGTCATCTTTACTGCTGCAGTGGTCAACTTGTAGCACCCCTAAGCTCGCAGGACATATGCTTCAACTGGCATTTCACAATCAACAGTATGTGGCAGCTTGAGTCATTGTGAGCTCACATCCTGGAAATCACCAGCATCCCATATCCCATT-GCAAGGAGCTCAGCACTGCTCCTTGGATAACCAAACCTATTCCCAAATCCCATCTGTGTGCGTCTATCTCCTGGTACCCTTCCTAGCATCAATTCTGTATTTGTAGGAGTCCAATCAGGAGACACAAACCACTCAAAAGTTTAAACTAGAATGAGCAAgatggctcacacctgtaatcccagaactctgggaggccaaggtgggtggactgctttgagctcaggagtttgaga acagtctgggaaacatggcgaaacctcgtctctacaaaaaacacaaaaatcagctgggtgtggtggcacttacctgtaatcccagctactcgggaggctgaggcaggagaattgcttgagcctggcaggtggaggctgcagtgagcagaggttgtgccactgtactccagcctgggtgacagtgtgagacccggtatcaaaaagaaaaaaCGtatatatatatatatatatatatatatatatatatatatatatatatatgtaAATTTAATATAAAAAGTATTAATTTTggccaggcaaaatggctcatgcctgtaatcccagcactttgggaggccaaggcagacagatcacctgaggtcaggagttcgagaccagcctgaccagcacagagaaaccccatctctactaaaaatacaaaattagctgggcatggtggcacatgcctgtaatcccaactactcgggaggctgaggcaggagaattgcttgaacccagaaggtggaggttgcgctgagccgagatagcgccattgcactccagcctgggcaacaagagtgaaactccatctc---aaaaaaaaaaaaGGGTATTAATTTTTACAGAGGATCAGCACAATGAGGGACACACTAGCACAAAGTAAAGACAACTCTAGAGAATACGGAACTAGCAGAggccaggcattgtggctcatgcctgtaatcccagcaatttgggaagcctaggcaggaggatcgcttgaggccaggagttggagaccaatcagtgctaaatagtgagactctgtgtctaccaaaaaaaagagacattagccaggtgtggtggtggtgcacacccgtagttccagctacttgggagtctggggtgggagaaatcccttgagcctgggaagtctacactacagtgagccaagattgtgccactgcactccagcctgggcgacagagtgagaccctgtcttagaaagaaaaaagaaaagaaaGTGTTAA TCCCCCTATGGGAATCTCCTCTTCTCCTGCCCTCTCTGGAACCTCACTTGTCAGTTCTTCCTCCCACTTTCCTGTATCTTTAACCTATCCCCCACTTTTAGCTCCTTCCCATCATCATTTAAATTACTCAAACTTCTTCTGTTTTAAAAACCTCTCCCTAAACTCAGGGAGAGGTCTTCTGCACACACATTGAGCCATCTGCTCTTCCCGGTGCCTTCTCTACAGCAGCCTGAGCCATGTCTCTAATCTATGAATCTCATCATGTTACTCCCCCATTTACATCACTTCTCCTTGCCTCAGGGATTAAGTCCAAACTCCTTAACAGCCCCTGCTCTGCCCTGCCTTGCAAGGCAGcctcactgcttgcccctctccatttcatctgctatggagtccaactgagcctcatctgccccttgaacgcacactctttctcctctgggagtctctgaagtgggtaatatcctctgcttataatatgcttccccttaaacctctactctcttcctagctagctttgactcctctgtcacttgtccgctttggcatcacctcctcatagaagacttctatgactcccgagATTCTCAGGAGCATGGCAGGTGAAGTGctcctcccatgaatggatggagattagggagtgtgtgttattcatgcttaattcaccagtgcttagctgagtacctggcataaaatagttactGTGGTGGCCAAAGTAATAACCCCCACCGCCACCAATTGCTCATGTCCtatgttacacagcacagttacagaggaagggggaattaagagtgcagataaaattaatgttgctcatcagctgaccttaaaacaagattatcctggagtatctaggagagcccatgtaattacaagcattctttaaaactggaagagggaggcagaaggttaagaaccagagacggTgggcacaatggctcatgcctgtaataccaatactttgggaggccagggtaggaaaatccctt gagtgcaggagttcaaggtcagccatggcaacatactgaggtcccatctctacaacaaaataaaaacaaaattcactgagtgtcacgatgcttacctgtagtcccagctactgggaaggctgacatggtaggattgcttgagcctgggagtttgaggctataatgagccatgataggaccactgaactccatcctgagtgacagggcaaggtcctgtttctgaagaaaaaaaGGACATTGGAATCAGGGCCCTCTCCATCCTGAGGTGCCTACAAGGCATCTCTCTCTGCAAACGAGTAAACATCACCCTCCAACTCCTTACAGAGTGGAGCAACAGGAAAACTCCTTCACCTCATTTCTGTGCTGCTTGGGAGGCCTGGACAGCCCAATAACCAGCTCCTCGCTGATGAAGCAATCAGGAAATGGCTCGAGTTGAGCTAAGGAGAATTTGGATCCTTCCTTTGGTTCTCAGTAGGCAGGGTAGGggccaggcatggtggctcatacctgtaatccttgcactgtggggggccaaggtgagaggattgcttgaggccaggagctcaagaccagcctggacaacatagcaagacctgggtggcacacacctgtggtccctactacttggtaggatgaggtgggaggattgatcacttgatcccaggagtttcaggctgcagtgagccatgatcacaccactgcacttcagcctgggtgacagagccagaccatgtcacaaaaagttag------aaaaaaaaaaGAGAGAGGGAGAgagactatacacaggcaccaccacatttggctaatttttaaatattctgtagagacaaggtcttgctaggttgcccaggctagtctaaaactcctggcatcaggctgggcatggtggctcatgcttgtaatcgcagcactttgggaagctaaggcaggcaaatcacctgaagtctggagttcgagaccagcctggccaacacggtgaaactctg actctatcaaaaatacaaaaatcagctgggcagtagtggcgtgtgcctgtagtctcacctactcgggaggctgaggcaggagaatcacttgaacctgggaggtggaggttgcagtggaccccatcactgcactccaccctgggtgacagagcgaga--ctGTc---aacaacaacaacaacaacaaaaacaaaaacaacaacaacaaaaaaaactcctggcatcaagacatcttcctgtcttagcctcccaaagccctgggattataCTGTTTCCTATAATTGAAGACACTTGTTCTTATACTGCTTTAAGGTATAAAGGAAGAAAaaaaaaacagataatggcaaatgttggtgaaggccgggcatggtggcagcctgtaattccagaacttagggaggctgaggtgggcagatcacttgaggccaggagtatgagaccagcctgggcaacatggtaaaatcccaccactacagaaaaatctaaaaattagccaggcatggtggcgtacacctgtaattttcagctacccaggaggctgagatgagagaatcacttgtgcctgggaggtcacggctgcagtgaactgtgatggcatcattgcactgcggcctgagagacagagcaagcccctatctag-aaaaaaaaaatgtcagtgaagatgtggaggaattggaacccacaaacattactggtgggaacataaaattgtgtaaccattttgTTTGGGTATTTCTTTTCTTGTCATTTTAATTGGATTTTTAAAAAATCAagacggggtttcactatcttgcccaggctggtcttgaattcacgggctcaagccatcctcctagctgagcctcctgagtagctgggattacaggtgtgagccattgcacccaactggtatagccacgttagaaaacattctggcagtttctcaaaaggctaaatgtacagtcatcctataatgcaacaatttcactcctaggcatatatcccagaaa aataaaaatatatgtccacacaaaaacttgtacaacaatcttcatagcagcattattcataatgaccaatacatggaatacatggaaacaacccaaatatccaccaactgatgaacagataaacaaaatgcagtgtgtctctaccatggaatactgccatagaaggaatgaaatattgatacacactatgacataaaggaactttgaaaacactgtgctaagagggaaaaaaagccacaaaagatcacatattgtacaattctatttgtccagattaggcaaatctatagtgacaaaaaaattaatcaatggttgcctaaggctgggggcaaaggtaggtggggagagtaggaggtagtggctaaggggtatggatttctctatagggtaatgaaaggttctaaaagtgactgtggtgatcgatgcacagctctgtgaatattctaaaacctactgaattgcagatttcaataaataaagtgaatggtatgtgaatattttaataaagctattaTTTAAAATAATAATAATAGGGggctgggcacaggtggtcatgcctgcctgtaatcccagcactttgggaggctgaggcaggaggatcacttgaggtcaggagttttgagcccagtcggagcaacatggcaagatcccgtctctatgataaaaaattagctggacatggtggcacatgtctgtagtcccagctacttgggagactgaagtgagagaaccacttgagcccaggagtttgaggctacagtgaaccatgatcatgtcactgtactgtagcctaagcaacagagcaagacgctgtctctgaaaaggaaagaaaacaaaTGCAAGTTTTTATCACTTTGTGAGTGTAGCCAAGTTGGAGGAGAAATAGACAATAATAAAAGAGCACTGAATAATGACAGTGAGTGGCTGGTTAGGCTCAGTTGCTAGCTAAATGGCTTCTAAAAAATTCAATAAAGTTACAGCTCTGGGGA CAGTCATGTAGTCAAAGAATGAAGGCGAAATTCATTACAATTGCCCATGGTCTTTATTTACATGCCTTCTAGTGAAAAATTCCTAAGTGCCTAAACAGCAAGTCTGCAATGATAGCAGCTGTTTATTAAAGACTACAAAAAAGAAATGGAggccgggcgtggttgttcacatctgtactccttgaattttgggaggctgaggcaggcagattgcctgaggtcaggagctccagaggagcctggccaacatggtgaaatcccatctctactaaaaatacaaaaattagctgggtatggtggcgggcacctgtaatcccagctactcgggaggctgaggcaggagaattgcttgaacccagaaggtgaaggttgcagtgagccaaaatcgcaccattgcactccagcctgggtgacaagagaaagactcttatctt---aaaaaaaaaaagaaaaaaaagaaaTGGCATCTTCTTCAAGAATTACATCGTGTTTCATGATAAAGAAGCTCTAATTTTGCATTTGTTCAAGTATTGATGAGATTTACCCAATATGACACCCATCTTGGATAAAATGCAAACAACACAATTTCATTTTGTCATTAACAAAACCGATTAAGTAGTCTaatataaattgcgatcttattaaaaactgatccgatttaaaaaattatggaattatggagccaataagatgttacaacctgttccaaggggaattccaaaatccacacatatctgagaccatcaagtatgatgaaatatatttgATTACTATATTGAAAAATAAACTGATTACATAGCCAACAATTGGACAGGGGTCTCCTCATCCACAGCCACACAAACCCGATCATGCAGCTGTATGGTTACAAGGCCTACATAGCCTAGAAGGGACTGGTCTGACTTGAGATTTCAtttgtatttgtattttgagacagggtcccactctgtcacccaggatggagtgcagtggtataatcatagctcactgca accttgaccaactgggctcaagagatgctcctgcctcagctgcccccatacctgggaatacaggcaagtatcaccatgtcaggcatttttttcatttttgtagagagagaagacttgctatgttgcccaagctggcctcaaactcctagaatcaagagatctgcccatctcagccacatgagtaactggggccataggtacataccatcatgcctggctatatttattttattttattaaatttattttttttatttttgtagagaggaggtcttgctgtgttgcccaggctgctctcaaactcatggccttaaaacatactcccatctcctctgcctctcaaactgttggaactataggtgtgagccactgtacctggccTGACTTGGGATTTCTTTTATCTAGCATCCTTTACTTGGTAGGATTGGGAAAAGCAGTAGTGTTTTTTAAAATTACTTAATAATTCAATCAGAATCAAACtcaaccttgaccactgccttctctcacagctcacatccagtctgtcaggaaatcctactgactgacttcaacatgtatccaggctctaaccatctctcaccaccaccatgaaccccgtcaggatcactatcatctcccaccgggatgttgccacagcttggctcccatgcttctacccaaatcttcccatagtctttctcaactcggcagccaggtcgtgcttttaaatcaggagacggatcatgtcgcctctctgctcagaagccctcggtggttcccattttagtcagagcaaaagccaaagccccagcaatagcgtcccagggcttacacgatctgtaccgatcccagcccagcaactccctggcctcctcgctgacttcgctcc----atctctttgctccactggcctccttccagagcctcagacacaccagagagtttcctcctaatgcctttatcctgttgactcagcctacaatgctcttccctcagcaccttggccagc tccatcacctgcttcaaacttttgctcaatattcacttatgaggccaaccctgaccactctacttaacactgccatctgtccccattcccaccatgctcatttctttctttctttttgaaacaagatcttgctttattgcccaggctggagtacactggtgcaatcacagctcacagcaacttcaacctcccaggcttaaacaatcctcccgcctcagccaccctaggaactgagactacagctgcatgccacaacacatggc------ttttatttttttttttttgagacggagtctcggtcgcccaggctgaagtgtaagggtgcgatcttggctcactgcaatgtctgccttttgggttcaagtgattctctgcctcccaagtagctgggattacaggcacccaccaccacacctggctaatgtttgtatttttagtagagatggggtttcaccatcttggctaggctggtcttgaacttctgacctcgtgatccaccctcctcggcctcccaaagtgctgggattacaggcgtgagccactgcgcctggcctttaaaaaaatattttttttagacatgaggtctcattatgttgcccaggctggtcttaagctcctgggcttaagcgatcctcccacctcagcctcctaaagttctgggattacaggcgtgagcaactgTAACATGAGGTCCCAGCTTCgtgttcattttttgttgttgctacaacaaagtaccctacatttagtggcatcaaacaccacaaatctaccatcttacagttctgggggccagaagcccaactaggtctattaaggctaaagtcaaggtgtcagagaggctgcattccttctgggggaggctctagacagaatgtgctcctttgccttttccagcttctagaagccacccccattccttgacttacctcgtgactccatattcaaggccagaagtgcagcatcttcaaatctccctctctgacctc ttcttccattaccacatcactttctctaattctgactctcctacctcattctcttataaagatccttgtgattGGTgggtatgggggctcccatctgtaatcccaacattttgggaggccaaagaggaaggattgcttgaggccaagagttagagatcagcctggggaaaataggaagatcctgcctttac------aaaattaaaatcagctggacatggtgatgcatgcctgtagttccagctactggagaggctaaggtgggaggattgctttagcctaggaggtcaaggctgcagtgagctatgatcacatcactgcactccagcctcagtggcaga--gtgagactctgtctccgatataagaaaagaaatatacatttggtctctgcccgtggttcctggcatagagcttccaaagctcttataaagcccttcgtgacagaggtaataggagcattttctgttttgatatttagtcttagtcccaggttcctgacacaagggcctctaaggtctttcagatctgcagcatggtaagaatgcatgtgggatgctgttgagctaacggggtggctgcaagctccgagactgcttcaggaggagggctagctgccagagaaagcaaccacattttttttttaaaacagagtttggctcttgtagcccaggctggagtgcaatggcacaatctcagcttgctac +s panTro2.chr1_random 7184740 12479 + 9420409 tacttgagaggctgaggtgagacagtcgatttagccgaggagtttgagatcagcctggacgacataactaaatctcatctctacaaggacgaggtgggaggatcacttgagcccaggaatttgtggccagcctgggcaacaaaagaagaccccatctggccgacatggccaacctggccaccatggtgaaactctgactctacaaaaatgagctgggcatgggtgacatgcatgtgtagtcctagctacttgggaggttgagatgggaggattgcttgatctcagaaggccaaagctatagtgagctatgatcacatcactgcactccagcctggatgacacagggagattctgtctcaaaaaaaagaaaagaaatatatatttaatctctgtccctggttcctggcacagagcttctaaagctcttacaaagacctcagtgatagatgtgacaggaacatcttttgttttaatatttggtcttggtcccaggtttctaacacaagagcctctaagaactttgggatctccagcatggtaagaatgcatttggggatgttgttgagatgaccgggtgactgcaagctcctaaatttcttcaagaggagggctgattaccatgcaaccacatggtaagaggcttggaactttcagcctcatgcactgaactccagggggaagaggggctggagactgacttaatcatcaacagccaaagattttatcaatcatgcttgcataataaagcctccataaacaccctgaaaggggtttgcagagctttcagggttgctggacacaggagatgctgggagggtcgcatgttcaacagagggcatgggagctctgtgcccctccgaacttaacttgccctgggtatctttctttttttttgagacaggatcaggctcttttgtccaagctggagtgcagtggcacaa tctcagcttactgtaacctaagcctccccagtccccagctcaaggtatcctctcatctcagcttccctagtagttggaactctaggtgcacaccaccacaccggttattattattattttttaattttttatagagacaggttttcaccatgttgcccaggctggtctcaaactcctgagtttcagcaatcctcccaccttggcctcccaaagtgctgagattacaggcatgagccactgcatccagcatgcacgtctctttcattgactgtttctgagatgtatccttcacaatgaaccagtaataggaaatgaactggccagatgcggtggctcacatctgtaatcccagcactttcagaggctgaggtgggaggatcacttgagaccaggaatttgtggccagcctggccaacacaacaagaccccatctatacaaaaaataaaagaaactagccagatgtggtggtgcaggcatgtagtctcagctactagggaggctgaggtgggagaaccactggaacccagacaatcaaggctgcaatgagctatgactgcaccattgcacaccagcctgggcaacaaaataagaccctctctctcagaaaaaaagaaaataaaccgtttttctgagttccgtaaactgttctagcaaattattaaacccaagaagacagttatgggaacccccgattggtaacaggttggtcaaaagtatggtgacaacttaggacttgccattggcagctgaagtgaggatggcctcgtgggactgagcccctaacttgtggggtctgtgctaacttcaggtagtgtcagaataaagtcatgggatacccagttaatatccagagcactgaagaatttggtgtagaaactccatacatacattcagtcggaagtgtgtgagtagagacaaacaTGGGCTTTTCTGTCACCTACCTGCTTAACTGCATAGgagaggcaatatgtggtgctcatgaacaaag caaacattaaagtcagaccagacccaacatttgactcagtcttaatatccaggtgagcctgcgcaaatcattcattattcctaaggctt-catcactccattcataaaatggggataactgtggcacctacatgtgattctgtgagaattaatgaaatattatgcttgGGGTTATTGTGATCATTATACCTGTTCCAAACTATTTGACAAGGACAGTGATGGATGAAGACATCAAAAAATCAGAAACTGCAATGAGGTCTCTCAGGCAAAATTCCATACAAGCAAATTACTGTGTCTACAAAGCATTCCTGCCACACTTAATTCACCATTCCCTGAACAAAATATGCCATCTTCGTTGTTCAGGTCTGTACAGTGCTGGTTTCCCTTCCCGGGCAGTTTGCGCTATCCCATCCCGGCCCATTCCCCATCCCTCCACCTCCCCCTTCCCTCCCCACTCTCATACAACTCTTCCTCATCTTTCAGGACTTGGCTTCAATGTCACCTTAACTGGAAGCTTCTCTCACTCTCCAGAAGAGCTTCCCATTGCACTTGATGCATGC--ACTATTATTTGATCATTTTTAAGTTACAGTCCAAATCTTTTTGTACCTGAATAACATGTTGCCCAGTCAGTCTCTCTTCCTGGATTCAGAAGTCCTTCATGGTAGATCCAGCTGGAAGTGACAAAAAGATATCTTTTGACATAAAGGGATGACACAGACAGACATAAGTTCTTAAATGTCTTAAATGTTATGTGAAAATTAAACAGAATTCAAAGACTTGTGGGGAACACTTAGGAAGTTACTGGGAATGTCATAAAGGGTTAAtttg---tttttttttttttttgagacagtctcattctgtcacctaggctggagtgcagtggtgcaatcaggctcactgcagccttgaccacctgggctcaagtaatcTC----AATTTTTATTTGGTTTAAGAAAGTCTTGGTTGAGGgtggtggcttatgc ctgtaatctcagcactttgggaggctgagagaggtatattacttgaggccaggagtttgagatcagcctgggcaatatattaagaccctgcctctaccaaaaaACAGAGTGAATGTgtggaagacaatttttccacagactgggagtgagggaataatttcaggatgattcaagtgcattacatatattgtgcactttctttctattattactacatagtaatatataatgaaatgattctacaactcactataacgtagactcagtgggatctctgagcttgttttcctggaactagactgtccatctggggtgatgggagacagtaacagaatatcaggcattagattctcataaggagtacacaacctagatccctcgcatgcacacttcacaacagagtttgtgctcctatgagaatctaatgctgctgctgatctgacaggacatggagctcaggtggtcatgcaagtgatgggaggggctagaaatacagatgaagtttcccttcacttgcctgctgctcacctccagctctgtggccctgtGGTTGGAGACCGCTGCTCAAGTGCATTTGAAAGGATCCATCCCACGCCATTCTTCAGAGTCATCTTTACTGCTGCAGTGGTCAACTTGTAGCACCCCTAAGCTCACAGGACATATGCTTCAACTGGCATTTCACAATCAACAGTATGTGGCAGCTTGAGTCATTGTGAGCTCACTTCCTGGAAATCACCAGCATCCCATATCCCATTAGCAAGGAGCTCAGCACTGCTCCTTGGATAACCAAACCTATTCCCAAATCCCATCCATGTGCGTCTATCTCCTGGTACCCTTCCTAGCATCAATTCTGTATTTGTAGGAGTCCAATCAGGAGACACAAACCACTCAAAAGTTTAAACTAGAATGAGCAAgatggttcacacctgtaatcccagcactctgggaggccaaggtgggtggactgctttgagctcaggagtttgaga acagtctgggaaacatggcgaaacctcgtctctacaaaaaacacaaaaatcagctgggtgtggtggcacttacctgtaatcccagctactcgggaggctgaggcaggagaattgcttgagcctggcaggtggaggctgcagtgagcagaggttgtgccactgtactccagcctgggtgacagtgtgagacccggtatcaaaaagaaaaaaC------------------------------atatatatatatatatatatgtaAATTTAATATAAAAAGTATTAATTTTggccaggcaaaatggctcatgcctgtaatcccagcactttgggaggccaaggcagacagatcacctgaggtcaggagttcgagaccagcctgaccagcatagagaaaccccatctctactaaaaatacaaaattagctgggcatggtggcacatgcctgtaatcccaactactcaggaggctgaggcaggagaatcgcttgaacccggcaggtggaggttgcgctgagccgagatagtgccattgcactccagcctgggcaacaagagtgaaactccatctcaaaaaaaaaaaaaaaaGGTATTAATTTTTACAGAGGATCAGCACAATGAGGGACACACTAGCACAAAGTAAAGACAACTCTAGAGAATACAGAACTAGCAGAggccaggcattgtggctcatgcctgtaatcccagcaatttgggaggcctaggcaggaggatcgcttgaggccaggagttggagaccaatcagtgctaaatagtgagactctgcgtctaccaataaaaagagatattagccaggtgtggtggtggtgcacacccgtagttccagctacttgggagtctggggtgggagaaatcccttaagcctgggaagtctacactacagtgagcccagattgtgccactgcactccagcctgggcgacagagtgagaccctgtcttagaaagaaaaaagaaaagaaaGTGTTAA ACCCCCTATGGGAATCTCCTCTTCTCCTGCCCTCTCTGGAACCTCACTTGTCGGTTCTTCCTCCCACTTTCCTGTATCTTTAACCTAACCCCCACTTTTAGCTCCTTCCCATCATCATTTAAATTACTCAAACTTCTTCTGTTTTAAAAACCTCTCCCTAAACTCAGGGAGAGGTCTCCTGCACACCCATTGAGCCATCGGCTCTCCCTGGTGCCTTCTCTATAGCAGCCTGAGCCATGTCTCTAATCCATGAATCTCATCATGTTACTCCCCCATTTACATCACTTCTCCTTGCCTCAGGGATTAAGTCCAAACTCCTTAACAGCCCCTGCTCTGCCCTGCCTTGCAAGGCAGcctcactgcttgcccctctccatttcatctgctatggagtccaactgagcctcatctgccccttgaacacacactctttctcctctgggagtctctgaagtgggtaatatcctctgcttatagtatgcttccccttaaacctctactctcttcctagctagctttgactcctctgtcacttgtccgctttggcatcacctcctcatagaagacttctatgactcccgagATTCTCAGGAGCATGGCAGGTGAAGTGctcctcccatgaatggatggagattagggagtgtgtgttattcatgcttaattcaccagtgcttagctgagtacctggcataaaatagttactGTGGTGGCCAAAGTAATAACCCCCACCGCCACCAATTGCTCATGTCCTATGTTACACAGCACAAttacataggaagggggaattaagagtgcagataaaattaatgttgctcatcagctgaccttaaaacaagattatcctggagtatctaggagagcccatgtaattacaagcattctttaaaactggaagagggaggcagaaggttaagaaccagagacggTgggcacaatggctcatgcctgtaataccaatactttgggaggccagggcaggaaaatccctt gagtgcaggagttcaaggtcagccgtggcaacatactgaggtcccatctctacaacaaaataaaaacaaaattcactgagtgtcacgatgcttacctgtagtcccagctactgggaaggctgacatggtaggattgcttgagcctgggagtttgaggctataatgagccatgataggaccactgaactccatcctgagtgacagggaaaggtcctgtttctgaagaaaaaaaGGACATTGGAATCAGGGCCCTCTCCATCCTGAGGTGCCTACAAGGCATCTCTCTCTGCAAATGAGTAAACATCACCCTCCAACTCCTTACAGAGTGGAGCAACAGGAAAACTCCTTCACCTCATTTCTGTGCTGCTTGGGAGGCCTGGACAGCCCAATAACCAGCTCCTTGCTGATGAAACAATCAGGAAATGGCTCGAGTTGAGCTAAGGAGAATTTGGATCCTTCTTTTGGTTCTCAGTAGGCAGGGTAGGggccaggcatggtggctcatacctgtaatccttgcactgtggggggccaaggtgagaggattgcttgaggccaggagctcaagaccagcctggacaacatagcaagacctgggtggcatacacctgtggtccctactacttggtaggatgaggtgggaggattgatcacttgatcccaggagtttcaggctgcaatgagccatgatcacaccactgcacttcagcctgggtgacagagccagaccatgtcacaaaaagttagaaagaaaaaaaaaaaaGAGAGAGGGAGAgagactatacacaggcaccaccacatttggctaatttttaaatattctgtagagacaaggtcttgctaggttgcccaggctagtctaaaactcctggcatcagactgggcatggtggctcatgcttgtaatcgcagcactttgggaagctaaggcaggcaaatcacctgaagtctggagttcgagaccagcctggccaacatggtgaaactctg actctatcaaaaatacaaaaattagct-ggcagtagtggcgtgtacctgtagtctcacctactcgggaggctgaggcaggagaatcacttgaacctgggaggtggaggttgcagtggaccccatcactgcactccaccctgggtgacagagcgagactctgtcaaaaacaacaacaacaataacaaaaacaaaaacaacaacaacaaaaaaaactcctggcatcaagacatcttcctgtcttagcctcccaatgccctgggattataCTGTTTCCTATAATTGAAGACGCTTGTTCTTATACTGCTTTAAGGTATAAAGGAAG-AAaaaaaaacagataatggcaaatgttggtgaaggccgggcatggtggcagcctgtaattccagaacttagggaggctgaggtgggtagatcacttgaggccaggagtatgagaccagcctgggcaacatggtaaaatcccatcactacagaaaaatataaaaattagccaggcatggtggcgtacacctgtaattttcagctactcaggaggctgagatgagagaatcacttgtgcctgggaggtcaaggctgcagtgaactgtgatggcatcattgcactgcagcctgagagacagagcaagcccctatctagaaaaaaaaaaatgtcagtgaagatgtggaggaactggaacccacacacattactggtgggaacataaaattgtgtaaccattttgTTTGGGTATTTCTTTTCTTGTCATTTTAATTGGATTTTTAAAAAATCAagacagggtttcactatcttgcccaggctggtcttgaattcatgggctcaagccatcctcctagctgagcctcctgagtagctgggattacaggtgtgagccattgcacccaactggtgtagccacattagaaaacagtctggcagtttctcaaaaggctaaatgtacagtcatcctatgatgcaacaatttcactcctaggcatatatcccagaaa aataaaaatatatgtccacacaaaaacttgtacaacaatcttcatagcagcattattcataatgaccaatacatggaatacatggaaacaacccaaatatccaccaactgatgaacagataaacaaaatgcagtgtgtctctaccatggaatactgccatagaaggaatgaaatattgatacacactatgacataaaggaactttgaaaacactgtgctaagagggaaaaaaagccacaaaagatcacatattgtacaattctatttgtccagattaggcaaatctatagtgacaaaaaaattaatcaatggttgcctaaggctgggggcgaaggtaggtggggagagtaggaggtagtggctaaggggtatggatttctctatagggtaatgaagggttctaaaagtgactgtggtgatcgatgcacagctctgtgaatattctaaaacctactggattgcagatttcaataaataaagtgaatggtatgtgaatattttaataaagctattaTTTAAAATAATAATAATAGGGggctgggcacaggtggtcatgcctgcctgtaatcccagcactttgggaggctgaggcaggaggatcacttgaggtcaggagttttgagcccagtcggagcaacgtggcaagatcccgtctctatgataaaaaattagctggacatggtggcacatgtctgtagtcccagctacttgggagactgaagtgagagaaccgcttgagcccaggagtttgaggctacagtgaaccatgatcatgtcactgtactgcagcctgagcaacagagcaagatgctgtctctgaaaaggaaagaaaacaaaTGCAAGTTTTTATCACTTTGTGAGTGTAGCCAAGTTGGAGGAGAAATAGACAATAATAAAAGAGCACTGAATAATGACGGTGAGTGGCTGGTTAGGCTCAGTTGCTAGCTAAATGGCTTCTAAAAAATTCAATAAAGTTACAGCTCTGGGGA CAGTCATGTAGTCAAAGAATGAACACAAAATTCATTACAATTGCCCATGGTCTTTATTTACATGCCTTCTAGTGAAAAATTCCTAAGTGCCTAAACAGCAAGTCTGCAATGATAGCAGCTGTTTATTAAAGACTACAAAAAAGAAATGGAggccgggcatggttgctcacatctgtactccttgaattttgggaggctgaggcaggcagattgcctgagatcaggagctccagaggagcctggccaacatggtgaaaccccatctctactaaaaatacaaaacttagctgggtatggtggcgggtgcctgtaatcccagctactcgggaggctgaggcaggagaatggcttgaacccagaaggtgaaggttgcagtgagccaaaatcgcaccattgcactccagcctgggtgacaagagaaagactcttatcttaaaaaaaaaaaaaagaaaaaaaagaaaTGGCATCTTCTTCAAGAATTACATCATGTTTCATGATAAAGAAGCTCTAATTTTGCATTTGTTCAAGTATTGATGATATTTACCCAATATGACACCCATCTTGGATAAAATGCAAACAACACAATTTCATTTTCTCATTAACAAAACCGATTAAGTAGTCTAATATAAATTCTGATCTTATTAAAAACTGATCAGATTTTAAAAATTATGGaattatggagccaataagatgttacaacctgtaccaaggggaattccaaaatccacacatatctgagaccatcaagtatgatgaaatatatttgATTACTATATTGAAAAATAAACTGATTACATAGCCAACAATTGGACAGGGGTCTCCTCATCCACAGCCACACAAACCCGATCATGCAGCTATATGGTTACAAGGCCTACATAGCCTAGAAGGGACTGGTCTGACTTGAGATTTCAtttgtatttgtattttgagacagggtcccactctgtcacccaggatggagtgcagtggtataatcatagctcactgca accttgaccaactgggctcaagagatgctcctgcctcagctgcccccatacctgggaatacaggaaagtaccaccatgtcaggcatttttttcatttttctagagagagaagacttgctatgttgcccaagctggcctcaaactcctagaatcaagagatctgcccatctcagccacatgagtaactggggccataggtacataccatcatgcctggctatatttattttattttattaaatttattttttttatttttgtagagaggaggtcttgctgtgttgcccaggctgctctcaaactcatggccttaaaacatactcccat---ctctgcctctcaaactgttggaactataggtgtgagccactgtacctggccTGACTTGAGATTTCTTTTATCTAGCATCCTTTACTTGGTAGGATTGGGAAAGGCAGTAGTGTTTTTTAAAATTACTTAATAATTCAATCAGAATCAAACtcaaccttgaccactgccttctctcacagctcacatccagtctgtcaggaaatcctactgactgacttcaacatgtatccaggctctaaccatctctcaccaccaccgtgaacccggtcaggatcactatcatctcccaccgggatgttgccacagcttggcccccatgcttctacccaaatcttcccatagtctttctcaacttggcagccaggtcgtgcttttaaatcaggagacagatcatgtcgcctctctgctcagaagccctcggtggttcccattttagtcagagtaaaagccaaagccccagcaatagcgtcccagggcttacacgatctgtaccgatcccagcccagcaactccctggcttcctcgctgacttcgctccctctatctctttgctccactggcctccttccagagcctcagacacaccagagagtttcctcctaatgcctttatcctgttgactcagcctacaatgctcttccctcagcaccttggccagc tccatcacctgcttcaaacttttgctcaatattcacttatgaggccaaccctgatcactctacttaacactgccatctgtccccattcccaccatgctcatttctttctttctttttgaaacaaggtcttgctttattgcccaggctggagtacactggtgcaatcacagctcacagcaacttcaacctcccaggcttaaacaatcctcccgcctcagccaccctaggaactgagactacagctgcatgccacaacacatggcttttttttttttttttttttttttgagaaggagtctcggtcgcccaggctgaagtgtaagggtgcgatcttggctcactgcaatgtctgccttttgggttcaagtgattctctgcctcccgagtagctgggattacaggcacccaccaccacacctggctaatgtttgtatttttagtagagatggggtttcaccatcttggctaggctggtcttgaacttctgacctcgtgatccaccctcctcggcctcccaaagtgctgggattacaggcgtgagccaccgtgcctggcctttaaaaaa--attttttttagacatgaggtctcattatgctgcccaggctggtcttaagctcctgggcttaagcgatcctcccacctcagcctcctaaagttctgggattacaggcgtgagcaactgTAACATGAGGTCCCAGCTTCAtgttcattttttgttgttgctacaacaaagtaccctacatttagtggcatcaaacaccacaaatctaccatcttacagttctgggggccagaagcccaactaggtctattaaggctaaagtcaaggtgtcagaggggctgcattccttctgggggaggctctagacagaatgtgctcctttgccttttccagcttctacaagccacccccattccttgacttacctcgtgactccatattcaaggccagaagtgcagcatcttcaaatctccctctctgacctc ttcttccattaccacatcactttctctaattctgactatcctacctccttctcttataaagatccttgtgattGGTgggtatgggggctcccatctgtaatcccaacattttgggaggccaaagaggaaggattgcttgaggccaagagttagagatcagcctggggaaaataggaagaccctgcctttacaaaattaaaattaaaatcagctggacatggtgatgcatgcctgtagttccagctactggagaggctaaggtgggaggattgctttagcctaggaggtcaaggctgcagtgagctatgatcacatcactgcactccagcctcagtggcagagtgtgagactctgtctccaatataagaaaagaaatatacatttggtctctgcccctggttcctggcatagcgcttccaaagctcttataaagcccttcgtgacagaggtaataggagcattttctgttttgatatttagtcttagtcccaggttcctgacacaagggcctctaaggtctttcagatctgcagcatggtaagaatgcatgtgggatgctgttgcgctaacagggtggctgcaagctcctagactgcttcaggaggagggctagctgccagagaaagcaaccacaatttttttttaaaacggagtttggctcttgtagcccaggctggagtgcattggcacaatctcagctcactac + +a score=294155 +s hg18.chr1 142760 3236 + 247249719 aacctccacctcccgggttcaagcaattctcctgcctcggcctcccgagtagctggaattataggggtgtgccacaatgcctagctaactgttgttatttttagtagaaacggggtttcaccatgttggtcaggctggtctcaaactcttgacctcaagtggtccatgtgcctcagccttccaaactgctaggattacaggagtgagccaccgcacctggccccaaccacattttttgaggcttggaactttcagcctcacctgctgaactccaggaggcaaaaggaactggagattgacttaactaccaatggccagtgattttatcaatcatgcctccataaacacccaaacagcagggtttggagagcttctgtgttgctaaacacaaggaggtcctgggagggtagtgtgcccaacagagggcatggaagctctgtgcccctccccacttaccttgtcctgtgcatctctttcattggctgttcctgagatggagccattacattgagccagtaatagaaaataaggtggccagatgcactggctcatgcccgtaatcccagcactttgggaggcagaggtgggcggaatcacttgagcctaggaatttgagaccaacctgggcaacataagaagaccccatctatacaaaaaataaaagaaattagccaaatgtggtggtgggaaccctgtaattccagctacttgagaggctgaagcaggagaatcacttgagccctggacgttgaggcttcaataagctatgattacaccactgcacaccagcttggacaacagagcgaggccctgtctcttaaaaagaaaagaaaaaaaacttgtttttctaagttctgtgagttgttctagtaaataattaaactcaacaagagggtcatgggaaaccctgatttctaactggttggtcaaaatacaggtgac aacctaggacttgcaactggcatctgaagtgagggtggtcttgtgggactgagcccctaacctgtgggttctgtgctaactctaggtagtgtcagaatggaattgtgggatacgcggttggcatccagagagttggagaactggtgtagaaactctgcacacacatttggtcagaagtctgtgagtagagagaaacGtgttgcaggaagtcagggaccccaaacggagggactggctgaagccacagcagaagaatataaattgtgaagatttcatggacatttattagttccccaaattaatacttctataatttcttaggcctgtcattactgcaatctctgaacataaattgtgaagatttcatggacacttatcacttccccaatcaatacccttgtgattttctatgcctgtcttta-----atctcttaatccggtcatcttcgtaagctgaggatgaatgtccccgcaggaccctgtgataattgcgttaactgcacaagttgtttaaacaatatgaaacctgggcaccttgaaaaaagaacaggataacagcaatttcagggaacaagggagataaccttaaactctggctgcctgtgggccgggttgaacagagccatatttctcttctttcaaaagcaaataggagaagtattgctgaattctttttctcagcaaagaacatccctgagaaagagaatgcatccctaaggggaggcctctgaaatggccgctttggggacggctgtcttttacagtcatagataagggatgaaataagccctgggttcgcgtggcgctcccaggcttatcaggacaaggaaattcccgcctaataaatgttggtcagatgggttgtctgctctcaaaccctttctcctgataagatgttatcaatgacaatgcgcgcccgaaacttcattagcaattttaatttcgccccagtcctgtggtcctgtgatcttgccctgcctccatttgc cttgtgatattttattaccttgtgaagcatgtgatctctgtgacccacaccctattcgtacactccctcaccttttgaaaatcactaataaaaacttgttggttttgcggcttggggggcatcacggaacctgccgacgtgtgatgtctcccctggacatccagctttaaaatttctctcttttgtactctttccctttatttctcagactggctgacactcagggaaaatagaaaagaacctacatgaaatatcaggggtgaatttcccccgataTCACACTGGCTCTTCTCTCACCTGTCTACCTGCTTAACTTAATAGgagaggcaatgcatggtgctcatgaacaaggcaagcattaaagtcagaccagactaacatttgactcagtcctaatattcaggtgagcttgggcaaatcgctcattaaccccaagtcttcatcattttgtgcatataatggggataactgtggcacccacctgtttttgtgagaatcaatgaaatattatgcttgATGTTATTGTGATCATGATACTATCTGACAAGGGCAGTGATGCATGATAACATCAAAAAATTAGAAACTGTAATGAGGTCTCTTGGGCAAAATTCCATACAGGCAAATTACTGTCTCTACAAAGCATTTCTGCCACACTTAATTCACCATACCCTGAACAAAATGTGCCATCTTCATTGTTCAGGTCTGTATAGTGCTGGTTTCCCTGCCTGGGcagctcactccatcccatcccagcccaatccccatccctccacctcccccttccctccccactcTCATACAACTCTTCCTTATCTTACAGGACTTGGCTTCAATGTCACCTTAACTGGAAGCTTCTCTCCCTCTCCAGAAGAGCTTCCGATTGCACTTGATGCATGCACTATTATTTGATCATTTTTGAGTTACAGTCCAAGTCTTTTTGTACCTGAATAACATGTTGCCCAGTCAGTTTCTCTTCCTGGATTCAGAAG TCTTTCATGGTAGGTCCAGCTAGAAGTGACAAAAAGACATTTAAAAAAAAAAAAAAAGAGGGATGACACAGACAGACATCAGCACTTAAAAGTTTTAAACGATATGTGAAAAACAAAATTTAAGGGCTTCTAGGAGAAATGTAGGAGGGAAGGTGTTACTGGGAAATATGATAGAAGGTTAAtttttattttattttatttttagagaaagggtcttgctctatcacctaggctggactgcagtggtgcaatcacagttaactgcagcctcaacctccagggcttgagcaatattcccatctAAtttttattttgtttaag +s panTro2.chr1_random 7199179 3214 + 9420409 aacctccacctcccgggttcaagcaattctcctgcctcggcctcccgagtagctggaattatagggatgtgccacaatgcctagctaactgttgttatttttagtagaaacggggtttcaccatgttggtcaggctggtctcaaactcttgacctcaagtggtccatgtgcctcagccttccaaactgctaggattacaggagtgagccactgcacctggccccaaccacattttttgaggcttggaactttcagcctcacctgctgaactccaggaggtaaaaggaactggagattgacttaactaccaatggccaatgattttatcaatcatgcctccataaacacccaaacagcagggtttggagagcttctgtgttgctaaacacaaggaggtcctgggagggtagtgtgcccaacagaggacatggaagctctgtgcccctccccactt----------gtgcatctctttcattggctgttcctgagatggagccattacattgagccagtaatagaaaataaggtggccagatgcgctggctcatgcccgtaatcccagcactttgggaggcagagatgggcggaatcacttgagcctaggaatttgagaccaacctgggcaacataaaaagaccccatctatacaaaaaataaaagaaattagccaaatgtggtggtgggaaccctgtaattccagctacttgagaggctgaagcaggagaatcacttgagccctggaggttgaggcttcaatgagctatgattgcagcactgcacacaagcttggacaacagagcgaggccctgtctcttaaaaagaaaagaaaaaaaacctgtttttctaagttctgtgagttgttctagtaaataattaaactcaagaagagggtcatgggaaaccctgatttctaactggttggtcaaaatacaggtgac aacctaggacttgcaactggcatctgaagtgagggtggtcttgtgggactgagcccctaacctgtgggttctgtgctaactctaggtagtgtcagaatggaattgtgggatacgca-ttggtatccagagagttggagaactggtgtagaaactctgcacacaaatttggtcagaagtctgtgagtagagagaaacGtgttgcaggaagtcagggaccccaaacggagggaccggctgaagccacggcagaagaacataaattgtgaagatttcatggacatttattagttccccaaattaatacttctataatttcttaggcctgtctttactgcaatctccaaacataaattgtgaagatttcatggacacttatcacttccccaatcaatacccttgtgatttcctatgcctgtctttactttaatctcttaatccggtcatcttcgtaagctgacgatgaatgtccccgcaggaccctgtgataattgcgttaactgcacaagttgtttaaacaatatgaaacctgggcaccttgaaaaaagaacaggataacagcaatttcagggaacaagggagataaccttaaactctggctgcctgtgggccgggtggaacagagccatatttctcttctttcaaaagcaaataggagaaatattgctgaattctttttctcagcaaagaacatccctgagaaagagaatgcatccctaaggggaggcctctgaaatggccgctttggggacggctgtcttttacagtcatagataagggatgaaataagccctgggttcgcgtggcgctcccaggcttatcaggacaaggaaattcccgcctaataaattttggtcagatg-----tctgctctcaaaccctttctcctgataagatgttatcaatgacaatgcgtgcccgaaacttcattagcaattttaatttcgccccggtcctgtggtcctgtgatcttgccctgcctccatttgc cttgtgatattttattaccttgtgaagcatgtgatctctgtgacccacaccctattcgtacactccctcaccttttgaaaatcactaataaaaacttgttggttttgcagcttggggggcatcacggaacctgccgacatgtgatgtctcccctggacatccagctttaaaatttctctcttttgtactctttccctttatttctcagactggctgacactcagggaaaatagaaaagaacctacatgaaatatcaggggtgaatttcccccgataTCACACGGGCTCTTCTCTCACCTGTCTACCTGCTTAA-----TAGgagaggcaatgcatggtgctcatgaacgaggcaagcattaaagtcagaccagactaacatttgactcagtcctaatattcaggtgagcttgggcaaatcgctcattaaccccaagtcttcatcattttgtgcatataatggggataactgtggcacccacctgtttttgtgagaatcaatgagatattatgcttgATGTTATTGTGATCATGATACTATCTGACAAGGGCAGTGATGCATGATAACGTCAAAAAATTAGAAACTGTAATGAGGTCTCTTGGGCAAAATTCCATACAAGCAAATTACTGTCTCTACAAAGCATTTCTGCCACACGTAATTCACCATTCCCTGAACAAAATGTGCCATCTTCATTGTTCAGGTCTGTATAGTGCTGGTTTCCCTGCCTGGGcagctcactccatcccatcccagcccaatccccatccctccacctcccccttccctccccactcTCATACAACTCTTCCTTATCTTACAGGACTTGGCTTCAATGTCACCTTAACTGGAAGCTTCTCTCCCTCTCCAGAAGAGCTTCCGATTGCACTTGATGCATGCACTATTATTTGATCATTTTTGAGTTACAGTCCAAGTCTTTTTGTACCTGAATAACATGTTGCCCAGTCAGTTTCTCTTCCTGGATTCAGAAG TCTTTCATGGTAGGTCCAGCTAGAAGTGACAAAAAGACATTT-AAAAAAAAAAAAAAGACGGATGACACAGAAAGACATCAGCACTTAAAAGTTATAAACGATATGTGAAAAACAAAATTTAAGGGCTTCTAGGAGAAATGTAGGAGGGAAGGTGTTACTGGGAAATATGATAGAAGGTTAAt-----ttttattttatttttagagaaagggtcttgctctatcgcctaggctggactgcagtggtgcaatcacagttaactgcagcctcaacctccagggcttgagcaatattcccatctAATTTTTATTTTGTTTAAG + +a score=112167 +s hg18.chr1 145996 1215 + 247249719 aaatgcagtcttgctcttagcaaagctaaagtgcaatggtgtgatcatagcttactgcagcctcaaccttctagactcaagtgatcctccagtcttagcctccccagtagctcggactacaggtgtgcactgcaacgtgtagctcattttttttttttaatttttagtagagacaaagtgtcactatgttgaccaggttggtggtgatctcctacactcaggcagttctctcacctcagccttccaaaatgctgggattacaggtgtgagctgccacacctggctGAGGGGGTTAATTTTTAATTATATAAAGAGCTCAAAGCaaatattagaaggagcctaaatgcctccagcagttgactggtactggtaaattgtgatacatccatataataaaatattatgcaaccatgaaaaggattaagatagatcaataggtattgGCACAAATGTCCACGAAATATGAAAATATGAAGTGATGTTCAATCACCATGTACGTATCTTGAAGGATATGGCCCATTTTCTCAACTGCAATTATTTCCTGAGATAAGATTATGGGTCTAAAGAGTGAAGGACATTTTTCACttatttaaaagtatttatcatttttataatttaataaaaGATTAAACAGATCATTGAATTAGTAAAAGACAAAGTAACTCTATAAATAAATGGAAAAGACACAGATACCccaggcatggtggctcatgcttataataccagtactttgggagggggtggtggggggattgcttgaggccaggagttccagaccagcctaagaaacaaagcaagacctcctctctagtaaaaataaaaaaataaaaataattggccaggcatagtggcatgtgcctatagtcccaactactgaggtggaaggatcacctgagcctaggaggtcaaggctgcagtgagttgagactgtgccactacact gaagcctaggagacagagcgagacttcatctcaaaaaaaaaaaaaaggacaataaagaaaTAAAGCTAATAAGCTAACATAAGGAAAGATAAAATATGTGACAAATAggctgggcacatggctcacagctgtaatcaagcactttgggaggccaaggcgggtagatcttgagatcaggagttcgagaccagcctgatcaacatggtgaaaccacgtttctactaaaaatacaaaaattaaccaggcatggtggcatatgcctgtaatcccagc +s panTro2.chr1_random 7208475 1214 + 9420409 aaatGCAgtcttgctcttagcaaagctaaagtgcaatggtgtgatcatagcttactgcagcctcaaccttctagactcaagtgatcctccaggcttagcctccccagtagctcggactacaggtgtgcactgcaatgtgtagctcatttttttttta-aatttttagtagagacaaagtgtcactatgttgaccaggttggtggtgatctcctacactcaggcagttctctcacctcagccttccaaaatgctgggattacaggtgtgagctgccacacctggctGAGGGGGTTAATTTTTAATTATATAAAGAGCTCAAAGCaaatattagaaggagcctaaatgcctccagcagttgactggtactggtaaattgtgatacatccatataataaaatattatgcaaccatgaaaaggattaagatagatcaataggtattgGCACAAATGTCCACGAAATATGAAAATATGAAGTGATGTTCAATCACCATGTACGTATCTTGAAGGATATGGCCCATTTTCTCAACTGCAATTATTTCCTGAGATAAGATTATGGGTCTAAAGAGTGAAGGACATTTTTCACttatttaaaagtatttattatttttataatttaataaaaGATTAAACAGATCACTGAATTAGTAAAATACAAAGTAACTCTATAAATAAATGGAAAAGACACAGATACCccaggcatggtggctcatgcttataataccagtactttgggagggggtggtggggggattgcttgaggccaggagttccagaccagcctaagaaacaaagcaagacctcctctctagtaaaaattaaaaaataaaaataattggccaggcatagtggcatgtgcctatagtcccaactactgaggtggaaggatcacctgagcctaggaggtcaaggctgcagtgagttgagactgtgccactacact gaaacctaggagacagagcgagacttcatctcaaaaaaaaaaaaaaggacaataaagaaaTAAAGCTAATAAGCGAACATAAGGAAAGATAAAATATGTGACAAATAggctgggcacatggctcacagctgtaatcaagcactttgggaggccaaggcgggtagatcacgagatcaggagtttgagaccagcctgatcaacatggtgaaaccacgtttctactaaaaatacaaaaattagccaggcatggtggcatgtgcctgtaatcccagc + +a score=1066337 +s hg18.chr1 147211 11682 + 247249719 taATAGGAGGTCTTTCATTTATCACACAGAAAATAACTTGTTAAATTataatacctgtgtgggcgaaggtgcagtgaaatggccattttcttgtagtattagtggtgtttaaaatgtatataagccttccagcataaagcttggaaattttttttaaatcatacagacagtgactcattatactgcctcctccaactcctggcctcaagcaatcctcccacctcagcctcccaaagtgctggaattacaggctgacagccaccatgcctgaaagctttgcaatttacatcgagggtaataagaatgctcatgccctgtgactcacagtaatctcacttctggaaatttcacctttggatataattcaacctaaacaaaaggtcatatgcacaaACACAGTGAAAATCTGGGAGTAATTTTTTTCTCTTTTTTTAAaaaaatatggaatgcttcacaaatttgcatgtcattctttcacagaggccgtgccaatctctctattgttccaacttaagtatgtgtgctactgaggcaagcaTGAGTAATTTAAGATAGGGTGGTTAAGTGAAATAAGGAAGAATTATGGAGAATTTAAAAATCTATGCTATTTATAggcacctagtaacagctcagtaaatattagctgctactattATTATTTTTATGGTAATTTCACTCAATTAAAAACTGTCGTTAAAAATTGCCATTGTCATGGAACATAATGTCTCCTACTGTATAATTGTAGAAACAGATACAATttgtcccttggtatatggggggattagttccagctctcccatttctgtgtataccaaaatccacgcatactcaagttttcaaagtcagtcctgtggaatccacatataACACAAATGGGaaaattagtgaggtgtggtgacaagcacctgtagtcccagctacttgtgaggctgaggcaggag gattgcttgagcccaggaggttgaggctgcagtgagccataattgcaccactacactccagtctgggcaacagagtgagacAGAAGGTTGACTTTTTAATAGAATTTTTCTGTTCACTTGAAGATATGGTCAGGATTGTGGCATATGAAAATTCTTCATAAAATAACTATCTAATCCAATTAATGCTGGAATTGGGAACAGCAGAAGTGTCATCTCAGAGCTACTCGCAATGAAAGGTGATGTCTGGGGCTCAGGTGTGTTGAGGTCCCCATGCCTGGACTATGGGTGCTGAGTGGGATTTACTTGTCCATCCATTTTCTATATTCCAGCACTGGGAAACTAGGG-------------------------------------------------------------------------------ACAGTACTTGTTCTCAAGGGAATCTTCAGCTTAGGTGGCTCTGTAAAAGAGAAATTACATCATTGAAAAATCGTCGCAggtcaggtgaggtggctcatacctataatcccagcccactgggagactaaggcaggaggattccgtgaggccaggagttcaagaccagcctgagcaacacagtgaaacctcatctctacaaaaaattagaaaatgaactgggtgcggtaaaacattcgtatagtcccagctactctggaggctgaaataggaggatcgcttgagcccaggaagtggaagctgcagtgagctctgatctcaccactgcactctagccttggtgacagagtgagaccctgtctcaaGacacacacaaacacacacaca--------cacacacacacacCCCCAATCTCACTCTGTCCAGCCTTGACTAATCAAAAGGGCCTTCTGGTTACAGAAGAGGTATGCTCTTTTGTAGGACAGGGAGAGACCAGCAAGCTTGTTCACAGACTTTTCCTCATCCTCTGCTTAGTTTTCCAAGAACCCTCACAGTGGAAATGGAG TCTCTGGGAAAATGACCTAAATCTTTGGGTTACCAGGGGAGAAATATGCCTCCTTTGTCAATTAATAAATGGAACATCTGCCTTAAAATCCAGGGAGTTCTGCTAGAATGAATCACTCCCTAAGACCCTGACCAATGCATGGAACATGAAAAACTGAAGTTTAActgggcgcggtggatcacgcctgtaatcccagcactttgggaggctgaggcgggcggatcacctgaggtcaaaagttctagatcagcctggccaacatggtgaaaccccgtctctactaaaaatacaaaaattagttgggcatggtggtggacacctgtaatcccagctacttgggaggctgaggcaggaaaatcgcttgaacccggaaggcggaggttgcagtTACTTCTAGAAGAATTTCCATTAGCCCTTTGAAATCCTTCAACATTCATGAAGGCCAAAGAGTTTTCACCTAATTTAATCTGATGGGTATGTGACCAGAGTCTTTCTAGGGAATAGAGACTCCCAAACAGTTCGACTGGGAAGTGAGGAGAGAATTTATTACTCAAAACCAAAGGGAAATGAAAAGAGGCCAACATAGAATGTCATTATTCTTTCTTGGCGGGGAATGGATTCCAGAGTCATTCTGTGACCTTTACATGACCTCCTTATTAGCATCTAAAAGCTTCCAGTGTAGGATGCAGCCAGCTAGGTTCTCTTCTAATGTAATAAAATTTGCTTCGGCAAATCTTATGCAGAGCCATCTCCAGGCTCCAGAAACAATAGGCTATAAATTACTGGATCTCCCATTTGATACAATGAAGTATGAGCATGGTCCTGAATGACTCCTCTACATACTACTCTGGGTGGCTTGAAGTGAATTTGATACAAGAACTGGAGCGAGGGCAAAGCAGAGCTAGATCTAGGATTAATGTGCTTGGGCCCAGCTCCTCACTACTCACCTATGAGTCTAGTTCCAGAACCCAAGTAGAGGATGGGGAAAC AAGGCTCCTGACTTTTTTTCCCTAATATCTGCATCTCTTTCACATTTCTTATCTCCTTGCAAAGAAACTAAACAGGCTCAACTGAAATAACTAAATGATTAAACCCTATACAGAGAATCTCCAAAGACTGACAAAATATCATTCAAGACTGTTACACAGACAACCTTGAGGATGACTTGATGTACCAGTGATCTACAATATTTGGGATCATTCCAAATTCCCATCAAGGATCTGCCTATATCAACAAAGGAGCCAAGGACCAACCATTCAAATGGGCCCTGCTGCCAAGCC-TTTTTTTTTTTTTTTTAACAATGCCATCTCTTCATATTGTTCCATTTAACAAAACTGCAGCCCTTCATCTATCCTTAAGTCCCTTGGCCAGTGGTACAGAGCCAGAGTATGCTACTCCCTAGCAGGAAATCAACAGGATGACCTACTAAACACCATTCAGAAGATGCTAAGACCCATGAATTGCAACAGGAAAGAAAAGACAGAGAATTAGTCAGACAGGTACATGCTGTGCCAAAAGTGCACTACAGCCCCCACCCAATTCTGCCTAATCCTAGCTGGGCTGACACCAACCTGATGAGACAGGCCTATAAGATCTCAAACTAAAACAGAAACTCCTGAACTGGGTTCTTTCGAGCCCAGGAAGCAGCAGTAAATCATTAAAGAACAGATAAGTTCTTAAGGTGAGGGAGAGTTTCAGATAAATGGAATGCTGGTAGAACACAGGGCCCAAAGGAGCAAAAGTTAACCTAAGCCCAGGTAGAACCTTGTTTACTAGAGTATTAGGCATGGGTTTGGGCAACTATTCTAACCAGAGAAACTGGCTTCAGTGAGGGCAAGTTGGCAATCCAAGGTATAGCATGCATAGGGCTGGCAAAATTCAGGGTGACTGAAGCAAAAGCTTCATAACCAGAAAGACCACATCTGGGGGTAGAGCACAAAACTCTCAAGAGATGAATCTTTGTAAGAGTGAGGCAGA ACTATATAGCAGTTTTAGGAGATCTGTTGGTGCCCAGCAAGAGCTCCAAACGGGCTATATGCAGGGATGCAGGCTGTAGTCTCAGGAGAGGAGGTTCACAAAAGTCATTCAGTCCAAGACCTCAAACTGTGttctctactaaaaggaatcaaggttccctagagaaatggctgactccatgtatggtgcagtatattgatcctggaacatc-tgttttgccagaaagcaaggaagccatcaaagtccaacaggatcacttcaaaaagacatgaaagtcaacttgaagagataattattaacctagatgagacaatctaagcatccaaaacaataaagactgcaatggcctgaaatacatcaaatgcaaacaataatctatgagttcataatggtattcagaaaaaaaaactactggtcattagagggaaggttactaggtcactaacttactactctgaaaagtgACTTAAGATGAGAGGTAGGGTGGAAAATTAGCTATTTATTCAGTCTTTCCTGTACAAACATAAATTTTTAGGGAGATtgaagcagatgaaacaaatctggaaaaatggaggtaactgcttaatctgcgggttgggtgcatggaggttcaacatatttcttttgtgtatatttgaaCCCCCTACAAAAAAAGCACAAGAGAGAATGTGAGCCAAGCAGCTTAGGGTTTAGGCAAGGCTTCTGCCTACAAGAGACACTAGGATATGAGGGGTAGTTTTAGCCCTAATGGGCTGAGCCAACTGGAGGTATATAGGGAAGTGCTAAATTGCAGAGGTATCATGTTGCCCAGCACTTGATCAAATCCTAGATCCTAGGTCTGCTTGGTAGCATGCTTCCTAGGTAGTGGATCTGAGGCTACCTATAGAACTTCCTTTGCAGTCATAGTTCGCTCAGAAACTACAAAAGTGCTTGCTCTTGAAAATGGAgtctttgtccatttcatgcttctataaaagaataccacaga ctgcataatttataaaaaggaaaaaaggaaggaaagaaaaaaggaagggaggagggaaggagggaaaaagggaaggagggaaggaaaggaaggaagggaaagaaggaaaggaaggaagggaaagagagaaagagggaaggaggaagggagggaaggagggagggagggagagagagagggagggaggggaagggaagaaaagggaagagaagggaaaggaggaagaaaaggaaaggAaaggaataaattttatttcttaacagttctggatgttaggaagtccaaggttgaggggcctgcatctggtaaaggtcttcttgctgcatcatcccactacagaaggcagaaggaaaagagagtgcaagaaagcaagagggcaaaaggggctgaactctgttttataataagcccactctgtgattactaatctattaccacaataacaacattaactcattcatgaaggctattttattaggccccacatcccaactgttgcattgaggattgagtttccagcacataaactttgggggacacatttaaaccatagcaGAGCACTTAGGTTAATTCAACTAAGAGGAGCTGGGAAAATCAAAGGCATGAGAAAGACAGCAAAAGCTAGCAGAGAGAAATGCATAGGTTAAGGAAAAAAGTCACAGTGAATCCTGTAGTGCAGGCTACTTTATGAAAAGCACCTAAAAAAGATCTCATTAACTCCCCCAGCTCACCTCCACGCACATCTAAAGAGCCACACACAGCACCACCAAAGGCAGCACAATGAGAACAGCATTCTCCTCAACAGACAAGCTGGGAGTATCTAGACACCCGACCTCAATAGCTCCAGAACAGCCCTAAAACATTTCCTCCCTAACCACCACTCAAGTCACCAGCTTGGAAAGTATTAAGAAAACCCAAATCCTGACACACCACTATGAAACAACTTAAAACAGCAAAGAACAACCCATTTAAACAGCAATGCCAGCTGT TGGGAAAAAAAGGAACAATGAGTAGAGGAGAAACAGACCTCTCGGGGTCCACCAAGACCCAGTCTCTCAGCTTCAGCACTTTTAAATGCAGAATCCATACCCCTCTGGGGCCTGTGGAGCTCCACAAGGCATGTCGTCCTCAAAGATAAATGAGCAGGCAAGCTGGCTAGAAAACCACTAAGGGTATTTATTCTTTAAAGAATCTTTACAGGGTCAAAGAAGAATGGGTCTTAACTGGCTATGTGAACTCCCCACAGATTCTGAGGATGATGTCAGTATCCCTTTCCAGATGTGTTTAACACTTTGCAGTCACTTGTATTCCTGCTACTGAGTGCCAGTGCTTTGCTAATTTGAACTGATTCCAGCTCACGCTGACCCCAGCTCCCTGGATGTTACCATTAGCCAAGACTGTCACCCATACTGTACCCTTTCAAAGAGTCCTAAAAACAGCTCTTCACCTACTCTTCCAAGACAAGTAAAAATGTCTGCCAAAGAAATGGGGAAAAAAGATTCAGAGAGTGAAAACAATTAATATACTAACAAGAGAGCAAAAAGCAAAGGGGGAGGAGAAACTAGGAAAATCATATATGGGCTCTCACCTATTTCCAAAGCTGGGCTAATGTCCTTTTGCTTGTGTCTGAATAAGGCACCAATTTTAAGCTGATAATGAAAAAAAAAGAAAAAGAGAAAGAAGCAGGCCCAggctgggcgcagtggctcatgcctgtaatcccagcactttgggaggccgaggcgggtggatcacccaaggtcaggagttctagaccagcctggtcaacatggtgaaacaccatctctactaaaaatacaaaaaattagccaggcatggtggcgcatgcctgtaaatccagctactaaggaggctgaggcaggagaattgcttgaacctggaaggcagagaatgtggtgacctgagatcacgtcattgccctcaagccacggcaatgagaacaaaattcggtAaaaac aaaacaaaacaaaacaaaaTCACCATAAAATAACTCAGACTTAATTAAATACAACCCTAGTGGTGAATGACTAAAGATGGATTACTCATAACAGAGACAACAGTCCAATAAGAATCCAGGAATCTTACCTTTTAATAAC-AAAAAAATCCTTTCCTTCTAAAGTAACATCCTCTCAAGGCCAGGAATTCCATTAGTAGAAAGCCTTCCTAAAAAACAAAATTCCTggccaggcatgggttcacgtctgtaatctcagcactctgggaggccgaggcgggaagatcacttgatatcaggagtcgaggcgggaagatcacttgacgtcaggagttcgagactggcccggccaacatggtgaaaccgcatctccactaaaaatacaaaaattagcctggtatggtggtgggcacctgtaatcccagtgacttgggaggctaaggcaggagaatttcttgaacccaggaggcagaggttgcagtgaccagcaaggttgcgccattgcaccccagcctgggcgataagagtgaaaactccatctcaaaaaaaaaaaaaaaaaaaaaaTTCCTTTGGGAAGGCCTTCTACATAAAAATCTTCAACATGAGACTGGAAAAAAGGGTATGGGATCATCACCGGACCTTTGGCTTTTACAGCTCGAGCTATAAGAAAAAAAAGAAAAAGGGATATCATTTAAACACAGTATGTAGAAAAGAATAATTATTGAATCTGTACTGGTCTTTAACTTTTACACTTTGATCTTTAATTCTGTTATTGTGATTGAGTCCAAAGAAAAACAGTATGAGTAAAATAAAAAGAACACCAAAAATGCTAATATTCTGTTTACCGAAGTCTGTAGTGAAATATCCCATTAAATccaagtgcagtgacacacccataatcccaagcactttgggaggctgaggcgggtgaatctcctgaagtcaggagttcaaggccagcctggccaacatggtgaaaccccaactctac tacaaatacaaaaattaggcaggcgtggtggcagaggcctgtaatcccagctacttaggaggctgaggcagggagaattgcttgaacacaggaggtgagcttgccatgagctgagatcataccactgcactccagcgtgcgtgacagaacaaaacttcaacctcc-aaaaaaaaaaaaaaaaaaaaaaaCAGCTAGCAGGTGACATTTGCTATAGGGAGACTAGGGATATGATCTTGCTGCAATCTTTCCATTTTAGTAAATCTAAACAAGTGTGAATCCATTCTGTTTCGTCCCCACTCCACTCCAGAGCCAAAACAAGAAAAACAATTATATTTCTAGTTCTTTAAAAACATATCTAACTAAATCATCTAATTAAAAGATAATATGCATGGTTCCATACTCTAAAAGAAAACTTATGTCCTGCATATCATGGACATTTGATGAATGCTTATTCAGTTGACTGGTGTAGACTTCAATAATAACCTGTTCAATGCATTATGCCAGATGAATCTTGCATCTCAAAAGTAGAACAAATATTGTTCTTTCAGTTTTGTCTACCCATAAATGCAATATTTACTAATAAAAAGAAAATGAGTTTATTGTTCTAGAGAGTATGAGAATTTTGACAACATGAATTCTCCTGTCCTAGGACATAATTAATACTTAGAGGCATACTATTTCATGTGGAAGCTACCATTAAATCAATGTTAAGTGTTAATTACCTCACATAATCTTCTAATCTGACTT--GACTGAAGACGTACCTGACAAAGTTGATTTATCAAGTTGTAAATCTTCACCTGTTGAATTCATAAGTTCATGTCTGAAAGGTGAGAATAAATACTTAATATTCATTAGGCAATATTCAGCAAAGTAATATCCACTAGTACATATTTAATATTTCATCATGAACTGCGGGTGTGAAGAGAAAGGACAggctgggcacagtggctcacacctgtaatcccagcagtttgggaggccgaggc aggcagatcatgaggtcaggagttcgagaccagcctggccaacatggtaaaaccccgtctgtactaaaagtacaataattagctgggcatggtggcaggcacctgtaatcccagctactcgggaggctgaggcaggagaattgcctgaacccaggaggtggaggttgcagaaaccattatcacgccactgcattccagcctgggcaagagagcaagattctgtctcCATCAATCAATCAATAAAAATATAAGAAGGAAGcatttactgtgtatttatatgtctggtattatgtgaagcactttactatcttatcaaatcttcgggacagatcttcagttctcatgaccacaaaagaggatactaaagctcagacaggagaagagacgtggccaGCCTGTGTCCCCAGGGCCTATGGTCTTACCACTAGGTTACAGTGTTTCCAGATATCACATGTTGTGAGATTTTTGCTTTAAAATGAACCAAAAAAAAACCAAAGGTGAAAAAGGCATAAGCTATTAAAAAGTGGGAGAAACACTAAGAGAACCTTAAGCATGTAACTAAAAATATTATGGAAATGTTATTGAATACATTAGCAAATTTAGTGCTAGGTTTTCATTGAGGAGTAGGTTATATTACTCATGATGAAGAAAAATGTTCATTTTAAGTATATTAACATAAATACCATCAATATTGTTTATCATGTTTAAATGTTCACTTAAAGCAATTCAGTTAAAATTCTGCATATCATACAATTTTATAGTTTGCTAGTAGGTTACAAGTAAATAGTCACCCAAATAAAAACATCATGTTTTCCACTGGTTGTTGCTCTTTTTTAGGTGAGTATTTGATATATACCAACAGAGAGAGGATAATAACAAATCGCTAATTTCTTTCATCACTATATAAAGGTGGCTTCAGGATAGAATAGTATCAGTGTAATGATGAATTTGAAATCTAACATCAATTCAGTGATGCATCAAGATAAAAG TAGAGACAACAGGGGCACCTTGGTGAGTACTGAACAttttatttatttatttattttgagatggagttttgctctttttgcccaggctacagtgcaatggtgccaacctcgcctcactgcaacctctgcctcctgggttcaagcgattctcctgccttggcctcccgaatagctgggattacagacatgcgccaccacacccgtctaattttgtatttttagtagagacggggtttctccatgttggtcaggctggtctcgaactcccgacctagatatctgcctgccttggcctcccaaagtgctgggattacaggtgtgagccaccacgcccagATGAATTCCAAATTTAACAAAGCAGACTAAGAGAAACAATTCATTTAAAAAAATAATATTTggccaggcatggtggctcacacctataatcccagcactttgggaggctgaggtgagtggatcaggaggtcagcagttcaagaccagcctagccaagatcatgaaaccccgtctctactaaaaatacaaaaatcagccaggcgtggtggctggtgcctgtaatcctagctgctcgggaggctgaggcagagaactgcttgaacccgggaggcggaggttgcagtgagccgagatcgtgccactgcactccagcctgggcgacagagtgaggctccgtctcaaaaaaaataaataaaTAATTCAATGAAATTCCTAAGATCCAGGGCTTTGCAATAAATATGTAAATAAATTTCCAATCTCCATACTGAAAGTTTAAAAGAAATGCTAACTAATAACTAAAGAAATACAACTTTTCCTCAGCTTTGCAGCAATCTAGAAACAAAGTGTGTAGACACTACAAAGCACCTTACAAGGAGAAACATGTAAGGATGGCATGACTCGCCGGCAGCCCTGGGATTGTCCACGGTACCCCCATGATGAACAGTAACTCCACTGTGTAAACGCCCATGAACCTAAGATTACAAGACTTTTCC AGTTTAGACATACCATATTTTCTTTCAGACAATTCTTCAGTTTGTTTACGTAGATCAGCGATACGATGATTCCATTTCTCTGAAAACCAAGCAAAAGTTGCTTCTCAATAACACGTCCCTATGTCAGAGCAGCACTAACATATAATGACTGATTTCATATATTTTACATTCTAACAGTCCATATCATTTTACTGCTTTCAAGAAAAAATTTCCCCTTCTTGGTGGTTCTTAGAATTGGTTTAATGGGAGACTATTAGAGAAGCTGAAAAGCAGGAGGGCAGAAAAGCTCAATCAAATTAAACACAATAACAGGGAGGTCACAATGAGGCGGTCTCCAGGGGTCTTTTAGCAAACTTCCTAAAACATGTCTCAGCTGTGTGAAATAAGACTTTACAGCagccgggtgcagtggtgcaggcctgtaatcccagcactttggcagcagaggcaggcggatcactttgagctcagggcaacatagccaaaacccccctccctagccccacccccaccccgtccctaccaaaaatacaaaacagcagggcatggtggcgggcgcctgtagtcccagctactcaggaggctgaggcaggagaatcacctgaacccaggaggcagacattgcagtgagccaagatcacgccactgccagcctggatgacagagcaagactccacctcaaaaaaaacaaaaacaaaaaCACAAGGTTAAGAGGGACCCCCGACCTTACAGATACAAGTTTAAGAGGGACCCCTAAGCAAAAAATGCCAACCCTTTTTCTCCCAATCATTGAAACACCAGGAGGGTGTAACAGTTTTGCAGCCTAGCtgtagcaggctgatgcccccaagatgcccatatcctaatcccgggaactagtgaacatgaccttat-atggcaaaaggaactttgcagatataatgaagttaagggtctttggcttt +s panTro2.chr1_random 7209832 11753 + 9420409 TAATATGAGGTCTTTCATTTATCACACAGAAAATAACTTGTTAAATTacaatacctgtgtgggcgaaggtgcagtgaaatggccattttcttgtagtattagtggtgtttaaaatgtatataagccttccagcataaagctgggaaattttttttaagtcatacagacagtgactcattatactgcctcctccaactcctggcctcaagcaatcctcccacctcagcctcccaaagtgctggaattacaggctgacagccaccatgcctgaaagctttgcaatttacatcgagggtaataagaatgctcatgccctgtgactcacagtaatctcacttctggaaatttcacctttggatataattcaacctaaacaaaaggacatatgcacaaACACAGTGAAAATCTGGGAGTAATTTTTTTCTCTTTTTTAAAaaaaatatggaatgcttcacaaatttgcatgtcattctttcacagaggccgtgccaatctctctattgttccaacttaagtatgtgtgctactgaggcaagcaTGAGTAATTTAAGATAGAGTGGTTAAGTGAAATAAGGAAGAATTATGGAGAATTTAAAAATCTATGCTATTTATAggcacctagtaacagctcagtaaatattagctgctactattatTATTTTTATGGTAATTTCACTCAATTAAAAACTGTCATTAAAAATTACCATTGTCATGGAACGTAATGTCTCCTACTGTATAATTGTAAAAACAGATACAATttgtcccttggtatatggggggattagttccagctctcccatttctgtgtataccaaaatccacgcatactcaagttttcgaagtcagtcctgtggaatccacatataACACAAATGGGaaaattagtgaggtgtggtgacaagcacctgtagtcccagctacttgtgaggctgaggcaggag gattgcttgagcccaggaggttgaggctgcagtgagccataattgcatcactgcactccagtctgggcaaaagagtgagacAGAAGGTTGACTTTTTAATAGAATTTTTCTGTTCACTTGAAGATATGGTCAGGATTGTGGCATATGAAAATTCTTCATAAAATAACTATCTAATCCAATTAATGCTGGAATTGGGAACAGCAGAAGTGTCATCTCAGAGCTACTCACAATGAAAGGTGATGTCTGGGGCTCAGGTGTGTTGAGATCCCCATGCCTGGACTATGGGTGCTGAGTGGGATTTACTTGTCCATCCATTTTCTATATTCCAGCACTGGGAAACTAGGGTTTATCCATCTTGGTAAGATGTCATTTAAATTCCACTTCGCAAGAACCACAAATGGAAGAAAGGCCATGAAACCGCAGGACAGTACTTGTTCTCAAGGGAATCTTCAGCTTAGGTGGCTCTGTAAAAGAGAAATTACATTGTTGAAAAATCGTCGCAggtcaggtgaggtggctcatacctataatcccagcccactgggagactaaggcaggaggattccgtgaggccaggagttcaagaccagcctgagcaacacagtgaaacctcatctctacaaaaaattagaaaatgaactgggtgcagtaaaacattcgtatagtcccagctactctggaggctgaaataggaggatcgcttgagcccaggaagtggaagctgcagtgagctctgatctcaccactgcactccagcctcggtgacagagtgagaccctgtctcaaGATacacacaaacacacacacaaacacacacacacacacacacacCCAATCTC----TGTCCAGCCTTGACTAATCAAAAGGGCCTTCTGGTTACAGAAGAGGTATGCTCTTTTG----------AGAGACCAGCAAGCTTGTTCACAGACTTTTCCTCATCCTCTGCTTAGTTTTCCAAGAACCCTCACCGCGGAAATGGAG TCTCTGGGAAAATGACCTAAATCTTTGGGTTACCAGGGGAGAAATATGCCTCCTTTGTCAATTAATAAATGGAACATCTGCCTTAAAATCCAGGGAGTTCTGCTAGAATGAATCACTCCCTAAGACTCTGACCAATGCATGGAACATGAAAAACTGAAGTTTAActgggcgcggtggatcacgcctgtaatcccagcactttgggaggctgaggcgggtggatcacctgaggtcaaaagttctagatcagcctggccaacatggtgaaaccccgtctctactaaaaatacaaaaattagttaggcatggtggtggacacctgtaatccgagctactcgcgaggctgaggcaggaaaatcgcttgaacccggaaggcggaggttgcagtTACTTCTAGAAGAATTTCCATTAGCCCTTTGAAATCCTTCAACATTCATGAAGGCCAAAGAGTTTTCACCTAATTTAATCTGATGGGTATGTGACCAGAGTCTTTCTAGGGAATAGAGACTCCCAAACAGTTCAACTGGGAAGTGAGGAGAGAATTTATTACTCAAAATCAAAGGGAAATAAAAAGAGGCCAACATAGAATGTCATTATTCTTTCTTGGCGGGGAATGGATTCCAGAGTCATTCTGTGACCTTTACATGACCTCCTTATTAGCATCTAAAAGCTTCCAGTGTAGGATGCAGCCAGCTAGGTTCTCTTCTAATGTAATAAAATTTGCTTCGGCAAATCTTATGCAGAGCCATCTCCAGGCTCCAGTAACAATAGGCTATAAATTACTGGATCTCCCATTTGATACAATGAAGCATGAGCACGGTCCTGAATGACTCCTCTACATACTACTCTGGGTGGCTTGAAGTGAATTTGATACAAGAACTGGAGCGAGCACAAAGCAGAGCTAGATCTAGGATTAATGTGCTTGGACCCAGCTCCTCACTACTCACCTATGAGTCTAGTTCCAGAACCCAAGTAGAGGATGGGGAAAC AAGGCTCCTGACTTTTTTTCCCTAATGTCTGCATCTCTTTCACATTTCTTATCTCCTTGCAAAGAAACTAAACAGGCTCAACTGAAATAACTAAATGATTAAACCCTATACAGAGAATCTCCAAAGACTGACAAAATATCATTCAAGACTGTTACACAGACAACCTTGAGGATGACTTGATGTACCAGTGATCTACAATATTTGGGATCATTCCAAATTCCCATCAAGGATCTGCCTATATCAACAAAGGAGCCAAGGACCAACCATTCAAATGGGCCCTGCTGCCAAGCCTTTTTTTTTTTTTTTTTTACAATGCCATCTCTTCATATTGTTCCATTTAACAAAACTGCAGCACTTCATCTATGCTTAAGTCCCTTGGCCAATGGTACAGAGTCAGAGTATGCTACTCCCTAGCAGGAAATCAACAGGATGACCTACTAAACACCATTCAGAAGATGCTAAGACCCATGAATTGCAACAGGAAAGAAAAGACAGAGAAATAGTCAGACAGGTACATGCTGTGCCAAAAATGCACTACAGCCCCCACCCAATTCTGCCTAATCCTAGCTGGGCTGACACCAACCTGATGAGACAGGCCTATAAGATCTCAAACTAAAACAGAAACTCCTGAACTGGGTTCTTTCGAGCCCAGGAAGCAGCAGTAACTCATTAAAGAACAGATAAGTTCTTAAGGTGAGGGAGAGTTTCAGATAAATGGAATGCTGGTAGAACACAGGGCCCAAAGGAGCAAAAGTTAACCTAAGCCCAGGTAGAACCTTGTTTACTAGAGTATTAGGCATGGGTTGGGGCAACTATTCTAACCAGAGAAACTGGCTTCAGTGAGGGCAAGTTGGCAATCCAAGGTATAGCATGCATAGGGCTGGCAAAATTCAGGGTGACTGAAGCAAAAGCTTCAGAACCAGAAAGACCACATCTGGGGGTAGAGCACAAAACTCTCAAGAGATGAATCTTTGTAAGAGTGAGGCAGA ACTATATAGCAGTTTTAGGAGATCTGTTGGTGCCCAGCAAGAGCTCCAAATGGGCTATATGCAGGGATGCAGGCTGTAGTCTCAGGAGAGGAGGTTCACAAAAGTCATTCAGTCCAAGACCTCAAACTGTGttctctactaaaaggaatcaaggttccctagagaaatggctgactccatgtatggtgcagtatattgatcctggaacatctttttttgccagaaaggaaggaagccatcaaagtccaacaggatcacgtcaaaaagacatgaaagtcaacctgaagagataattattaacctagatgagacaatgtaagcatccaaaacaataaagactgcaatggcctgaaatacatcaaatgcaaacaataatctatgagttcataatggtactcagaaaaaaaaaatactggtcattagagggaaggttactaggtcactaatttactactctgaaaagtgACTTAAGATGAGAGGTACGGTGGAGAATTAGCTATTTATTCCATCTTTCCTGTACAAACATAAATTTTTAGGGAGATTGAAGCAGACAAAACAAATCTGGAAAAATGGAGGTAACTGCTTAATCTGCGGGTTGGGTGCATGGAGGGTCAACATATTTCTTTTGTGTATATTTGAACCCCCTACAAAAAAAGCACAAGACAGAATGTGAGCCAAGCAGCTTAGGGTTTAGGCAAGGCTTCTGCCTACAAGAGACACTAGGATATGAGGGGTAGTTTTAGCCCTAATGGGCTGAGCCAACTGGAGGTATATAGGGAAGTGCTAAATTGCACAGGTATCATGTTGCCCAGCACTTGATCAAATCCTAGATCCTAGGTCTGCTTGGTAGCATGCTTCCTAGGTAGTGGATCTGAGGCTACCTATAGAACTTCCTTTGCAGTCATAATTCGCTCAGAAACTACAAAAGTGCTTGCTCTTGAAAATGGAgtctttgtccatttcatgattctataaaagaataccacaga ctgcataatttataaaaaggaaaaaaggaaggaaagaaaaaaggaaggaaggagggaaggagggaaaaagggaaggagggaaggaaaggaaggaagggaaagaaggaaaggaaggaagggaaagagagaaagagggaaggaggaagggagggaaggagggagggagggagagagagagggagggaggggaagggaagaaaagggaggagaagggaaaggaggaagaaaaggaaaggAaaggaataaattttatttcttaacagttctggatgttaggaagtccaaggttgaggggcctgcatctggtaagggtcttcttgctgcatcatcccactacagaaggcagaaggaaaagagagtgcaagaaagcaagagggcaaaaggggctgaactctgttttataataagcccactctgtgattactaatctattaccacaataacaacactaactcattcatgaaggctattttataaggccccacatcccaactgttgcattgaggattgagtttccagcacataaactttgggggacacatttaaaccatagcaGAGCACTTAGGTTAATTCAACTAAGAGGAGCTGGGAAAATCAAAGGCATGAGAAAGGCAGCAAAAGCTAGCAGAGAGAAATGCATAGGTTAAGGAAAAAAGTCACAGTGAATCCTGTAGTGCAGGCTACTTTATCAAAAGCACCTAAAAAAGATCTCATTAACTCCCCCAGCTCACCTCCACCCACATCTAAAGAGCCACACACAGCACCACCAAAGGCAGCACGATGAGAACAGCATTCTCCTCAACAGACAAGCTGGGAGTATCTAGACACCTGACCTCAATAGCTCCAGAACAGCCCTAAAACATTTCCTCCCTAACCATCACTCAAGTCACCAGCTTGGAAAGTATTAAGAAAACCCGAATCCTGACACACCACTATGAAACAACTTAAAACAGCAGAGAACAACCCATTTAAACAGCAATGCCAGCTGT TGGGAAAAAAAGGAACAATGAGTAGAGGAGAAACAGACCTCTCGGGGTCCACCAAGACCCAGTCTCTCAGCTTCAGCACTTTTAAATGCAGAATCCATACCCCTCTGGGGCCTGTGGAGCTCCACAAGGCATGTTGTCGTCAAAGATAAATAAGCAGGCAAGCTGGCTAGAAAACCACTAAGGGTA-TTATTCTTTAAAGAATCTTTATAGGGTCAAAGAGGAATGGGTCTTAACTGGCTATGTGAACTCCCCACAGATTCTGAGGATGATGTCAGTATCCCTTTCCAGATGTGTTTAACACTTTGCAGTCACTTGTATTCCTGCCACTGAGTGCCAGTGCTTTGCTAATTTGAACTGATTCCAGCTCACGCTGACCCCAGCTCCCTGGATGTTACCATTAGCCAAGACTGTCACCCATACTGTACCCTTTCAAAGACTCCTAGAAACAGCTCTTCACCTACTCTTCCAAGACAAGTAAAAATGTCTGCCAAAGAAATGGGGAAAAAAGATTCAGAGAGTGAAAACAATTAATATACTAACAAGAGAGCAAAAAGCAAAGGGGGAGGAGAAACTAGGAAAATCATAGATGGGCTCTTACCTATTTCCAAAGCTGGGCTAATGTCCTTTTGCTTGTGTCTGAATAAGGCACCAATTTTAAGCTGCTAATG--AAAAAAAGAAAAAGAGAAAGAAGCAGGCCCAggctgggcgcagtggctcatgcctgtaatcccagcactttgggaggccgaggcgggtggatcacccaaggtcaggagttctagaccagcctggtcaacatggtgaaacaccatctctactaaaaatacaaaaaattagcgaggcatggtggcacatgcctgtaaatccagctactcaggaggctgaggcaggagaattgcttgaacctggaaggcagagaatgcggttacctgagatcatgccattgccctcaagccacggcaatgagaacaaaattcggtAaaaac aaaacaaaacaaaacaaaacCACCATAAAATAACTCAGACTTAATTAAATACAACCCTAGTGGTGAATGACTAAAGATGGATTACTCATAACAGAGATAACAATCCAATAAGAATCCAGGCATCTTACCTTTTAATAACAAAAAAAATCCTTTCCTTCGAAAGTAACATCCTCTCAAGGCCAGGAATTCCATTAGTAGAAATCCTTCCTAAAAAACAAAATTCCTggccaggcatgggttcacgtctgtaatctcagcactctgggaggctgaggcgggaagatcacttgatgtcaggagtcgaggcgggaagatcacttgacgtcaggagttcgagactggcccggccaacatggtgaaaccccatctccactaaaaatacaaaaattagcctgctgtggtggtgggcacctgtaatcccagcaacttgggaggctaaggcaggagaatttcttgaacccaggaggcagaggttgcagtgaccagcaaggttgtgccattgcaccccagcctgggcgataagagtgaaaactccatctc--aaaaaaaaaaaaaaaaaaaaTTCCTTTGGGAAGGCCTTCTACATAAAAATCTTCAACATGAGACTGGAAAAAAGGGTATGGGATCATCACCAGACCTTTGGCTTTTACAGCTCGAGCTATAAGAACAAAAAGAAAAAGGGATATCATTTAAACACAGTATGTAGAAAAGAATAATTATTGAATCTGTACTGGTCTTTAACTTTTACACTTTGATCTTTAATTCTGTTATTGTGATTGAGTCCAAAGAAAAATAGTATGAGTAAAATAAAAAGAACACCAAAAATGCTAATATTCTGTTTACCAAAGTCTGTAGTGAAATATCCCATTAAATccaagtgcagtgacacacccataatcccaagcactttgggaggctgaggcgggtgaatctcctgaagtcaggagttcaaggccagcctggccaacatggtgaaaccccaactctac tacaaatacaaaaattaggcaggcgtggtggcagaggcctgtaatcccagctacttaggaggctgaggcagggagaattgcttgaacccaggaggtgagcttgccatgagctgagatcataccactgcactccagcgtgggtgacagaacaaaacttcaacctccaaaaaaaaaaaaaaaaaaaaaaaaCAGCTAGCAGGTGACATTTGCTATGGGGAGACTAGGGATATGATCTTGCTGCAATCCTTCCATTTTAGTAAATCTAAAC-AGTGTGAATCCATTCTGTTTCGTCCCCACTCCACTCCAGAGCCAAAACAAGAAAATCAATTATATTTCTAGTTCTTTAAAAACATATCTAACTAAATCATCTAATTAAAAGATAATATGCATGGTTCCATACTCTAAAAGAAAACTTATGTCCTGCATATCATGGACATTTGATGAATGCTTATTCAGTTGACTGGTGTAGACTTCAATAATAACCTGTTCAATGCATTATGCCAGATGAATCTTGCATCTCAAAAGTAGAACAAATATTGTTCTTTCAGTTTTGTCTACCCATAAATGCAATATTTACTAATAAAAAGAAAATGAGTTTATTGCTCTAGAGAGTATGAGAATTTTGACAACATCAATTCTCCTGTCCTAGGACATAATTAATACTTAGAGGCATACTATTTCATGTGGAAGCTACCATTAAATCAATGTTAAGTGTTAATTACCTCACATAATCTTCTAATCTGACTTAAGACTGAAGACGTACCTCACAAAGTTGATTTATCAAGTTGTAAATCTTCACCTGTTGAATTCATAAGTTCATGTCTGAAAGGTGAGAATAAATACTTAATATTCACTAGGCAATATTCAGCAAAGTAATATCCACTAGTACATATTTAATATTTCATCATGAACTGTGGGTGTGAAGAGAAAAGACAggctgggcgcagtggctcacacctgtaatcccagcagttggggaggccgaggc aggcagatcatgaggtcaggagttcgagaccagcctggccaacatggtaaaaccacgtctgtactaaaagtacaataattagctgggcatggtggcaggcacctgtaatcccagctactcgggaggctgaggcaggagaattgcctgaacccaggaggtggaggttgcagaaaccattatcacgccactgcattccagcctgggcaagagagcaagattctgtctcaaTCAATCAATCAATAAAAATATAAGGAGGAAGcatttactgtgtatttatatgtctggtattatgtgaagcactttactatcttatcaaatcttcgggacagatcttcagttctcatgaccacaaaagaggatactaaagctcagacaggagaagagacgtggccaGCCTGTGTCCCCAGGGCCTATGGTCTTACCACTAGGTTACAGTGTTTCCAGATATCACATGTTGTGAGATTTTTGCTTTAAAATGAACCAAAAAAAAACCAAAGGTGAAAAAGGCATAAGCTATTAAAAAGTGGGAGAAACACTAAGAGAACCTTAAGCATGTAACTAAAAATATTATGGAAATGTTATTGAATTCATTAGCAAATTTAGTGCTAGGTTTTCATTGAGGAGTAGGTTATATTACTCATGATGAAGAAAAATGTTCATTTTAAGTATATTAACATAAATACCATCAATATTGTTTATCATGTTTAAATGTTCACTTAAAGCAATTCAGTTAAAATTCTGCATATCATACAATTTTATAGTTTGCTAGTAGGTTACAAGTAAATAGTCACCCAAATAAAAACATCA-GTTTTCCACTGGTTGTTGCTCTTTTTTAGGTGAGTATTTGATGTATACCAACAGAGAGAGGATAATAACAAATCGCTAATTTCTTTCATCACTATATAAAGGTGGCTTCAGGATAGAATAGTATCAGGGCAATGATGAATTTGAAATCTAACATCAATTCAGTGATGCATCAAGATAAAAG TAGAGACAACAGGGGCACCTTGGTGAGTACTGAACAttttatttatttatttattttgagatggagttttgctctttttgcccaggctagagtgcaatggtg-caacctcggctcaccgcaacctctgcctcctgggttcaagcgattctcctgccttggcctcccgaatagctgggattacagacatgtgccaccacacccgtctaattttgtatttttagtagagacggggtttctccatgttggtcaggctggtctcgaactcccgacctagatatctgcctgccttggcctcccaaagtgctgggattacaggtgtgagccaccgcgcccagATGAATTCCAAATTTAACAAAGCAGACTAAGAGAAACAATTCATTTAAAAAAATAATATTTggccaggcatggcggctcacacctgtaatcccagcactttgggaggctgaggtgagtggatcaggaggtcagcagttcaagaccagcctagccaagatcatgaaaccccatctctactaaaaatacaaaaatcagccaggcgtggtggctggtgcctgtaatcctagctgctcgggaggctgaggcagagaactgcttgaacccgggaggcggaggttgcagtgagccgagatcgtgccactgcactccagcctgggcgacagagtgaggctccatctcaaaaaaaataaataaaTAATTCAATGAAATCCCTAAGATCCAGGGCTTTCCAATAAATATGTAAATAAATTTCCAATCTCCATACTGAAAGTTTAAAAGAAATGCTAACTAATAACTAAAGAAATACAACTTTTCCTCAGCTTTGCAGCAATCTAGAAACAAAGTGTGTAGACACTACAAAGCACCTTACAAGGAGAAACATGTAAGGATGGCATGACTCGCCGGCAGCCCTGGGCTTGTCCACGGTACCCCCATGATGAACAGTAACTCCATTGTGTAAACGCCCATGAACATAAGATTACAGGATTTTTCC AGTTTAGACATACCATATTTTCTTTCAGACAATTCTTCAGTTTGTTTACGTAGATCAGCGATACGATGATTCCATTTCTCTGAAAATCAAGCAAAAGTTGCTTCTCAATAACACGTCCCTATGTCAGAGCAGCACTAACGTATAATGACTGATTTCATATATTTTACATTCTAACAGTCCATATCATTTTACTGCTTTCAAGAAAAAATTTCCCCTTTTTGGTGGTTCTTAGAATTGGTTTAATGGGAGACTATTAGAGAAGCTGAAAAGCAGGAGGGCAGAAAAGTTCAATCAAATTAAACACAATAACAGGGAGGTCACAATGAGGCGGTCTCCAGGGGTCTTTTAGCAAACTTCCTAAAACATGTCTCAGCTGTGTGAAATAAGACTTTACAGCagccgggtgcagtggtgcaggcctgtaatcccagcactttggcagcagaggcaggtggatcgctttgagctcagggcaacatagccaaaacccccctccctagccccaaccccaccccgtccctaccaaaaatacaaaacagcagggcatggtggcgggcgcctgtagtcccagcttctcaggaggctgaggcaggagaatcacccgaacccaggaggcagacattgcagtgagccaagatcacgccactgccagcctggatgacagagcaagactccacctcaaaaaaaacaaaaacaaaaaCACAAGGTTAAGAGGGACCCCCGACCTTACAGATACAAGTTTAAGAGGGACCCCTAAGCAAAAAATGCCAACCCTTTTCCTCCCAATCATTGAAACACCAGGAGGGTGTAACAGTTTTGCAGCCTAGCtgtagcaggctgatgcccccaagatgcccaaagcctaatcccgggaactggtgaacat-accttctnaatgagggagggnctttgcagatataatgaagttaagggtcttTGGCTTT + +a score=376695 +s hg18.chr1 158893 4074 + 247249719 tggggttgatgtactcactcggatccttgtaagagcagagcaggtgatgg-agagggtgggaggtgtagtgacagaagcaggaaactccagtcattcgagacgggcagcacaagctgcggagtgcaggccacctctacggccaggaaacggattctcccgcagagcctcggaagctaccgaccctgctcccaccttgactcagtaggacttactgtagaattctggccttcagacctgtaagggaatacattttggttgttttaagtcactaagtgtgtggtaatttgttgcagcagccacaggaaactagtaTTGTAGTGAAGCCTCAAAACCCCCCTGAAGGggctgggctcagtggctcatgcctgtaatcccagcactttgggaggccgagatgggtggatcacttgaggtcaggagttcgagaccagcccagccaacatggtgaaatgccatctatacaaaaaatacaaaaactagccgggcatggtggcacatgcctgtaatctcagctactcaggaggctgagacaggagaattgtttgaacccaggggggcagaggttgcagtgaactgagattccaccactgcactccagcctgggtgacagagcgacgctccatctcgaaaacaaaacaaaacaaaaaaaCCCCACCTGAAGGTTTCCAGTTCTGCCAGCACTCTCCCACCCAACCCCCAGAAACAGACATTCCATTGCTGTGGGCCACGGACAGGCAGAAGGAAGCACCTCCTCATGGCAGAGGCCTACCCAGGAGAAACCCAAGGGAAGGCACTACTGGGCTGGCCCCTCTCTGCCAAGGCCATAttcttttttttttttt-----gaggccagtttcactctgtctcccagactggagtgcaggggcacaatctcggctcacttcgacctctgcctccccagttcaagtgattctcctgcctca gtctcctgagtagctgggatgacaggagtgtagcatgcctagctaatttttgtatttctagtagagatgcggttttgccatgttgcccaggctggactcgaactccttgcctcaagtagtccacctgtctcagccccgcaaagtgctgctattataggagtgagccactgcacccagcATTTGCCAAGACCTTTGATGGCAGGCTTTTTCCAGGTGATCAGTCCTTGTCTGGTCTGGCTCTGCCCCACTCTCCTTCTCACCTAGTTGGAATCCCTAGCTACTTTTCAGTAGAGGAGAGTGTGTACCCCAATCCCAGCTTGGTTCAGATCTGCATTTAACTCATGGAACCTGGCTGCTCCCCAGGTTCTGAAGAAAAAAACGGTCTCTCTGTGGGTATGATAAAGGATGGGCCTGTCCCCAGGACCCTGTGAGAGGGAAGCCCAATGTCCCACCAGGTTGGCAGGGCTGGGGAAGGGAAAGTGTTATGGCAGCCCCAAGAAAAAAAAGAGGCAGCAGAGGGAGCAGGAGAGCGCTCACATGGAACTCATGCCACTGCCTGAG----GGGAGGGAGGAGTGCACGCCAGTGACGTCAGGGGGCAGAGAGGCGCAGTTCCAGGGCGGCTTTCCCCCTCACTTCCTGCCATGTTACTCTGATCGCCTCCACGTGAGCCTGCCCACTTTGTGCCCAGGGGCCTGTAGAAAACCACAGCTCCCCATGGTTATGGCCCCAGGAGTGGGGCAGAGCAGGGAGGAGTCCTGCACAGAGGAGAGGCAGGGGCAGGAGGGAGTGGGCCTCAAACTCCAGGAGGGGGCCCTTCTCATGGGTCCTGCTTTCTGGCTTCTCCTTCCTTACCCCTGGGCTGATCACTTGGGGAAGAACTGAGACAAAGTTTCTCACCCTCAGGCCCAAAGGGTTTAATTACTGGGCCCTTAGGGAGGTGTGAGCCCCCTGAAAGGATGCAAGgttttgttttgttttgtttttt gagacagagtttcgctcctgtcgcccaggctggagtgcagtggcgtgatctcaccacactacaacctgcgcctcccaggttcaagtgattctcctgcctcagcctctggagtagctgggattacaggtggctgccaccacgcctggctaattttttgtatttttagtagagacagggtttcgccatgttgggcaggctggtcttgaactcctgacctcaggtgatccgactggctccgcctcccaaagttctgggatcacatcagccactgtgcttggccACGATGAAAGGTTTTGTGTGGAGAGCATGTACATGCCTTTCTGGGAAAACAGTCCACAGCTCTTATTCTCAGCAGGCTTCACGGTGAAAAAAGGTTAGAACTCTTGCTACAGAGCTGTGGAAGCAGCCAGGTGAGGGGCCTGCCAAGGGCACTCTGGGCACTACCTGGGCACTCTCGAGCCCATCATCCCCTAGGCAGGCTGCACTGCTTGGTATTTGCAGAGCTGAGGGGGTGGGGCATGTGGGGACTGTGAAATCGCCCTGAGATGACCCACAGTCCTCAGCTAGGAAGTAAGCGCTGCATCTCCTGCAGCGTCCTCCATCCCTAGAGCCATGGGGCCAGGAGAACCGGCCCTTGCAGCAAGTGAAAAGCCTATTATTGATTCCCTCCCTAGCCATGTAGACAGTGAACCAAGACACTCATATCAGGTAAATGCCTTGTTCTCTGTTACCAAGGTAACCAGTAGGCATTCCCAGATACAGCGAAGGTCCTCACACCAAGATATGCACCTGGCCACCTGAGGAAAGAGAAAGGACTATCTGAGGGGACGGGGCTGAGCTGGGTGTGGAGTGGTCCTTGTGGGTCTTGGAGAGTGGGAGGGGGAACAGCATGAGCCAGGCCTCGAGGCAGAAGGACAACCAGGAGACAGCCTGGAAAAAGTGCTGGACCCACAAGGGCTCAAGGCTGGCCAGAGGGGAGGTGGGATAGG CTGTAAAGTCCTGAGGTCTGAAGATTGGCCCTGGCAGGAAGAAACCAGGTAAGGTGGGGTGTTACCTACACCCTCGGGGCCAGATGCAGGCCAGAGCCAGCCAATTACCAGGCCCTTAGGGAGGTGTGAGCCCCTTGAAATGATGCAAGGttttttgtttttgttttggagacggagtttcgctcttgtcacacaggctggCACCTTTGCCCAGAGCAGGCACCAAGACTTCTGGCTCTGGGTGTGACCTCAGTCTGGGTAAAAGCCCCAGCCCCCACCAGCACCACCTACCCCCTAGACTACTTCAGGTGCTGAGCCCAAGCCAGGGGCAGGAAGCTAAACTGATGCCTAGGGTAATCCCAACAAAGTCCCTGGTTCCCCGCAGCTATGGGGCTGACGGGGAATTACAGCCCAAACCCCAGATGCTGGCTCTCAAACTAACACTGAGCCCTCAGtgcccacagggagatacaatcagcgcactttccagatggggaaatgggatcagagaagtgcaacagccttgcccaatgccccagaccagGGCTCCAGGCCCAGAGTGTTCTTTTGTCACTGTGTTCAGAGGGCAGCAGCTGCTGTGATGTACCCACCTGAGCCTGGCAGCTCTCTCCAACTTTGGAAGCCCAGGGGCATGGCCCCTGTCCACAGATGCACCTGGCATGAGGCGTGCCCAGAGGGACAGAGGCAGATGAGTTTCGTCTCCTCCACTGGATTGTGAGGGCCTAGAAGGAGACAAGGGTCTGCTTGAGAAGGCAGTGAACAGCGAGCAGCCTGAGGCAGTGCCCCTCTGGATGGATGCGCAGTGCCTGGATGGAACCTGGCTCAGACAGAGCTCAGTTCTGCAGGTCCCTGAGGCATGGAGAGTTcacagctaccaagtgtaggagtctggattcaaagccaacggcgtgactccaaagtccctgccctagcccctggaccaccctTGCAGGCCCATCAGATGCCCA GGCCAGCAGCACAGCCGGCCAAGACCAGGGAAACTTGGGGAGCCTCAGAGCACCCCCAGGTATTCCAACCTAACCCTGGTGCCCCGCCTCTCACCACCCTTCTTCCTGCTTTAACCTCAACCCCTACACAAAGCCTGGGCCACTTAATGTGGCATCAAACAGACGCCTCA +s panTro2.chr1 224073421 4083 + 229974691 tggggttgatgtactcactcggatccttgtaagagcagagcaggtgatgggagagggtgggaggtgtagtgacagaagcaggaaactccagtaattcgagacgggcagcacaagctgaggagtgcaggccacctctacggccaggaaacggattctcccgcagagcctcggaagccaccgaccctgctcccaccttgactcagtaggacttactgtagaattctggccttcagacctgtaagggaatacattttcgttgttttaagtcactaagtgtgtggtaatttgttgcagcagccacaggaaactagtaTTGTAGTGAAGCCTCAAAACCCCCCTGAAGGggctgggctcagtggctcatgcctgtaatcccagcactttgggaggccgaggtgggtggatcacttgaggtcaggagctcgagaccagcccagccaacatggtgaaatgccatctatacaaaaaata-aaaaactagccaggcatggtggcacatgcctgtaatctcagctactcaggaggctgagacaggagaattgtttgaacccagtggggcggaggttgcagtgaactgagattccaccactgcactccagcctgggtgacagagagacgctccatctcgaaaacaaaacaaaacaaaaaaaCCCCACCTGAAGGTTTCCAGTTCTGCCAGCAGTCTCCCACCCAACCCCCAGAAGCAGACATTACATTGCTGTGGGCCATGGACAGGCAGAAGGAAGCACCTCCTCATGGCGGAGGCCTACCCAGGAGAAACCCAAGGGAAGGCACTGCTGGGCTGGCCCCTCTCTGCCAAGGCCATAttcttttttttttttttttttgaggccagtttcactctgtctcccagactggagtgcaggggcacaatctcagctcacttcgacctctgcctccccagttcaagtgattctcctgcctca gtctcctgagtagctgggattacaggagtgtagcatgcctagctaatttttgtatttctagtagagatggggttttgccatgttgcccaagctggactcgaactccttgcctcaagtagtccacctgtctcagccccgcaaagtgctgggattacaggagtgagccactgcacccagcATTTGCCAAGACCTTTGATGGCAGGCTTTTTCCAGGTGATCAGTCCTTGTCTGGTCTGGCTCTGCCCCACTCTCCTTCTCACCTAGTTGGAATCCCTAGCTACTTTTCAGTAGAGGAGAGTGTGTACCCCAATCCCAGCTTGGTTCAGATCTGCATTTAACTCATGGAACCTGGCTTCTCCCCAGGTCCTGAAGAAAAAAAGGGTATCTCTGTGGGTATGATAAAGGATGGGCCTGTCCCCAGGACCCTGTGAGAGGGAAGCCCAATGTCCCACCAGGTTGGCAGGGCTGGGGAAGGGAAAGTGTTATGGCAGTCCCACGAAAAAAAAGAGGCAGCAGAGGGAGCAGGACAGCGCTCACATGGAACTCATGCCACTGCCTGAGTGAGGGGAGGGAGGAGAGCACGCCAGTGACGTCAGGGGGCAGAGAGGCGCAGTTCCAGGGCGGCTTTCCCCCTCACTTCCTGCCATGTTACTCTGATCGCCTCCAGGTAAGCCTGCCCACTTTGTGCCCAGGGGCCTGTAGAAAACCACAGCTCCCCATGGTTATGGCCCCAGGAGTGGGGCAGGGCAGGGAGGAGTCCTGGACAGAGGAGAGGCAGGGGCAGGAGGGAGTGGGCCTCAAACTCCAGGAGGGGGCCCTTCTCATGGGTCCTGCTTTCTGGCTTCTCCTTCCTTACCCCTCGGCTGATCACTCGGGGAAGAACTGAGACAAAGTTTCTCACCGTCAGGCCCAAAGGGTTTAATTACTGGGCCCTTAGGGAGGTGTGAGCCCCCTGAAAGGATGCAAGgttttgttttgttttgtttttt gagacagagtttcgctcctgtcgcccaggctggagtgcagtggcgtgatctcaccacactacaacctgtgcctcccaggttcaagtgattctcctgcctcagcctccggagtagctgggattacaggtggctgccaccacgcctggctaattttttgtatttttagtagagacagggtttcgccatgttgggcaggctggtcttgaactcctgacctcaggtgatccgactggctccgcctcccaaagttctaggattacatgaggcactgtgcttggccACGATGAAAGGTTTTGAGTGGAGAGCATGTACATGCCTTTCTGGGAAAACAGTCCACAGCTCTTATTCTCAGCAGGCTTCACGGTCAAAAAAGGTTATAACTCTTGCTACAGAGCTGTGGAAGCAGCCAGGTGAGGGGCCTGCCAAGGGCACTCTGGGCACTACCTGGGCACTCTCAAGCCCATCATCCCCTAGGCAGGCTGCACTGCTTGGTATTTGCAGAGCTGAGGGGGTGGGGCATGTGGGGACTGTGAAATCGCCCTGAGATGACCCACAGTCCTCAGCTGGGAAGTGAGCGGTGCATCTCCTGCAGCGTCCTCCATCCCTAGAGCCATGGGGCCAGGAGAACTGGCCCTTGCAGCAAGTGAAAAGCCTATTATTGACTCCCTCCCTAGCCATGTAGACAGTGAACCAAGACACTCATATCAGGTAAATGCCTTGTTCTCTGTTACCGAGGTAACCAGTAGGCATTCCCAGATACAGTGAAGGTCCTCACACCAAGATATGCACCTGGCCACCTGAGGAAAGAGAAAGGACTATCTGAGGGGATGGGGCTGAGCTGGGTGTGGAGTGGTCCTTGTGGGTCTTGGAGAGTGGGAGGGGGAGCAGCATGAGCCAGGCCTCGAGGCAGAAGGACAACCAGGAGACAGCCTGGAAAAAGTGCTGGACCCACAAGGGCTCAAGGCTGGCCAGAGGGGAGGTGGGATAGG CTGCAAAGTCCTGAGGTCTGAAGATTGGCCCTGGCAGGAAGAAACCAGGTAAGGTGGGGTGTTACCTACACCCTCGGGGCCAGATGCAGGCCAGAGCCAGCCAATTACCAGGCCCTTAGGGAGGTGTGAGCCCCTTGAAATGACTCAAGGttttttgtttttgttttggagacggagtttcgctcttgtcgcacaggctggaACCTTTGCCCAGAGCAGGCACCAAGACTTCTGGCTCTGGGTGTGACCTCAGTCTGGGTAAAAGCCCCAGCCCCCACCAGGACCACCTACCCCTTAGACTACTTCAGGTGCTGAGCCCAAGCCAGGGGCAGGAAGCTAAACTGATGCCTAGGGTAATCCCAACAAAGTCCCTGGTTCCCCGCAGCTATGGGGCTGACGGGGAATTACAGCCCAAACCCCAGATGCTGGCTCTCAAACTAACAGTGAGCCCTCAGtgcccacagggagatacaatcagcgcactttccagatggggaaatgggatcagagaagtacaacagccttgcccaatgccccagaccagGGCTCCAGGCCCAGAGTGTTCTTTTGTCACTGTGTTCAGAGGGCAGCAGCTGTTGTGATGTACCCACCTGAGCCTGGCAGCTTTCTCCAACTTTGGAAGCCCAGGAGCATGGCCCCTGTCCACAGATGCACCTGGCATGAGGCGTGCCCAGAGGGACAGAGGCAGATGAGTTTCGTCTCCTCCACTGGATTGTGAGGGCCTAGAAGGAGACGAGGGTCTGCTTGGGAAGGCAGTGAATAGCGAGCAGCCTGAGGCAGTGCCCCTCTGGATGGATGCGCAGTGCCTGGATGGAACCTGGCTCAGACAGAGCTCAGTTCTGCAGGTCCCTGAGGCATGGAGAGTTcacagctaccaagcgtaggagtctggattcaaagccaacggcgtgactccaaagtccctgccctagcccctggaccaccctTGCAGGCCCATCAGATGCCCA GGCCAGCAGCACAGCCGGCCAAGACCAGGGAAACTTGGGGAGCCTCAGAACACCCCCAGGTATTCCAACCTAACCCTGGTGCCCCGCCTCTCACCACCCTTCTTCCTGCTTTAACCTCAACCCCTACACAAAGCCTGGGCCACTTAATGTGGCATCAAACAGATGCCTCA + +a score=232090 +s hg18.chr1 162967 2659 + 247249719 ATAAATCAGTCTAATCTCGAAAATAAAAAAGACTTAACAGATATACAATTGCACGTTAGAATGCTAAAAACCATAAACATATAACAACTTAAAGTACATATAAATTCAATATATATCCAATCATTGTAACTATGACACAGTAGAATATTAAAATACTATTTTCAAAATGTATACAAGCTTAATGTTCTATGTATTCAAACTATTTATTCAAAATACAAATCATCAACATACATTGCCACTAATATTCAGTCCCTTCACAGGACA--TGATTCACTGGGAGTTAATAAATTAGCAGCCAGCAGGCAGTGACACACCGCAAAAATGAAAACCAAGAGGTGAAATAGTTCTGAAATAAAGGTTTTAAAGCTAACAGAAATCACTGAATTACTAAGTCATTAGCACTAATTTTGAGCCAACTAACTAATTAATATGAGATGATACAATGTCCTATACTTTGGTAAATACAGACTATGTTTAAACAATGTCTGTAACGTGACTTGTAAAATGCTCCTGGCTTTACAAAGATGTGATTAAGATGTAGTAACACATGCTAAACCATTTCCCCCTGCAGAGCATGTGGTAACTTTCATCAGTCACACTGAGAGTACAGAAGATAAAGGAAAAGGTCATGGATTTCGCTGAGAACTTACCAGAGTTGAACTCCCTCATTTTCCGTTCCCCAGCATTGGCAGGTTCTGGGACTGGTGGCTGTGGTGGCTCGTTGGTCTTTGTCTCTTAGAAGGTGGGGAATAATCATCATCTTGAAAAAGAAAAAATGGTCATTACTGAAGGAACCATCTTAGGTTACAGCCACCTCTGGGTCAATTCCCAACATTCAAAAGCTGAGCAGGGCTTTAAAGCTATCTTATTAATAATTATTTCTGTATTGCGAACTTCAGCATACTTTTTTCTAGTTACATTTGAAATGTTATTCTTTTGGGA TGTGCTCAAGTGAGTACTGCTTTTTCCTCTGCCTTGCTTCATTACTTTTTAGTTTCCTTCATTTGAATCATCATTGTAAGTCTCCCCTTCTCCTCAAATAACTTTCAAATTGCTGCCAAGAACTACGTTCTATCTTAAGGCTTTTGAGAAAAAACTTTCAATGAAGATAGCCGCCTAAAGTTATACAAATATAGAAGAAACGGGATAAAATAAAGCTTAGATTGG-AAAAAATATTTAAGATTCTACAAAATTCACGCGTAAACAAGGGAAGCTGAGTAATTGTATGTTCAAATACTTTTAACAAGTGCAAAACATGTAGGCTTAAAGAAATAGAGCTggccaggcatggtggttcatgcctgtaattccaacagtttgggaggccaaggcaggcagataacttgaggtcaggaattcgagaccagcctggccaacagagtgaaaccctctctctactaaaaatacaaaaattaggccaggagtgatggctcacgcctgtgatcccagcactttgagaggccgaggcgggtagatcacctgaggtcaggagtttgagaccagcctaaccaacatagggaaaccccgtctctactaaaactacaacattagccgggtgtggtggcacatgcctgtaatcccagctactcgggaggctgaggcaggagaatcccttgaacccaaaaggcaaagattgtggtgagccgagattgtgccattgcactccagcctgggcaaaaacagcgaaactccgtctcaaaaaaaaaaaaaagaaaaaattagccaggcatgg-------------------------------------------------------------------tgaagttgcagtgagctgagactgcaccattgcactccagcctgggtagcagagcaagaccctgtctcaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagagagagagagaaagaaagaaagaGGGCTACA TTATTTATGAAACAGATACTGTTAACTCAGTCACCAGAAAGCCTGTGTATAAATGAGCAGTGAGATATTCAAGCACAGCACACACACACTTCTCAGGACAGCTGTCGTGAGTGTTCCATGCTCGTTTCCTTCTGGATACATCAGCAACTCACTCTGCTATGATCCTGCAATACATCTCATGTTAGAATTAGAGACATCTGggccaggcacagtggctgacgcctgtaatcctaacactttgggaagccgaggcaggcagatcacctaaggtcaggagttcgagaccagcctggccaacatggtgaaatgctgtctctaccaaaaatacaaaaaattagctgggcatggtggcgcgcgcctgtaatcccagctactcgggagcctgaggcaggagaatcgcttgaacccgggaggtggaggttgcagtgagccgagatcgtgccactgcactccagcatgggggacggagcaaggctctgtcaaaaaaaaaaaacagaaaaagaaaaagaaaaaAGAATTAGAGACATCTGGATCAAATCAGCTGCCAGTCTCGCAAAGTGTCGGGTAACATCCTATTAAGCTTGCTGCTTACACATCATCTATAAAATACTGAAAATATCATTTTAAGAAATCttttttttattttgagacagagttttgctcgttgcccaggctggagtgcaatggtgcgatctcagctcactgcaatctctgccccctgggttcaagcaattctccttcctcagcctcctgagtagctgggattacaggcatgcaccaccacgcctggctaatttt +s panTro2.chr1_random 7293350 2697 + 9420409 ATAAATCAGTCTAATCTTGAAAAATAAATCTACTTAACAGATATACAACTGCACGTTAGAATGCTAAAGACAATAAACATATAACAACTTAAAGTACATATAAATTCAATATATATCCAATCATTGTAACTATGACACAGTAGAATATTAAAATACTATTTTCAAAATGTATACAAGCTTAATGTTCTATGTATTCAAACTATTTATTCAAAATACAAATCATCAACATAAATTGCCACTAATATTCAGTCCCTTCACAGGACACATGATTCACTGGGAGTTAAT----TAGCAGCTGGCAGGCAGTGACACACAGCAAAAATGAAAACCAAGAGGTGAAATAGTTCTGAAATAAAGGTTTTAAAGCTAACAGAAATCACTGAATTACTAAGTCATTAGCACTAATTTTGAGCCAACTAACTAATTAATATGAGATGATACAATGTCCTATACTTTGGTAAATACAGACTATGTTTAAACAATGTCTGTAACGTGACTTGTAAAATGCTCCTGGCTTTACAAAGATGTGATTAAGATGTAGTAACACATGCTAAACCACTTCCCCCTGCAGAGCATGTGGTAACTTTCATCAGTCACATTGAGAGTCCAGAAGATAAAGGAAAAGGTCATGGATTTCGCTGAGAACTTACCAGAGTTGAACTCCCTCATTTTCCGTTCCCCAGCATTGGCGGGTTCTGGGACTGGTGGCTGTGGTGGCTCGTTGGTCTTTGTCTCTTAGAAGGTGGGGAATAATCATCATCTTGAAAAAGAAAAAATGGTCATTACTGAAGGAACCATCTTAGGTTACAGCCACCTCTGGGTCAATTCCCAACATTCAAAAGCTGAGCAGGGCTTTAAAGCTATCTTATTAATAATTATTTCTGTATTGCGAACTTCAGCATACTTTTTTCTAGTTACATTTGAAATGTTATTCTTTTGGGA TGTGCTCAAGTGAGTACTGCTTTTTCCTCTGCCTTGCTTCATTACTTTTTAGTTTCCTTCATTTGAATCATCATTGTAAGTCTCCCCTTCTCTTCAAATAACTTTCAAATTGCTGCCAAGAACTATGTTCTATCTTAAGGCTTTTGAGAAAAAACTTTCAACGAAGATAGCCTCGTAAAGTTATACAAATATAGAAGGAACGGGATAAAATAAAGCTTAGATTGGAAAAAAATATTTAAGATTATACAAAATTCACGCGTAAACAAGGGAAGCTGAGTAATTGTATGTTCAAATACTTTTAACAAGTGCAAAACATGTAGGCTTAAAGAAATAGAGCTggccaggcatggtggttcacgcctgtaattccaacagtttgggaggccgaggcaggcagataacttgaggtcaggaattagagaccagcctggccaacagaatgaaaccctctctcgactaaaaatacaaaaattaggccaggagtgatggctcatgcctgtgatcccagcactttgagaggccgaggtgagtagatcacctgaggtcaggagtttgagaccagcctaaccaacatagagaaaccccgtctctactaaaactacaacactagccagatgtggtggaacatgcctgtaatcccagctactcgggaggctgaggcaggagaatcccttgaacccgaaaggcaaagattgtggtgagccaagattgtgccattgcactccagcctgggcaaaaacagcgaaactccctctc-aaaaacaaaaaaagaaaaaattagccaggcgtggtggcgcatgcctgtaatcccagctacttgggaggctgaggcaggagaatcgcttgaacccaggaggctgaagttgcggtgagctgagactgcaccattgcactccagcctgggtagcagagcaagaccctgtctc----------aaaaaaaaaaaaaaaaaaaaaGAGAGAGAGAGAAAGAAAGAAAGAGGGCTACA TTATTTATGAAATAGATACTGTTAACTCAGTCACCAGAAAGCCTGTGTATAAATGAGCAGTGAGATATTCAAGCACAGCACACACACACTTCTCAGGACAGCTGTCGTGAGAGTTCCGTGCTCATTTCCTTCTGGATACATCAGCAACTCACTCTGCTATGATCCTGCAATACATCTCATGTTAGAATTAGAGACATCTGggccaggcacagtggctgacgcctataatcctaacactttgggaagccgaggcaggcagatcacctaaggtcaggagttcgagaccagcctggccaacatggtgaaacgctgtctctaccaaagatacaaaaaattagctgggcatggtggcgcgcgcctgtaatcccagctactcgggagcctgaggcaggagaatcgcttgaacccgggaggtggaggttgcagtgagccgagatcgtgccactgcactccagcatgggggacggagcaaggctctgtcaaaaaaa--------------aaaaaaaaaaaaaaaTTGGAGACATCTGGATCAAATCAGCTGCCAGTCTCGCAAACTGTCGGGTAACATCCTATTAAGATTGCTGCTTACACATCATCTATAAAATACTGAAAATATCATTCTAAGAAATCtttttt---ttttgaaacagagttttgctcgttgcccaggctggagtgcagtggtgcgatctcggctcactgcaatctctgccccctgggttcaagcgattctcctgcctcaggctcctgagtagctgggattacaggcgcgcgccaccatgcccagctaatttt + +a score=90424 +s hg18.chr1 165626 1010 + 247249719 gtattttcagttgagacagggtttctccatattggtcaggctggtctcgaactcctgacctcaggtgatccactgaccttggcctcccaaagtgctgggattacaggtgtgagccaccatgcctagccAAGAAACCCTTATTTTAAAACAagccaggcgcggtggctcatgcctataatcccagcactttgggaagccaaggcaggtggatcacttgac-gtcagtagtttgagaccagcccgggcaacatgttgtaaccccatctctactaaaaatatattttaaaaattagctgggcatggtggtgggcacctgtaatcccagcttctcaggaggctgaggcaggagaaccacttgaacctgggaggtggaggttgcagtgagcggagatcacgccactgcactctagcctgggtgacaatagaaagactccatctcaaaaacaaaacaaaacaaaacaaaacaaaaAACCACTAAAAAAAAGACTCCATTTCAAAAACAAAACTAAAACCAAAAACACAACACAAATGTAGTACACAAATGAAGATAATTACTGTGTTAAACACAGTTTCATAGAAAATAAAAGACCAATCAAATACAATAAGCTGACTTTTTagatgggtatgttattcttctttcacagctaaagaaacaggctcagagaatgttatttgattggaccGTGTTGCATTTCTGGACAGTGCAGCTGAGATCAGACTTTGTGTGTAACTCCACTAGCCTACCAGGGTGCCTCTCATAAAGGTAAGAAATGTAAATTTGGCCTAATATACAAAGTTGCCAGGGCAGCACTGGGTCAATTCTACATACAGTACTTCTATGTTCATCAAGGGAAACCTTAAGGGAAAGTGAAAATGCTTCTAGAAGGCGACTGGACACCAGCGCCTTTGCTTGTTGCCTTTGGGCTCTTCTTCTAAGGCCAACAGTG ACCTGAAATTATTGACTGGCTTTTCCAATCAAGTGGACAAAATGGTACCAAGGTCACCAACATC +s panTro2.chr1 224080226 1004 + 229974691 gtattttcggtagagacagggtttctccatattggtcaggctggtctcaaactcctgacctcaggtgatccactgaccttggcctcccaaagtgctgggattacaggtgtgagccaccatgcctagccAAGAAACCCTTATTTTAAAACAagccaggcgcggtggctcatgcctataatcccagcactttggggagccaaggcgggtggatcacttgactatcagtagtttgagaccagcctggacaacatgttgtaaccccatctctactaaaaatatatttaaaaaattagctgggcgtggtggtgggcacctgtaatcccagcttctcaggaggctgaggcaggagaatcacttgaacctgggaggtggaggttgcagtgagtggagatcacgccactgcactctagcctgggtgacaacagaaagactccatctca-----aaaacaaaacaaaacaaaacaaaaAACCACTAAAAGAAAGACTCCATTTCAAAAACAAAACTAAAACCAAAAACACAACACAAATGTAGTATACAAATGAAAATAATTACTGTGTTAAACACAGTTTCATAGAAAATAAAAGACCAATCAAATacaataagctgcctttttagatggg--tgttattcttctttcacagctaaagaaacgggctcagagaatgttatttgattggaccGTGTTGCATCTCTGGACAGTGCAGCTGAGATCAGACTTTGTGTGTAACTCCACTAGCCTACCAGGGTGCCTCTCATAAAGGTAAGAAATGTAAATTTGGGCTAATATACAAAGTTGCCAGGGCAGCACTCGGTCAATTCTACATACAGTACTTCTATGTTCATCAAGGGAAACCTTAAGGGAAAGTGAAAATGCTTCTAGAAGGCGACTGGACACCAGCGCCTTTGCTTGTTGCCTTTGGGCTCTTCTTCTAAGGCCAACAGTG ACCTGAGATTATTGACTGGCTTTTCCAATCAAGTGGACAAAATGGTACCAAGGTCGCCAACATC + +a score=3684 +s hg18.chr1 166636 39 + 247249719 GATGTAGAACATCGATGTTCTACAACATTGCTTAACGCA +s panTro2.chr1_random 1501241 39 - 9420409 GATGTAGAACATCGATGTTCTACAACATTGCTTAACGCA + +a score=51959 +s hg18.chr1 166675 605 + 247249719 AGGGGAGACGCTCCTGACTCAGAGTGTTTAATTGCTCACCTACTTCTTTTTCTGCCCTCTTGGGCTTCTGAAATGAAAAGAACCCTGGGGTGATACAGTGAGTCAAAGGGGTGCCAGCCGCATCACAGCAAAATAGATTCCTAAAAAATCCCTGGCCTAAGATGACAGCCTTGGCTGGATCAGTTTGAATGTGCTGATAGTGGACATGGTAGAATGAAGGTGGTTGAAATGTTCATATTAAAGAACTTCCACCCAGATTGCAAGAAAAGAGAGAAGAATGGAGACGGCAGCACGAGCCCCTACAATAAAAGCAGATGTTTTGAGATCAGTTATATTTCTTCTGACAAAAATTAAAGACAGAAACCAAAGTTTAGCCTGAGACTACAATTAATTGGGCAATAAGCCAGAGGCACATATGGCATAAGACAGATTTAAACATTTCTCCCTGATATTAATACAAACACTAAAATTACAAATACTTTGATTCCaaataaaacaaatatttaaaaaatttaatGAATAAACACTGGGGTCTACAGTAGTATTTGA---AGATCTCACAAACAGGTTTGGTTTTTGAAGGTTAGAACTGGTGGTCTAGAGAATTC +s panTro2.chr1_random 7554708 605 + 9420409 AGGGGAGACGCTCCTGACTCAGAGTGNTTA-TTGCTCACCTACTTCNTTTTCTGCCCTCTNAGACTTCTGAAATGAAAAGACCCCCGGGGTGATACAGGGAGTCAAAGGGGTGCCAGCCGCATCACAGCAAAATAGATTCCTAAAAAATCCCTGGCCTAAGATGACAGCCTTGGCTGGATCAGTTTGAATGTGCTGATAGTGGACACGGTAGAGTGAAGGTGGTTGAAATGTTCATATTAAAGAACTTCCACCCAGATTGCAAGAAAAGAGAGAGGAATGGAGATGGCAGCACGAGCCCCTA-AATAAAAGCAGATGTTTTGAGATCAGTTATATTTCTTCTGACAAAAATTAAAGACAGAAACAAAAGTTTAGCCTGAGACTACAATTAATTGGGCAATAAGCCAGAGGCACATATGGCAT-AGACAGATTTAAACATTTCTCCCTTATATTAATACAAATACTAAAATTACAAATACTTTGATTCCAAATAAAACAAATATTTTAAAACTTTAATGAATAAATACTGGGGTCTACAGTAGTATTTGAAGGAGATCTCACAAACAGGTTTGGGTTTTGAAGGTTAGAACTAGTGGTCTGGAGAATTC + +a score=16857 +s hg18.chr1 217280 205 + 247249719 GATTCATGGCTgaaatcgtgtttgaccagctatgtgtgtctctcaatccgatcaagtagatgtctaaaattaaccgtcaGAATATTTATGCCTGATTCATGGCTgaaattgtgtttgaccagctatgtgtgtctcttaatccactcaagtagatgtctaaaattaaccatcaGAATATTTATGCCTGATTCATGGCTgaaatcac +s panTro2.chrUn 47945019 205 - 58616431 GATTCATGGCTgaaatcgtgtttcgccagctatgtgtgtctcttagtccagtcaagtagatgtctaaacttaaccatcaGAATATTTATGCCTGATTCGTGGCTgaaattgtgtttgaccagctatgtgtgtcccttagtccagtcaagtagatgcctaaagttaaccatcaGAATATTTATGCCTGATTCATTGCTgaaatcgt + +a score=175275 +s hg18.chr1 217485 2070 + 247249719 gtttgaccagctatgtgtgtctcttaatccagtcaagtagatgtctaaaattaaccatcaGAATATTTATGCCTGATTCATGGCTgaaatcgtgtttgaccagctatgtgtgtctctcaatccgatcaagtagatgtctgaaattaaccatcaGAAtatttatgcctgattcatggctgaaatttcaggatgaaagctatgaaatctctatttgtgtttgtgtatctattaatgtatgttatgtatatgtgatattttcttaactccagagagcattgcaaaattcatttatgaaaacctctaaaagtgctctattctaacttggcttggaaaaaaataagcatttataaataaatattcaccaaactcctagaaatataggaactgatcaaatgtttcttaagttaacatgatttggataaaacttagttaaataagattaatatagtatttttggtgtaataaaacaactatatcttcaaaattatcattattgaatataaaacaagcataaattcctattctgcttgagttctagtcaaataagctaatattatacttactagaaacgtaaaatcttaaagcttatagatttgattctaaTTAAGTTGTCATTCTTATGAAAAACATTATTTTTTTTATGCTGAAAAGATACACATATATTTAGAGTTAGCCAGCTGGACTCAGTTTAGGTGATCCCAATTTTGTTACAACATCGAAAGCATCATAATCAGGAGCAAGTCGAACATATGCCTTCT---CTTTATCAGGACAAATCAGGGTGGTGACCTTGGCCACATCACTGTCATAGAGCTTCTTCACAGCCTGTCTGATCTGGTGCTTGTTGGCTTTAACATCCACAGTGAACACAAGCGTGTTGTTTTCTTCTATCTTCTTCACGGCCGACTCAGTGGTCAGCGGAAACTTGATGATAGCATAGTGGCCAAGC TTGTTTCTCCTGGGGGTGCTCTTCCGAGGATATCTGGGCTGCCTCCGGAGTCGCAGTGTCTTGGGCCGCCTGAAGGTGAGTGACATGCGGATCTTCTTTTTTGCGTGTGGCTGCGGACACCTTTCAACACTGCCTTCTTGGCCTTTAAGGCCTTCGCTTTGGCTTCGGCTTTAGGAGGAGCAGGAGCTTCCTTCGCTTTCGGTGCCGTCTTGTGAAAAGCGAAAAACATTATTTCAAAAATAATTTGTTTACAGTAAATCTgcctaagaatagtttccaaagtacttttggtaatttttaaccttaaagttaagctaagtaaaagatttgcattaaatatctagaccatttataaataagatacaatactaaaacattaattactgaacataaataattcaagtttatatacttttggcttcctgtttttacagagagactaaagatattttggcccgttaataaacatgtttttttctgccacactgaggaattgtattatgagaaaacacatccctctagatgttgggagatggtatattcatacattttctaacctactatagaatgctaatatatgacagtttataaccgtctacttcctagttttctctggaaaataaaagattactaagtattaaaattataatcaatatatgtaaataaaactactagaaataatagaataactagaaacaactctatgcaaagcatgcaagaaaagtagggcatgtttcgcaagtaaagtaggttgcattttttataaggaaaaCCATACAGAAGATAcaaataaaaagagatacctaaccttccctgtgttatatttgtatgggtaaaatgttatgttttcagaaattatataaaattcctggaagtttgtcaatgtcctccttatccatgctatgtgccactatagagtaatgagtcataattccaattattactttaaatgttgtgccaggcacagtggctcatgcctataatcccag cactttaggaggctgaggcgggtggatcacaaggtcaggagatccagaccatcctggttaactcggtgaatctccatctctattaaaaatataaaaaattagccgggcgtgatggaaggcacctgtagtcccagc +s panTro2.chr19 196757 2066 + 64473437 gtttgaccagctgtgtgtgtcccttaatccagtccagtagatgtctagaattaaccatcggaatatttatgcctgattcatggctgaaatcgtgtttgaccagctatgtgtgtctcttaattcagtcaagtagatgtccaatattaaccatcaGAAtatttatgcctgattcatggctgaaatttcaggatgaaagctatgaaatctctatttgtgtttgtatatctattaatgtatgttatgtacatgtgatattttcttaactccggataccactgcaaaattcatttataaaatcctctaaaagtgctctattccaacttggcttggaaaaaaataaccatttataaataaatattcaccaaactcctagaaacatagtaactgatcaaatgtctcttaagttaccatgatttggataaaacttagttaaatgagattaatataatatttttggtgtaataaaacaactatgtcttcaaagttatcactattgaatataaaacaaacataaattcctattctgcttgagttctagtcaaataagctaatattatacttac-agaaatgtaaaatcttaaagcttatagatttGGTTCTAATTAAGTTGTCATTCTTATGAAAAACATTATTTTTT--ATGGTGAAAAGATACACATATATTTAGAGTTAGCCAGCTGGGGTCAGTTTAGATGATCCCAATTTTGTTGCAACATCCAAAGCTTCATAATCAGGAGCCAGTTGAACATATGCCTTCTTCTCTTTATCAGGACAAATCAGGGTGGTGACCTTGGCCACATCACTGTCATAGAGCTTCTTCACGGTCTGTTTGATATGGTGCTTGTTGGCTTTAACATCCACAAAGAACACAAGCATGTTGTTTTCTTGTATCTTCTTC-CAGCCGACTCAGTGGTCAGTGGAAACTTGAT---AGCATAGTGGTCAAGC TTGTTTCTCCTGGGGGTGCTCTTCCGAGGATATTTGGGCTGCCTCCGGAGTCGCAGTGTCTTGGGCCACCTGAAGGTGAGTGATATGCAGATCTTCTTTTTTGCGTGTGGCTGTGGACACCTTTCAACACTGCCTTCTTGGCCTTTAAAGCCTTCACTTTGGCTTCGGCTGTAGGAGGAGCAGGAGCTTCCTTCGCTTTCGGTGCCATCTTGTGAAAAGTGAAAAACATTATTTCAAAAATAATTTGTTTACAGTAAATCTgcctaatagtagtttccaaagtacttttgctaatttttaaccttaaacttaagctaagtaaaagatttgcattaaatatctagaccatttataaataagatacaatactaaaacattaattactgaacataaataattcaagtttatatacttttggcttcctatttttacagaaagactaaagatattttggcctgttaataaacatgtttttttctgccacattgagaaattgtattatgaggaaacgcatccctctagatgttgggagatggtatattcatacattttttaacctgctatagaatgctaatatatgacagtttataactgactacttcctagttttctctggaaaataaaagattactaagtattaaaattataatcagtatatgtaaatagaactactagaaataatggaataactagaaacaaccccatgcaaagcatgcaagaaaagtagggcatgtttcgcaagtaaagtaggatgtattttttataaggaaaaCCATACATAAGATAcaaataaaaagagatacctaaccttccctgtgttatatttgtatgggtaaaatgttatgttttcagaaatgatataaaattcctggaaatttgtcaatgtcctccttatccatgctatgtgccagtatagggtaatgagtcataattccaattattattttaaatattgtgctgggtgcagtggcttacacctgtaatcccag cactttgggaggctgaggaggatggatcacaaggtcaggagatccagaccatcctggctaacccggtgaatctccatctccactaaaaatataaaaaattagccggctgtggtggcaggcacctgtagtcccagc + +a score=13860 +s hg18.chr1 219555 161 + 247249719 tactcgggaggctgaggcaggagaatggcgtgaacccaggagacagagcttgcagtgagccgagatcgcactgctgcactccagcctgggcgacagagcaagactctgtctctaaataaataaataaataa----atgttgtctgccacagaaaaaatcgaatAT +s panTro2.chr3 77587300 165 + 203962478 tacttgggaggctgaggcaggagaatggcgtgaacccgggagacagagcttgcagtaagccgagatcgcaccactgcactccagcctgggcgacagagcgagactctgtctctaaataaataaataaataaatatatgttgtatgccacagaaaaaatcgaatat + +a score=33729 +s hg18.chr1 219723 401 + 247249719 gaaaccccgtctctaccaaaaatacaaaaattagatgggcaggacggcatgtgcctgtagtcccaggtaatcaggaggctgaggagggaggatcgtttgcacccaggaggtagaggttgcagtgagctgacattgcacctttgcactccagcctgggcgatagagccagaccctgtctcaaaaaaaaTTTTTTT-AAATgaaaactatagccattgtgagttatcagattctagtcttgtttcttgtttctgggctatttttacctctttgtaaactggatcctgccatctgatgaattttGTCCCACAATGATACTTGGGGAACAAGAAGCCAAGTATTGTCTCTCCTACTAATGTATCTATTGTCAGTTAATTTGAAGGTCTCCAACCCTGGAACAAAGT +s panTro2.chr19 200660 402 + 64473437 gaaaccccatctctaccaaaaatacaaaaatgagatgggcatgatggcatgtgcctgtagtcccagctaatcaggaagttgaggagggaggatcacttgcacacaggaggtagaggttgcagtgagctgagattgcacctttgcaccccagcctgggcaacagagccagaccctgtctcaaaaaaaattttttttaaaggaaaactatagctattgtggattatcagattctagtcttgtttcttgttttggggctatttttacctctttgtaaactggatcctgccatctgatgaattttGTCCCACAATGATACTTGTGGAATAAGAAGCCAAATATTGTCTCTCCTACTAATATATCTATTGTCAGTTAATTTGAAGGTCTTCAACCCTGGAACAAAgt + +a score=23697 +s hg18.chr1 220124 270 + 247249719 TAGAAGAGGAAGGTTCTACTCCCCAAaatgcataaccaaattgtgctacattcatgtaatggaatactatttagccatagaaaggaacaagatatcaacacacacaaagacatgagtgaatcttgcatgcacattgctaagtggaagaagacagtctgaggaggatacacatagtgtgacctcatttaatgagacactggggaaggcaaactacacagatgggaagccattggctccatggggtgggggtttgaggcattccatatgata +s panTro2.chrUn 1540276 270 + 58616431 TAGAAGAGGAAGGTTCTGCTCCCCAAaatgcataaccaaattgtggtacattcatgtaatggaatactatttagccatagaaaggaacaagctatcaactgacacaaagacatgagtgaatcttgcatgcacattgctaaatggaagaagacagtctgaggaggatacacacaatgtgatctcatttaatgagacactggagaaggcaaactatacagatgggaagccattggctccatggggtgggggtttgaagcattccatatgata + +a score=49220 +s hg18.chr1 220394 611 + 247249719 ctttaatagtgggatatctgccacaatgcatttgtcgaaatatgcagaattttacagccaaatggttaaagcaaactctattcaaattaaatcaaattactcaggatgtggagtatcccaggacagaatacatcatgtgaaaaagaatttatgctacaaattacgatggtttggatgtggtttgtccccacaaaaactcatgttgaaatttgactcccactgtgtcagtgtggggcggtggggcctagtggacggtgtttgggtcgtggggacggatccctcatgaaaggattaatgtcctccatgggggtgagtgagttctgttctcacaggaatagat-aattcctgcaggagcaggtaattaaaaagagtctggcttccttggcttccctcttgctttcacttctgctatgtgatctctggtgcaccccttgctccccttccactttccaccatgaggtgaaaaagactgaggccccgccagatgcaactgcccaatctcagacattccagccaccagtattgtgaaccaaatgaaacttttttacttataaattacgcagcctcaggtattctgttacagaagcacaaaatggactaagacacaaatc +s panTro2.chrUn 56831951 612 - 58616431 ctttaatagggggatatctgccacaatgcatttatcaaaatacacagaattttatgaccaaatgggtaaatcaaactctattcaaattaaacaaaattactcaggatgtggagtatcccaggacagaatgcatcacgtgaaaaagaatttatgctacaaattactatggtttggatgtggtttgtccccgcaaaatctcatgttgaaatttgacccccaatgtggcagtgtgaggcggtggggcatagtggatggtgtttgggtcatggggacggatccctcatgaatagattaatgtcctccacagggatgactcagttctgctctcataggaatggattaattcctgcaggagtgggtaattaaaaagagtctggcttccttggcttcccttttgctttcacttttgctatgtgatctctggtgcaccccttgctccccttccgctttccaccatgaggtgaaaaagactgaggccccaccagatgcaactgcccaatctcagacattccagctactagtattgtgagccaaatgaatcttttttacttataaattagccagcatcaggtattctgttacagaagcacaaaatggactaggtaaaaactc + +a score=282229 +s hg18.chr1 221014 3176 + 247249719 actttgaaaatgaatagaatctgtaggctgaaggcacatgaactatacttcattattggattccattttataaagttctttccaacagaagcaattgtgaacaattgtaaaaccacagtgtctgtatctggagtaaaacaatgacttacataagtcgcagatggtgggaaccagctttctcactgttgaagtgggaggttacaaattagcaagacgagaaggctagaatgattcctgtgatagtagatcagaggtggagacatcaacgtaaacttatgcttagtttaatatagatacacacagttctacatagaaaactttataattaggtgtgtgtaggtaggttagacacgcacatatacttcctagcattgctaatgagggacaagatacaatgtgcattcagcagccacatgtaagttttcccaccattctgaaaggaatcaggctctttgaagaaatgtctgatactagaactgggacagtaaatataggagccaggataatctggaagtatcagaaagtaagtactaaaaaaattaaaatatatcaaacaaaaataaaagccaataaaaacagctaccgatggccaacacaggaaggaattgtgcaacataatgctatagtgtcaaataataactaaagcttaaagtaattatctaggtgtctgtatttgtatacctaggtgaataagcaaatggagttgcatagaaatctcctttgcaaaagaattccaaataactgatgtagacactcagccatcaagaaggtggagccaactcctcactccgtaagtgtgggctctgcatagtgacttgctccaaaagaacacatgcagtacggacaaggaggaaaaataacttcacagtggagaaatctgacaaacagtagctctgccaaatgatccaagtgaatatcaaagctgacagttcaccttgagaacatga agtgacaatggggggcattctacaaaattcctgaccaatcctcctcagtgctatgaaggtcatcatgagatggaaagcctgacacactgtcacagccaggaagagcctatgtgatgactacatgccgtgcgggatcctggatgggatcctgggtcagagtaagatagaactaagggaatccaaatgaaatatgaacttcagttaataacagtctatcagtattggttcattaactgcggcaaattatgtaagatattaataagccatgtgagacacactgatagaagatgttaataagagaggaaactaggttgcggctacatgggaaatctctgctttttttttttgacgatttctgtgtaagtaaaaaaaagacgtaaaataaaactttatttaaaaCACAGTTTTTTTAACACTTCCTTGTTTAATTATTTATACCATGAATTACTAGTAATTGACACTGTTAACTAGTCCTGTTTTTTAAAATAAGAGCAATTATGACACAAAAAATTAAACAGTGCAGACTGATATATAAATCAAAACAAATGTCCTTTACATGTTTTCTGTTACAGTAGTAACA-ATATGTGTAAACTTAATTATCATATTTTTTTCTTGTGCTGTGGTTGTGTCCTGGGTTCATTCTCTAAAATGCTGTTCACCTTAGACCAGGAAAAATATTAACCATACAGACTCTGTTTCAAGTCATAGCTGAATATTTTCAAAAGAGTGACTTTGTAAAAACATGTTCCAATGGCAAATTGATTCATTGTGATGGGATCAATTATTCCAAAGACTTCTTGTCTTTATTTTGTTCCCATGCCTACCTTTTAGCCATAATACAACAGAATCAAATATTGGCCACTGGGAAAAAA--TATTCAAAGAAAGAAAGAATGTGAACAGAACTTATGACCATGATGATTCAATGTTTTACCACAATGCTTTCTAAAACAAAAGAGTCTAAAAGGATATTCAAAGTCAATTTCCTC AGCGAGGATTTGCAGAAAATGAGGAAACTAGAAAAACAAAAATGGCGGGACATTCTACGGGTGATTTTAAATGTTGCTATGTTTTATGGGAAAAAATACTTTACCTTTTAAAGAATCACAAAGAATTATTGGAAACCCAAACTCTGGAATGTTTGCAAATTTAGTTGAGCTTCTGTGTAATTATGTCTATATAGGTAGCCATGAAGTTGATGATTTCTTAAAAATCTGTGCCTTATTTGTGTAATAAAAGACACAATGAATAATTAATACTCATAGGAACACTTACgaagggaaaataaatcttggggactcaaaatcactaagctaaagggaaaagtcaagctgggaactgcttagggcaaacccgcctcccattctatccaaa-acacccgtctgatcacctagataaatgcatacctgattgcctcacatggagagggtaatcagcaatgcaaaagaatgaaaccatttgtctcttacctacctgtgacctggaagccccctgtctggccttctcacctttctggactgaaccaatgtacatcttacacgtattgattgatctctcgtgtctccctaaagtgtataaaaccaagctgtgccccgaccaccttgggcccatgttgtcaggatctcctgaggaggcatcacaggcgcacatcctcaagattggcaaaataaactttctaaaaaatctgagagctgtctcagattttcagggttcacaCATGTAATGTAGGATGTCAATGTTTATAAAAGGGATGTTATTCTATCTACTATTAGAAATATGCTGTCAATTAACCTTAAACTTTCTCAACACAATAAAAAATGTTGATGAGGTACAAATAATATATCTAGGCTTAAATAGTGTTGCAAGTTTTAATATGCCTACTTTTCAATTTTTCAATACTATCTTTACTAATTTAACACTGTAAGAAAAATGAGTAATTAAAACATGAATAAAAGTGTTTACAGGGGATGCACATGT TTCCTCCAGCCTCTGCCTATACCCAACTTTCATCCCAACTGTCCTGATGGTGGCTCTAAGCATTTCTCCTTTCTCTATACCAAGATATCTCCCCAGAAACAAACCCAAATCTTACTATATGTTATGGCACGCTATGATGATGAGCAGCGATGAGCAGCCGAAGCCTCAAGGAAGGGATGCTTTTGTAAAACAAGACTTGTGGAATATAACATGTGAAAGTAAAGCCCATGGCAGAACTCCCTCCTCAGCACACGG +s panTro2.chrUn 56832599 3177 - 58616431 actttgaaaatgaatagaatctgtaggctgaag-cacatgaactacacctcatcattggattccattttataaagttctttcca-cagaagcaattgtgaacaattgtaaaaccacagtgtctgtatctggagtaaaacaatgacttacataagtcgcagatggtgggaaccagctttctcactgttgaaatgggaggttacaaattagcaagacgagaaggctagaatgattcctgtgatactagatcagaggtggagacatcaacgtaaacttatgtttagtttaatgtagatacacacagttctacatagaaaactttataattaggtgtgtataggtaggttagacacacacatatacttcctagcattgctaatgagggacaagatacaatcttcattcagcagccagatgtaagttttcccaccattctgaaaggaatcaggctctttgaagaaatgtctgatactagaactgagacagtaaatataggagccaggataatctggaagtatcagaaagtaagtactaaaaaaattaaaatatatcaaagaaaaataaaagccaataaaaacagctaccgacggccaacacaggaaggaattgtgcaacataatgctatagtgtcgaataataactaaagcttaaagtcattatctaggtgtctgtatttgtatacatagctgaataagcaaatggagttgcatagaaatctcctttgcaaaagaattccaaataattgatgtagacactgagccatgaagaaggtggagccaactcctcactccgtaagtgtgggctctgcatagtgacttgctccaaaagaacacatgcagtacggacaagcaggtaaaataacttcacagtggagaaacctgacaaacagtagctctgccaaatgatccaagtgaacatcaaagctgacagttcaccttgagaacatgA AGTGACAAtggggggcattctacaaaattcctgaccaatcctcctcagtactatcaaggtcacc-tgagatggaaagcctgacacactgtcacagccaggaagagcccacgtgatgactacatgtcatgcgggatcctggatgggatcctgggtcagagtaagatagaactaagggaatccaaatgaaatatgaactttagttaataacagtctatcagtattggttcattaactgtgacaaattctgtaagatattaataagccatgtgagacacactgatagaagatgttaataagagaggaaactaggttgcggctacatgggtaatctctgcttttttttttggacgatttctgtgtaagtaaaaagaagatgtaaaataaaactttatttaaaaCACTGTTTTTTTAACACTTCCTTGTTTAATTATTTATACCATGAATTACTAGTAATTGACACTGTTAACTAGTCCTGTTTTTTAAAATAAGAGCATTTATGACACAAAAAATTAAACAGTGCAGACTGATATATAAATCAAAACAAATGTTCTTTACATGTTTTCTGTTACAGTAGTAACACATATGTGTAAATTTAAGTATCATATTTTTTTCTTGTGCTGTGGTGGTGTCCTGGGTTCATTCTCTAAAATGCTGTTCACCTTAGACCAGGAAAAATATTAACGTTACAGACTCTGTTTCAAGTCATAGCTAAATATTTTCAAAAGAGTGACTTTGTAAAAACATGTTCCAATGGCAAATTGATTCATTGTGATGGGATCAATTATTCCAAAGACTTCCTGTCTTTATTTTCTTGCCATGCCTACCTTTTAGCCGTAATACAACAGAATCAAATATTAGCCACTGGGAAAAAAAATATTCAAAGAAAGAAAGAATGTGAACAGAACTTATGACCATGATGATTCAATTTTTTACCACAATGCTTTCTAAAACAGAAGAGTGTAAAAGGATATTCAAAGTCAATTTCCTC AGCGAGGCTTTGCAGAAAATGAGGAAACTAGAAAAACAAAAATGGCAGGACATTCTACGGGTGATTTTAAATGTTGCTATGTTTTATGGGAAAAAATACTTTACCTTTTAAAGAATCACAAAGAATTATTGGAAACCCAAACTCTGGAATGTTTGCAAATTTAGTTCAGCTTCTATGTAATTATGTCTATATAGGTAGCCATGAAGTTGATGATTTTTTAAAAATCTGTGCCTTATTTGTGTAATAAAAGACACAATGAATAATTAATGCTCATAGGAACACTTACgaagggaaaataaatcttggagactcaaaatcactaagctaaagggaaaagtcaagctgggaactgcttagggcaaacccgcctcccattctatccaaagacacccgtctgatcaccgagataaatgcatacctgattgcctcacgtggagagggtaatcagcaacgcaaaagaatgaaaccatttgtctcttacctacctgtgacctggaagccccctgtctggccttctcacctttctggactgaaccaatgtacatcttacacatattgattgatctctcgtgtcttcctaaagtgtataaaaccaagctgtgccccgaccaccttgggcccatgttgtcaggacctcttgaggaggcatcacgggcgcacatcctcaagactggcaaaataaactttctaaaaaatctgagagctgtctcagattttcagggttcataCATGTAATGTAGGATGTCAATGTTTATAAAAGAGATATTATTCTATCTACTATTAGAAATATGCTGTCAATTAATCTTAGACTTTCTCAACAAAATAAAAAATGTTGATGAGGTACAAATAATATATCTAAGCTTAAATAGTGTTGCAAGTTTTAATATGCCTACTTTTCAATTTTTCAATACTATTTTTGCTAATTTAACACTGTAAGAAAAATGAGTAAATAAAACATGAATAAAAGTGTTTACAGGAGATGCACATGT TTCCTCCAGCCTCTGCCTATACCCAACTTTCATCCCAACTGTCCTGATGGTGGCTCTAAGCACTTCTCCTTTCTCTATACCAAGATCTCTCCCCAGAAACAAACCCAAATCTTACCATATGTTATGGCACGCTATGATGATGAGCAGCGATGAGCAGCCGAAGCCTCAAGGAAGGGACGCTTTTGTAAAACAAGACTTGTGGAATATAACGTGTGAAAGTAAAGCCCATGGCAGAGCTCCCTCCTCAGCACACGG + +a score=5815 +s hg18.chr1 224190 71 + 247249719 GGAGCAGACAGGAAGCTGTTGCCTCACCTTCCTCAATGGCCTACAGCCACATCTCCCCAGGTCAGTCTTAA +s panTro2.chr3 77593762 70 + 203962478 GGAGCAGACAGGAAGCTTTTGCCTCACCTTCCTCAATGGCCTGTAGCCACATCT-CCCAGGTCAGTCTTAA + +a score=101136 +s hg18.chr1 224261 1125 + 247249719 GGACAATGAAACTCTGGTCTTCACTGTGGACACACCACACTACCAGGCGCTCCAAAGCCATGGTGACCCACCCTCGGGTGGGTCCTGAGGAGAACAAAGCTCTGGTTCTAATTCTAACCCTAACCTTGTCCCAAGACTTTGACACTGAACCTAAATCCTGATCCCTATCCTGGTccctaattctgacccttactttgaccctgactttgatctcgaccctgaccatgaccccacctctaaccatacttctggccctgactctgacccagatcctaatcctatccctaaccctaTTATTATCTTTACAATCTATGTCTAATCTTACCCTCTAGTGCTAAATAGCTGTACCCAAAAGCACTTTAAAATTATTTAACTTCTTTTCCTTGAATTCTCTAAGGACATCCTAAAGGAGATGTCAATATGTATTTTGCATTCCCTCTGAGTGGTATGGCTTCAGATAAGAAGTTCTAATACTTTGCAAGACATAAAAAGTTTGGAGGGTGACAGCACTGGGTTGTTAGGGATGCATGTTGGCATTCgtggtagtcataggtgctgttctccagatattttcagttcatattttatgaatgcattctgactgttccatcccgcctacttacattttcacatggccacatgactttttttttgccaatggaggtgagaagaaataacatgtgactttttcaggagaaatctccaagaaacagagtgctattccgcatacttttttctcttttctatagcaatggggatcttattgattgtccctccttccgtctggattcctgtgttaggatgacacagcacagagctacctctcacctgacccatgatgaaatgtaaataaatgaggaagaagatttttgagccactgaaatttggaggttgtttgtcaccacagtttaacctagcccccatttactgatgcaCGGCTGAAGAAT GAGTCCGAACTGGATCTGGACAAGACATGTGAAGAGCGCTCCAGGCTGAGTAAAATTCAAGTGTTGTCTCAAAGATAACACTGAGCACGATATGTTATTGGGGTGGGTGTGGGATAAATAAGGTATATCAGGTGAGAATAACAAGAAACTCAACTTTAAAAGACGGTGCCGATTTGGA +s panTro2.chrUn 56835776 1123 - 58616431 GGACAATGAAACTCTAGTCTTCACTGTGGACACGCCACACTACCAGGTGCTCCAAAGCCATGGTGACCCACCCTCGGGTGGGTCCTGAGGAGAACAAAGCTCTGGTTCTAATTCTAACCCTAACCTTGTCCCAAGACTTTGACACTGAACCTAAATCCTGATCCCTACCCTGGTccctaattctgacccttaatttgaccctgactttgatcttgaccctgaccatgaccccacctctaaccatacttctggccctgactctgacccagatcctaatcctatccctaaccctaTTATTATCTTTACAATCTATGTCTGATCTTACCCTCTAGTGCTAAATAGCTGTACCCAAAAGCACTTTTAAATTATCTAACTTCTTTTCCTTGAATTCTCTAAGGACATCATAAAGGACGTGTCATTATGTATTTTGCATTCCCTCTGAGTGGTATGGCTTCAGATAAGAAGTTCTAATACTTTGCAAGACATAAAAAGTTTGGAGGGTGACAGCACTGGGTTGTTAGGGATGCATGTTGGCATTCgtggtagtcataggtgccgttctccagatattttcagttcatattttatgaatgcattctgac--ttccatcccacctacttacattttcgcatggccacatgactttttttttgccaatggaggtgagaagacataacatgtgactttttcaggagaaatctccaagaaacagagttctattccgcatgcttttttctcttttctatagcaatggggatcttattgatcgtccctccttccgtctggattcctgtgttaggatgacacagcacagagctacctctcacctgaccagtcatgagatgtaaataaatgaggaagaagatttttgagccactgaaatttggaggttgtttgtcaccacagtttaacctagcccccatttactgatgcaCAGCTGAAGAAT GAGTCCGAACTGGATCTGGACAAGACATGTGAAGAGCGCTCCAGGCTGAGTAAAATTCAAGTGTTTTCTTAAAGATAACAGTGAGCACGATATGTTATTGGGGTGGGTGTGGGATAAATAAGGTATATCAGATGAGAATAATAAGAAACTCAACTTTAAAAGACGGTGCTGATTTGGA + +a score=17379 +s hg18.chr1 225388 189 + 247249719 ACACCAAATTGGAAGACAGCAGGAGCTGCCCCATAATACCAGTAAAGTGAGAAGCAGAGATAAACTAGTCCTAGACAGCTGACTCATGTTGGGGGCAGCCCACTCACAGTGGCCCTGACCCAACTCTGACTAGAGGCCACTTGATCTCAACACCAGGGTGCTCAATGGCCCGTCCTGGTACTCTGCTCT +s panTro2.chrUn 56816265 189 - 58616431 ACACCAAATTGGAAGACAGCAGGAGCTGCCCCATAATACCAGTAAAGTGAGAAGCAGAGATAAATTAGTCCTAGACAACCGACTCATGTTGGGGGCAGCCCACTCACAGTGGCCCTGACCCAACTCTGACTAGAGGCCACTTGctctcaacaccagggtgctcaatggcccgtcctggtactctactct + +a score=80560 +s hg18.chr1 225577 931 + 247249719 ACACTGGTTGTAGGAAGGAATCTGCAGGTTGAAATAAGGAGATCATTTCCCTGAGGTTCCGAAGCTCATATTTACTCACCATTTGTTGTTTACTGCTAATGTTGAGCACTGTCAGTAAAATACATAAAACCCtttgccaatccaggaagtgaaaatgacactttactgttttaatttgcatttctctgcttacaagtggattacacacattttcgtgtgctgttggctacttattcattcagaaaacatactaagtgctggctctttttcatgtcctttatcaagtttggatcatgtcatttgctattttcttTCTGATGTAAACTCTCAAAGTCTGAAGTGTATTGTCTTTTCCTGACACATATGTTGTAAATAATTTTCTGGCTTACATTTTGACTTTTAATTTCATTCACGATGTTTTTAATGAATAATTTTAATTTTTATGAATGCAAGTTAAAATAATTCTTTCATTGTGGTCTCTGACATGTCATGCCAATAAGGGTCTTCTCCTCCAAGAGCACAGAAATATTTGCCAATACTGTCCTTAAAATCGGTCACAGTTTCATTTTTTATATATGCATTTTACTTCAATTGGGGCTTCATTTTACTGAATGCCCTATTTGAAGCAAGTTTCTCAGTTAATTCTTTTCTCAAAGGGCTAAGTATGGTAGATTGCAAACATAAGTGGCCACATAATGCTCTCACCTCctttgcctcctctcccaggaggagatagcgtccatctttccactccttaatctgggcttggccgtgtgacttgcactggccaatgggatattaacaagtctgatgtgcacagaggctgtagaatgtgcacgggggcttggtctctcttgctgccctggagaccagctgccccacgaaggaaccagagccaacctgctgcttcctggaggaagacagtccctct +s panTro2.chr1_random 7323839 929 + 9420409 acactggctgtaggaaggaa-CTACAGGTTGAAATAAGGAGATCATTTCCCTGAGCTTCCGAAGCTCATATTAACTCACCATTTGTTGTTTACTGCTAATATTGAGCACTATCAGTAAAATACATAAAACCCtctgccaatccaggatgtgaaaatgacactttactgttttagtttgtatttctctgcttacaaatggaatacacacattttcatgtgctgttggctacttATTCATTCAGAAAACTTA-TAACTGCTGGCTCTTTTTCATGTCCTTTATCAAGTTTGGATCATGTCATTTGCTGTTTTCTGTCTGATGTAAACTCTCAAAGTTTAAAGGGTATTGTCTTTTCCTGACACGTACATTGCGAATAATTTTCTGGCTTACATTTTGACTTTTAATTTCATTCACGATGTTTTTAATGAATAATTTTAATTTTTATGAATGCAAGTTAAAATAATTCTTTCATTGTGGTTCCTGACATGTCATGCAAATAAGGGTCTTCTCCTCCAAGAGCACAGAAATATTTGCCAATACTGTCCTTAAAATCGGTCACAGTTTCATTTTTTATATATGCCTTTTACTTCAATTGGGGCTTCATTTTACTGAATGCCCTATTTGAAGCAAGTTTCTCAGTTAATTCTTTTCTCAAAGTGCTAAGTATGGTAGATTGCAAACATAAATGGCCACATAATGCTCCCACCTCctttgcctcctctcccaggaggagatagtctccatctttccactccttaatctgggcttggccatgtgacttacactggccaatgggatattaacaagtctgatgtgcacagaggctgtagaacgtgcactggggcttggtctctcttgctgccctggagaccagctaccccacgaaggaaacagagccaacctgctgcttcctggaggaggacagtccctct + +a score=5330 +s hg18.chr1 226508 59 + 247249719 gtccctctgtctctgccaaccagttaacctgctgcttcctggagggagacagtccctca +s panTro2.chr1_random 8583060 59 + 9420409 GTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGAAGACAGTCCCTCT + +a score=223737 +s hg18.chr1 226567 2476 + 247249719 gtccctctgtctctgccaaccagttaacctgctgcttcctggaggaagacagtcactctgtctctgccaacccagttgaccgcagacatgcaggtctgctcaggtaagaccagcacagtccctgccctgtgagccaaaccaaatggtccagccacagaatcgtgagcaaataagtgatgcttaagtcactaagatttgggCAAAAGCTGAGCATTTATCCCAATCCCAATACTGTTTGTCCTTCTGTTTATCTGTCTGTCCTTCCCTGCTCATTTAAAATGCCCCCACTGCATCTAGTACATTTTTATAGGATCAGGGATCTGCTCTTGGATTAATGTTGTGTTCCCACCTCGAGGCAGCTTTGTAAGCTTCTGAGCACTTCCCAATTCCGGGTGACTTCAGGCACTGGGAGGCCTGTGCATCAGCTGCTGCTGTCTGTAGCTGACTTCCTTCACCCCTCTGCTGTCCTCAGCTCCTTCACCCCTGGGCCTCAGGAAATCAATGTCATGCTGACATCACTCTAGATCTAAAAGTTGGGTTCTTGgaccaggcgtggtggctcacacctgtaatcccagcactttgggaggccgaggcgggtggatcacaaggtcaggagatcaagacgattctggctaacacggtgaaaccccgtctctactaaaaatacaaaaaaattagccgggtgtggtggcaggtgcctgtagccccagctacttgggaggctgaggcaggagaatggcttgaacctgggaggtggagcttgcagtgagccaagatcacgccactgcactccagaatgggagagagagcgagactttctc-------aaaaaaaaaaaaaaaaCTTAGGTTCTTGGATGTTCGGGAAAGGGGGTTA-TTATCTAGGATCCTTGAAGCACCCCCAAGGGCATCTTCTCAAAGTTGGATGTGTGCATTTT CCTGAGAGGAAAGCTTTCCCACATTATACAGCTTCTGAAAGGGTTGCTTGACCCACAGATGTGAAGCTGAGGCTGAAGGAGACTGATGTGGTTTCTCCTCAGTTTCTCTGTGCAGCACCAGGTGGCAGCAGAGGTCAGCAAGGCAAACCCGAGCCCGGGGATGCGGAGTGGGGGCAGCTACGTCCTCTCTTGAGCTACAGCAGATTCACTCTGTTCTGTTTCA---TTGTTGTTTAGTTTGCGTTGTGTTTCTCCAACTTTGTGCCTCATCAGGAAAAGCTTTGGATCACAATTCCCAGtgctgaagaaaaggccaaactctggaaaaaattttgaatattttgagccaaatgtgaggactacaacctgtgagaacggaaaataaatcctgggaccccagactcactaagccaaagggaaaagccaagctgggaactggcttatgcaaacctgcttcccatctggttcctaaataagatagctattacacaaagataaaaaagctacatccctgcctctacctccatcgcatgtaaaatgtgtattcagtgaacgctgaccaaagacagaagaatgcaacaatttgcctctgatttacccacacccattttttccacttcttcccctttccccaatacccacacttttcccctttacttactgaggtccccagaaaatctttgggaaaagcacggaccacagtttttcctgtggttctctgttcttttctcaggtgtgtccttaaccttgcaaatagatttcttgaaatgattgagactcaccttggttgtgttctttgattAGTgcctgtgacgcagcttcaggaggtcctgagaacgtgtgcacagtttagtcggcagaaacttagggaaatgtaagaccaccatcagcacataggagttctgcattggtttggtctgcattggtttggtctggaaggaggaaaattcaaagtaatggggcttacaggtcatagatagattcaaaga ttttctgattgtcaattggttgaaagaattattatctacagacctgctatcaatagaaaggagagtctgggttaagataagagactgtggagaccGTGCATAGTTGCTTCCTGATCAGCTCTTTATTTGATTGAGAGTGAGGCAGGGAAGATTAGAGGGAAGCTTACAGTGGAATTCAGGGCTAAGGCTGCTATTCTTTTGCTCCTTGTAACTTCCTACAGTGTTGTCAGCATCCACATACTTCTCTGTGGGGTTggtctcagagccaggttaccttgtcttaggtccagtggcaccctgactggcttggtgtccttgaacaagttacctaacctctccatacctcagtccctcagctgtaaaattaaaaaaaaaaaaaaagaagaagaagagtacctactgtatagcattgatttgaagattgaatgagctggtattatacaacgtttagaagcagtgcctgacacgcaaaaggctctcaacaaatACTATCCTTTACTAATATCCTGTGTGTCTGTATCAGAGCTGGTGGGGTGGAGGGACAGAAACAAGTGGG +s panTro2.chr1_random 7324768 2478 + 9420409 gtccctctgtctctgccaaccagttaacctgctgcttcctggaggaggacagtcactctgtctctgccaacccagttgaccgcagacatgcaggtctgctcaggtaagaccagcacagtccctgccctgtgagccaaaccaaatggtccagccacagaatcgtgagcaaataagtgatgcttaagtcactaagatttgggCAAAAGCTGAGCATTTATCCCAATCCCAATACTGTTTGTCCTTCTGTTTATCTGTCTGTCCTTCTCTGCTCATTTAAAATGACCCCACTGCATCTAGTACATTTTTATAGGGTCAGGGATCTGCTCTTGGATTTATGTCGTGTTCCCACCTCGAGGCAGCTTTGTAAGCTTCTGAGCACTTCCCAATTCCGGGTGACTTCAGGCGCTGGGAGGCCTGTGCATCAGCTGCTGCTGTCTGTAGCTGAGTTCCTTCACCCCTCTGCTGTCCTCAGCTCCTTCACCCCTGGGCCTCAGGAAATCAATGTCATGCTGACATCACTCTAGATCTAAAACTTGGGTTCTTGgaccaggtgcggtggctcacacctgtaatcccagcactttgggaggccgaggcgggtggatcacaaggtcaggagatcaagaagatcctggctaacacggtgaaaccccgtctctactaaaaatacaaaaaaattagccgggtgtggtggcaggtgcctgtagccccagctactcgggaggctgaggcaggagaatggcgtgaacctgggaggtggagcttgcagggagccaagatcacgccactgcactccagactgggagagagagcgagactttctcaaaaaaaaaaaaaaaaaaaaaaaCTTAGGTTCTTGGATGTTCGGGAAAGGGGGTTCTTTATCTAGGATCCTTGAAGCGCCCCCAAGGGCATCTTCTCAAAGTTGGATGTGTGCATTTT CCTGAGAGGAAAGCTTTCCCACATTATACAGCTTCTGAAAGTGTTACTTGACCCACAGATGTGAAGCTGAGGCTGAAGGAAACTGATGTGGTTTCTCCTCAGTTTCTCTGTGTGGCACCAGGTGGCAGCAGAGGTCAGCAAGGCAAACCCGAGCCCAGGGATGCGGGGTGGGGGCAGGTACGTCCTCTCTTGAGCTACAGCAGATTAACTCTGTTCTGTTTCATTGTTGTTGTTTAGTTTGCGTTTTGTTTCTCCAACTTTGTGCTTCATCCGGGAAAGCTTTGGATCACAATTCCCAGtgctgaagaaaaggccaaactctggaaaaaa-tttgaatattttgagccaaatgtgaggaccacaacctgtgagaatggaaaatacatcctgggaccccagactcactaagccaaagggaaaagccaagctgggaactggcttatgcaaacctgcttcccatctggttcctaaataagatagctattacacaaagacaaaaaagctacatccctgcctctacctccatcgcatgtaaaatgtgtattcagtgaacgctgaccaaagactgaagaatgcaaccatttgcctctgatttacccacacccattttttccacttcttcccctttccccaatacccacacttttcccctttacttactgaggtccccagacaatctttgggaaaatcacggaccacagtttttcctgtggttctctgttcttttctcaggtgtgtccttaaccttgcaaatagatttcttgaaatgattgagactcaccttggttgtgttctttgattAGTgcctgtgacgcagcttcaggaggtcctgagaacgtgtgcacagtttagtcggcagaaacttagggaaacgtaagaccaccatcagcacataggagttctgcattggtttggtctgcattggtttggtctggaaggaggaaaattcaaagtaatggggcttacaggtcatagatagattcaaaga ttttctgattgtcaattggttgaaagaattattatctacagacctgctatcaatagaaaggagagtctgggttaagataagagactgtggagaccGTGCATAGTTGCTTCCTGATCAGCTCTTTATTTGATTGAGAGTGAGGCAGGGAAGATTAGAGGGAAGCTTACAGTGGAATTCAGGGCTGAGGCTGCTATTCTTTTGCTCCTTGTAACTTCCTACAGTGTTGTCAGCATCCACATAATTCTCTGTGGGGTTggtctcagagccaggttaccttgtcttaggtccagtggcaccctgactggcttggtgtccttgaacaagttacctaacctctccatacatcagtccctcagctgtaaaatttaaaaaaaaaa-----aagaagaagagtacctactgtatagcattgatttgaagattgaatgagctggtattat---acgtttagaagcagtgcctgacacgcaaaagactctgaacaaatACTATCCTTTACTAATATCCTGTGTGTCTGTATCAGAGCTGGTGGGGTGGAGGGACAGAAAGAAgtggg + +a score=198101 +s hg18.chr1 229043 2232 + 247249719 AGAAGGTAAAGAGATGGGCAAATGATCTCTAAACTCTCTCTGGCACTAACACAATTCTTTATTATGTGTTTTGTCTGGCTCTTTATATTGATAGCTGTTCCAGAGGCAATCAATAGCTATTAGTCGGTTTTATTCTTATTTTTCTGTCTGATCTTACAAGGGAGCAAACTGTGGCAAAGTATGAACTTACTTCTCAGGAAATTAACCATTATATTGGCAATCACTGTGATTATTTGAACTTCAGCGTCTGGACAAATTTAGTCACATGAAATACAGAAGAGAGATTTCTCATGGTTAAAACGAAGCTCTCTTTATTTGCTTCTGCTAATTAAAAAATCAGAGCTAAAGATACTTAAACACTACAGTTAAAATGCCATGGTTGTCTATTGGCTTAACGAATTCTCTTATGAAATCAACTCTAAAATGTTATCCATCATAAATCATGAAACGCAATTTTTCTTATTCTCTTTAGAGCTTTACAATTCATCTTAAAGACCAGTGTTTACACTCTCTTCTGTAGGTTGTACAATAACTTTTGGTGAGAAAAAATAAAAGTCTGGCTTTCTGACTCATAGGTGTGTTCCCTTTAACAGAAAAAGAAAATATGTCCTCTTTAAAACTGATGATCATTGGTCACCTCAATTTTATTGAAGTTCACTTCTGACCTCTTTAGATGTAGTTCTCTACATAAAACTGCCCAACAGAATTCTCTGTCTGAATGTCTCCTCCACAAACAAAATTTTAAGAACTAAAATTATCATCTTTCCTTCCAAATATGCTCTCCCTATGTCCCCAGGGCTCTCCATGTGTAGAGCTGAGACCATTTGCCACTCAGTTTCCTCACCCAATTAATTACAAGTCCCAACAATTTTCCGGtttttttgtttttgtttttgtttttagacggagtcttgctctgtcaccaggctggtgtgcggtggtgcaat ctcagctcactgcaacctccgctgcctgtgttcaagcgattctcctgcctcagcttcccaagtagctgggattataggtgtgtgccactacatccagataatttttgtatttttagtagagaggggatttcaccatattggcccagatgatctcaatctcttgacctcatgatctgcccaccttggcctcccaaagtgctgggattacaggcgtgagccgccatccctggccCAGTTTTGCCTTTTTAACATCCCTCAGCTCTTCAAATCCATTTTCTcttctctaacacctccccattccccagctcgtaatgaactcgtaagtaaattactacaatcacctcccaaatggtcttcctggctccatcagccttgtgaccttcaagttcattttccacatggatgtcagagtaactttctaaaatgaaaatctgaccacgttactctcttgcctaaatccgcctatggccgctcttaggatcaagtctaaactcccgaccctggaacatcaggtcttcgtgctctgttcactgcttctctacctcacctgcaaccaACACCACTCCCACATCCATATGCTGCTCACCGTGTATCAACATGAACAGGAGGTGGGTGTTTCAGTCCCCAGGAAGACACTGGGCCTTTTCAATCATCTACTGCTTTGTAATAACCACCCCGCAAACTGACCACATGATTTCATTTTGCAAGGGTTCCTTCCTTgggctgtgttcagcaaaagggtttactgagctggcaggtccaagatggcctcactcacaggactggctgttgatgggagccttgatgctcttgggctcaccccttatcctccagtaggttagagcttcttacagtggtttcaggcagcatctgaagacagtaaaagcagaagctccaaggcttcttacattctagcctggaaaattacatcacattgcttccttcata-tttttttggcaaatcaggttgcaaggcttgcccagattag ggtaaagaggcaaagaggctccttttcttttcttttcttttcttttttcttttttttttttttttgagtcagaatctcgctctgttgcccaggctggagtgcagtggtgcgatctaggctcactgcaagctctgcctcctgggttcacgccattctcctgcctcaggctcccaagtagctgagactacaggcacctaccaccacacccggctaa----ttttttttttttttttgtattttttagtagagactgtgtctcactgtgttagccaggatggtctccatctcctgacctcgtga +s panTro2.chr1 223988426 2212 + 229974691 AGAAGGTAAACAGATGGGCAAATGATCTCTAAAGTCTCTCTGGCACTAACACAATTCTTTATTATGTGTTTTGTCTGGCTCTTTATATTGATAGCTGTTCCAGAGGCAATCAATACCTATTAGTCGGTTTTATTCTTATTTTTCTGTCTGACCTTACAGGGGAGCAAACTGAGGCAAAGCATGAACTTACTTCTCAGGAAATTAACCATTATGTTGGCAATCGCTGTGATTATTTGAACGGCAGCATCTGGACAAATTTAGTCACATGAAGTACAGAAGAGAGAGTTCTCATGGTTAAAACGAAGCTCTCTTTATTTGCTTCTGCTAATTAAAAAATCAGAGCTAAAGATACTTAAACACTACAGTTAAAATGCCATGGTTGTCTATTGGCTTAATGAATTCTCTTATGAAATCAACTCTAAAATGTTATCCATCATAAACCATGAAACACAATTTTTCTTATTCTCTTTAGAGCTTTACAATTCATCTTAAAGACCAGTGTTTACACTCTCTTCTGTAGGTTGTACAATAACCTTTGGCGAGAAAAAATAAAAGTCTGGCTTTCTGACTCATAGGTGTGTTCCCTTTAACAGAAAAAGAAAATATGTCCTCTTTAAAACTGATGATCATTGGTCACCTCAATTTTATTGAAGTTCACTTCTGACCTCTTTAGATGTAGTTGTCTACGTAAAACTGCCCAACAGAATTCTCTGTCTGAATGCCTTCTCCACAAACAAAATTTTAAGAACTAAAATCATCATCTTTCCTTCCAAATGTGCTCTCCCTATGTCCCCAGGGCTCTCCATGTGTAGAGCTGAGACCATTTGCCACTCAGTTTCCTCACCCAATTAATTGCAAGTCCCAACAAttttcc------------tttttttttttttttaaatggagtcttgctctgtcaccaggctggtgtgcggtggtgcaat ctcagctcactgcaacctccgctgcctgggttcaagcgattctcctgcctcagcttcccaagtagctgggattataggtgtgtgccactacatccagataatttttgtatttttagtaaagaggggatttcaccatattggcccagatgatctcaatctcttgacctcatgatctgcccaccttggcctcccaaagtgctgggattacaggcatgagccaccatccctggccCACTTTTGCCTTTTTAACATCCCTCAGCTCTTCAAATCCATTTTCTcttctctaacacctccccattccccagctcgtaatgaactcttaagtagattactacaatcacctcccaaatggtcttcctggctccatcagccttgtgaccttcaagttcattctccacatggatgtcagagtaactttctaaaatgaaaatctgaccacgttactctcttgcctaaatctgcctatggccgctgttaggatcaagtctaaactcccgaccctggaacatcaggtcttcgtgctctgttcactgcttctctacctcacctgcaaccaacaccactcccacatccatattctgctcACCGTGTATCAACATGAACAGGAGGTGGGTGTTTCAGTCCCCAGGAAGACACTGGGCCTTTTCAATCATCTACTGCTGTGTAATAACCACCCCGCAAACTGACCACATGATTTCATTTTGCAAGGGTTCCTTCCTTgggctgtgttcagcaaaagggtttactgagctggcaggtccaagatggcctcattcacaggactggctgttgatgggagccttgatgctcttgggctcaccccttatcctccagtaggttagagcttcttacagtggtttcaggcagcatctgaagacagtaaaaacagaagctccaaggcttcttacattctagcctggaaaatcacatcacattgcttccttcatattttttttggcaaatcaggtttcaaggcttgcccagattag ggt--------aaagaggctccttttcttttcttttcttttctt-----ttctttttttttgtttgagtcagaatctcgctctgttgcccaggctggagtgcagtggcacgatctaggctcactgcaagctctgcctcctgggttcacgccattctcctgcctcaggctcccaagtagctgagactacaggcacctgccaccacgcccggctaattttttttttttttttttttgtattttttagtagagactgtgtttcactgtgttagccaggatggtctccatctcctgacctcgtga + +a score=81076 +s hg18.chr1 231275 904 + 247249719 tccTTGCAAAGGGACATGCAGACCACATTAGTGAGAATATGTGCCTGTATTTTGCAATCTGTAACATGGGCATAAACTAAATGTTTTCCAAAGGGAATAGGGCAAAACAAAAAGGACCTTGACCACTCCTT-GGCCCTGAATAAATCCAGGAAGCCTAAGAGTATGACTATCCTGAGGTAGAAAGAGGGTCACATGCTGGATAAGAGGTACCTGGGCTCTCCACTTACAAGAAGAGAGCATGGTTACATTTATAATCACCATTCCCAACATGCTGTGAGTGCAGGCAGCTACCAGGAGGAGAACAAAGGAAATAACCAGGACACTCATCTCTAAACCTGTTAATTTAATCACACGGAACACTTCTATTTAAAATTCCCGAGAGTTAAGATGTAAGAATGCTTATCAAGGTAAATGCTGTTCACACTGCTTGGAGTGTCAGGCCTAGATCTCTATCCATCAGAaacaacaatatcaataacaacaacagcaacaTGATGATGGGGCAATTTCTTAAAAGCACCATGTATTTTATCGatacatgtccgttgcagaaaatccaggtgaatccaaagaagaaataaatgtcttccacaatcccatagcccagagctaactaACCACTATAAAGAACCCAGCGTGGTTTTAACTCATGGATCAAAAGATGCTCATCAAAGGCTCTGAGCTTTCCTGAGTGCTAACAGGAAACATCCAGCATCACTGGTCTCTCCAAGGCTGCAGGTGTCTTTGCCCATAGTGCCTGTTTTGTGTCAGGGAAAGAATCAACCTGGGAGCCAAGCCCAGGAATCAGGATGACCAAGACATACTGCACAAGGAGGGAACAAACCCATCCAAGGACACTCAAGGACAAATCAAGCAAATGAATTTAAGGGAGACGTGCTCATGG +s panTro2.chr1_random 7327830 904 + 9420409 TCCTTGCAAAGGGACGTGCAGACCACATTAGTGAGAGTATGTGCCTGTATTTTGCAATCTGTAACATGGGCATAAACTAAATGTTTTCCAAAGGGAATAGGGCAAAACAAAAAGGACCTTGACCACTCCTTTGGTCCTGAATAAATCCAGGAAGCCTAAGAGTATGACTATCCTGAGGTAGAAAGAGGGTCACATGCTGGATAAGAGGTACCTGGGCTCTCCACTTACAAGAAGAGAGCATGGTTACATTTATAATCACCATTCCCAACATGCTGTGAGTGCAGGCAGCTACCAGGAGGAGAACAAAGGAAATAACCAGGACACCCATCTCTAAACCTGTTAATTTAATCACATGGAACACTTCTATTTAAAATTCCAGAGAGTTAAGATGTAAGAATGCTTATCAAGGTAAATGCTGTTCACACTGCTTGGAGTGTCAGGCCTAGATCTCTATCCATCAGAaacaacaatatcaataacaacaacagcaacaTGATGATGGGGCAATTTCTGAAAAGCACCATGTATTTTATCGATACATGTCCGTTGCAGAAAATCCAGGCGAATCCAAAGAAGAAATAAATGCCTTCCACAATCCCATAGCCCAGAGCTAACTAACCACTATAAAGAACCCAGCGTGGTTTTAACTAATGGATCAAAAGATGCTAATCAAAGGCTCTGAGCTTTCCTGAGTGCTAACAGGAAACATCCAGCATCACTGGTCCCTCCAAGGCTGCAGGTGTCTTTGCCCATAGTGCCTGTTTTGTGTCAGGGAAAGAATCCACCTGGGAGCCAAGTCCAGGAATCAGGATGACCAAGACATACTGGACAAGGAGGGAACAAAAGCATCC-AGGACACTTCAGGACAAATCATGCAAATGGATTTAAGGGAGACCTGCTCATGG + +a score=188515 +s hg18.chr1 232179 2073 + 247249719 TCTGCTTTGCTGCTCAGCATGGCTGGGAGGCACAGTGGAAGATCATGCATCCTGCCCCTGGGACTCCTCTGCCAGAGCCTGAGAGCTTTCTCCTGCCCACAGGCTAGGGGTAGGGCAGTTGGAATTGATCCATGCCTTCTAGCTAGACTGTGGGTCCCCTCAGTCTTGGGCATGGTGACAGCCCAGCATCAGACAGAGGTCAGTATCAAACTAGAAAATGTAATAAATACTGTCAGATTTGTAGACCCAAGAAAATATAAACTGCCAATCATGGAGGAAAAAAATCTCTCAATGATCTTATCTTTATATGATTCCCTTGCTGCCTGGAGATTGACATTTCCTTGGGGATAATCTGGTCATAGGATTGGTGAAGGTGGAAGGGAGGCAACCTCCAAAGGTGGGGCCCTCTGCTCACCTGGGACAGGGAGGGCCTGAGGTAGGTGTCTGTGTGGGCTGGGGAGGAGGATGGGAGCAGTGCTTCTAGATGTTTCCACTTTCTCCTCATTAGATAATAACGAATGGGTGATTTCCCTAGTCACTGCAGTGTGAGGAAATCTACAAAATTAATTTCACAATACACTTTACAGGATAGGTGGAGAAACACATGAAGCACAACTGCAGTGGGTTATAAAAAACGGCCTTTTGAGTTGAGCAATAAATTCGTTCAAGCAGCCATTCTGAAGGACAAAC-TGGCTCTGTATTTAAGAGGGGCATTCCAGCACTTCTCTAGCCACTGGGTTGACAATGACTCACCAAAGCCTCTGGTAGCCACCACAGGACACCCAGAGCATATGTTTTAAAGCTGAACACCAAACTGCGGACTTCGGGAGTAAGTGAACTGACTGGTTTTTATTTTGTTTTACTGCTTTTAACATTACAGTAACTGTTACAGGTTCCAGCAGGCTAACTGGGTGGAAATGAGTTTGGTTTCACTTAGTCTC TCTAAAGAGAAAGCAAGTCGGTAGACTAATACCTAATAAAAGCAAAGCTGCCAACAATTGAAATTGCCTAGGCTGCTCTGTGTGTCCCACAtgcatgggtgtgggtgccagtgtgtgtgcgtgtgtgcatgcatgtgcatgtgtgtTGGGATAGAGTGGTAAGAAAATGGGAAATAATAAGAATGTTCAGTCCATAGCCCTTCATTATAAAAAGGTGAGCTGTAATAAATACTAGTGCCACATTTAGCCAAAACTTTACTCCAGCCAAAGGTGATATTTTCATGATAACATCCTGTGATTGCTTTGTTCTTCGTCTTGTATGTTCTTCCTAGATGGGCTCAGAACATACAAGAATTAAGTACACATCTTATTTTCCAGTGATAATGCTACCGGCAAATTCTGTTGTTTGTATAAACATCAGCCAAGTTTATATAACTAAACTAGTGTTTTGTTTTGTCAATTCAGCAAGAAATTAGACCAAATGGTGGCTTAATGCTGCATTGATTTGACTATCAATTTGTTTTCACTTTTCTGCAAAATAATTAATACATTATTAAATTGAGTTATGCTGATGCCACAGTTGTTCTTATCTCAAGTGTCTTAAAATTCATTTAATTTGTTTTTCCTTTGGTTTCATTATTCAGATTTTAACTTCAGTTCTCAAGATTTTATCTGATGGAAGAGATGGAGTCCATTACTAAGGACTCCATTGTGCTCCATCATGCCAGAGTTGTAAAATAGATCTTTTAAAGGAAATTTACTGTGATTTTTTTTCTATTTAAGAGCTTCCTCTCCAGTTGAGCATGTAAGAAAATTATACCAGGAGAATACAGTAAACTCTATGAGGCAAGCTATAAACATGTAGCATTGTGATTAGGGctggttctccttctagagatatggtaggattgcaatttcataccatccttgaagttagagagagccatgtgactcatttagccaatgaactgtgagcagaatgacatgtc acttccagctgaagctttaaCAATCTGAGAGACATTCATACATTTTCCATGTGCTGTAGCCTTATACCCAAAGCCTGGGTCCCAAGTGACCATGACAGGCAGAGCTCCCTGGtgagccacagagatttagagaatggctgtta +s panTro2.chr1_random 8588109 2072 + 9420409 TCTGCTTTGCTGCTCAGCATGGCTGGGAGGCACAGTGGAAGATCATGCATCCTGCCCCTGGGACTCCTCTGCCAGAGCCTGAGAGCTTTCTCCTGCCCACAGGCTAGGGGTAGGACAGTTGGAATTGATCCATGCCTTCTAGCTAGACTGTGGGTCCCCTCAGTCTTGGGCATGGTGACAGCCCAGCATCAGACAGAGGTCAGTATCAAACTAGAAAATTTAATAAATGCTGTCAGATTTGTAGACCCAAGAAAATATAAACTGCCAATCACGAAGGAAAAAAATCTCTCAATGATCTCATCTTTATATGATTCCCTTGCTGCCTGGAAATTGACATTTCCTTGGGGATAATCTGGTCATAGGATTGGTGAAGGTGGAAGGGAGGCAACCTCCGAAGGTGGGGCCCTCTGCTCACCTGGGACAGGGAGGGCCTGAGGTAGGTGTCTGTGTGGGCTGGGAAGGAGGATGGGAGCAGTGCTTCTAGATGTTTCCACTTTCTCCTCATTAGATAATAACGAATGGGTGATTTCCCTACTCACTGCAGTGTGAGGAAATCTACAAAATTAATTTCACAATACACTTTACAGGATAGGTGGAGAAACACATGAAGCACAACTGCAGTGGATTATAAAAAATGGCCTTTCGAGTTGAGCAATAAATTCGTTCAAGCAGCCATTCTGAAGGACAATCGTGGCTCTGTATTTAAGAGGGGCATTCCAGCACTTCTCTAGCCACTGGGTTGACAATGACTCACCAAAGCCTCTGGTAGCCACCACAGGACACCCAGAGCATATGTTTTAAAGCTGAACACCAAACTGCGGACTTCGGGAGTAAGTGAACTGACTGGTTTTTATTTTGTTTTACTGCTTTTAACATTACAGTAACTGTTACAGGTTCCAGCAGGCTAACTGGGTGGAAATGAGTTTGGTTTCACTTAGTCTC TCTAAAGAGAAAGCAAGTCGGTAGACTAATACCTAATAAAAGCAAAGCTGCCAACAATTGAAATTGCCTGGGCTGCTCTGTGTGTCCCACAtgcatgggtgtgggtgccagtgtgtgtgcgtgtgtgcatgcatgtgcatgtgtgtTGGGATAGAGTGGTAAGAAAATGGGAAATAATAAGAATGTTCAGTCCATAGCCCTTCATTATAAAAAGGTGAGCTGTAATAAATACTAGTGCCACATTTAGCCAAAACTTTACTCCAGCCAAAGGTGATATTTTCATGATAACATCCTATGATTGCTTTATTCTTCGTCTTTTATGTTCTTCCTAGATGGGCTCAGAACATACAAGAATTAAGTACACATCTTATTTTCCAGTGATAATGCTACCGGCAAATTCTGTTGTTTGTATAAACATCAGCCATGTTTATATAACTAAACTAGTGTTTTGTTTTGTCAATTCAGCAAGAAATTAGACCAAATGGTGGCTTAATGCTGCATTGATTTGGCTATCCATTTCTTTTCACTTTTCTGCAAAATATTTAATACATTATTAAATTGAATTATGCTGATGCCACAGTTGTTCTTATCTCAATTGTCTTAAAATTCATTTAATTT-TTTTTCCTTTGGTTTCATTATTCAAATTTTAACTTCAGTTCTCAAGATTTTATCTGATGGAAGAGATGGAGTCCATTACTAAGGACTCCATTGTGCTCCATCATGCCAGAGTTGTAAAATAGATCTTTTAAAGGAAATTTACTGTGA-TTTTTTTCTATTTAAGAGCTTCCTCTCCAGTTGAGCATGTAAGAAAATTACACCAGGAGAATACAGTAAACTCTATGAGGCAAGCTATAAACATGCAGCATTGTGATTAGGGctggttctccttctagaaacacggtaggattgcaatttcataccatccttgaagttagagagagctacgtgactcatttagccaatgaactctgagcagaatgacatgtc acttccagcagaagctttaagaatctgagagacattcatacgttttccatgtgctgtagccttatacccaaagcctgggtcccaagtgaccatgacaggcagagctccctgttgagccacagagatttacagaatgtctgtta + +a score=322739 +s hg18.chr1 234252 3582 + 247249719 acacagcataatccagcccatcctgactaatCTGATATTAACATGTATAATAAAGAATTCTATCAATGCTGAGGGAAGATGACTAGTTAAGGTCCTAGGTTGCAAGTCTCAAAACCTCTTCTAAGGATTGTAGACAGGAAATTAAATGACTTCTAGTCCCTAGAGTTCCCAATCTCCT--ACCATCC-CATCCTAATATGACAGAAGTAATTCCTGAGTTGCTTCTGAAACCAGAGCTTCCCTCAGAACCCTTAGCCTGCCAGATGGCTTCTTGGAGAGCCCTCACTCACTTTTCTCCTTCTGCTATTGCTGCTCATTCATTCCAGCTTTTAAAAATTCATCTTTATCCAGGAACCTCGCTTCTAGAAAAGTCATACAGGTGCTTCCAGGAGGCTACATGGGCACCCATATTTTTCTAGCCACTTTCATTAGACCAATGCAGCAGAGAAGAAAAGCCTCAATAATTATTATGACATGGCATGTTAGGATACCAAGTAAATTGCATTTGTAAAATGTGATTTTCTGTTGGTGTTCACTTCTGCTCTACTGACATTTGGTAAGTATTATTGACTGACTGACTAACTAATGTGGTCATTAGTCTTCATAAAGAAAGGCTCTCTACAAAAACGGAAGGATGCCCTTTTTCTGGCATTTAATACGTAAGAAATTGCCTCCAATAGAAACCAGAGTTGCCTGATTACTATCAGCACAGGAGAAATGTATTAATGTGCCTTTCTAGTAACAGGTTTTTAGAAAGTCAAATATAAACAAATCTGTCTATTTGTGTGTGTGCATGTGGTAGTGGGGAGGGAAGAAAAAAGGAGGGGGAGAGAAAGAGAAATAAGAACCAAGTTTATTATACTGTATTCAGGGGGAAAAAATTTTCCCAAGGTTCTAACAGAAGAGCAAAGTGCCACTGTCAATAGCCTCAGTAGTGTTAGA GTTGCT------------tttatttatttatttatttatttatttatttttcctttttttt-ctttctctttttttcttcttttttttttcttttctttctttttttt----tttttttggacagagtctcacactgtcacctcggctggagtgcattggtgcaatctcgactcactgcaacttctgcctcccaggttcaagtgattctcctgcctcagccgcccaagtagctgggattacaggtgtctgccaccgtgcctagctaatttttttgtatttttagtagagatgaggtttcactatgttggccaggctggtctcaaactcctgacctcatgatccacccacgttggcctcccaaagtgctgggattacaggcgtgagccaccgcccctggccAGGATTGCTTTTACAGCCAGTCTTCAGGTGCCCACTGTAGGAACAATGTCATTTAACCCTCGGGATTATTCTGTGCCAAATATGGATAATGACTAATATCCAACACAGATATTCTCAGCTCAGAAGAGCAATTAGCAAATTCATAAATTAAGTGCTTGCTTCCTCTTTAGTCAAATACAAACGTTTGTTAAAAGATATTATTTTGCTTTACACTTTTTCTCTCAGAAATAAACAGATGCTTGAATTCCCACAGTGCTGCTTGAGCCTCACACCATGTCATCCTGCCAGGCACCCAGATCCAGTTCTAGAGTTTCACATGATCATGAgtgttggttaataagtcaatgcgaactgggaggggagatttttcaggagtgccacagggctctccctttaatcACATACACTCCCTGCTTTCATTGGAAAGTGTATAATGATGTCAGAGTGCCCCAGAATGGAGCTAGTTGGAAGACTGCCGTCATAGGGATGCCTTAGTGAATTAATAAGGTTTTAATTTCTGGCTCTCAACTTTGTAGATGTAAAAGTTGATTTATCAATATGTGAGAAAGGATGAATCTTTCTGAAGGTT ATGTCATCACACTCACTAAGCACACAGAGAATAATGTCTAGAATCTGAGTGCCATGTTATCAAATTGTACTGAGACTCTTGCAGTCACACAGGCTGACATGTAAGCATCGCCATGCCTAGTACAGACTCTCCCTGCAGATGAAATTATATGGGATGCTAAATTATAATGAGAACAATGTTTGGTGAGCCAAAACTACAACAAGGGAAGCTAATTGGATGAATTTATAAAAATATGCCTCAGCCAAAATAGCTTAATTCACTCTCCCTTATCATAAGGATAATCTTGCCTAAAGGGACAGTAATATTAAAGACACTAGGAATAACCTCTGTACTTTGGACAGTAGACCTGCATAGCCCATTAGGCCTCAATGAAGTCTTATGCAAGACCAGAAGCCAATTTGCCA-TTTAAGGTGATTCTCCATGTTTCTGCTCTAACTGTGCTTCACAATACTCAAAACACTAAATCAGGATGTTTCCTGGAGTTCAGGGAGCTGTCCGTGTTACTGAGCAGTTCTCAGCAACACAAAGATCCTACTGACTCCTCATCAGACTTCTTTCTCACTGGAATTTTACACCTGGGCTGTTAACACCAGGCCAGGTCAAATTCAAAGGAGAGAAAAAAGCTCATTATGAAGGGTAAAATCCAAAACACTGTGCATAAAGATATGTGTGCACAATTTTTATACATAAAGATTTCATAAAACCAAAGCATCAGGAAATGAAAAGAGATACAGAAAGAAAAATGATGGTAAATGAGACATTAATTTACCCTTCTAATCTCTATCACAGCAAAAAGATAATTAAAAAATCTATATGAGGACCACAAAATACACAAAAATTATGTAGCAAAGCCTATAGCCTGAAAAAGTAAACATTGAAATTTGTATGTCCATAAAATGTTTACAAAATTCAGTACATATTACACACCCCACCCTAAAAACATCTAAGCAAAGTAGAGAATGTAGAAATGCTACAGATTATATTCTCT GATTATGACACAACAAAACTAGAAATTACAGCATGGAAATTTAAAAGCTTTCTCTTAAATAATTCTGTGTCAAAAAGAAATCCAggccgggtacagtggctcatgcctgtaattccagtactttgggaggccaaggtgggcaggtcacttgaggtcagcagttcaagaccagcctcgtcaacatggcgacaccctgtctctactaaaaatacaaaaattagctgggcctggtggctcatgcctgtaatcccagctacttaggaggctgaggcaggagaattccttgaacccagaaggtggaggttgcagtgagctgagattgcaccactgcactccagcctaggtgacacagcaagactctgtc--aaaaaaaaaaaaagaaaTCCAAATAAAATTTCCAGAATATGTGGAAAATAGTGACAATAAAAATATTAcacatgtgtaatcccagcattttgagatgccaaggtggcaggatcacttgagaccaggagttcgcaaccagcctggacaacatagggagactccatctccacacatgccaaaaaaa-tttttaaatagccaggtatagtggtacttcttgtaatcccatctacttgggaggctaaggtgggagaatcacccaacctcaggagttcagggcttcagcaagccatgatcatatcactgcactccagcctcagca +s panTro2.chr1_random 7330233 3600 + 9420409 ACACAGCATAATCCAGCCCATC-TGACTAATCTGATATCA-CATGTATAATAA-GAATTCTATCAATGCTGAGGGAAGATGATTAGTTAAGGTCGTAGGTTGCAAGTCTCAAAAC-TCTTCTAAAGGATGTAGACAGGAAATTAAATGACTTCTAGTCCCTAGAGTTCCCAATCTCCTTACCCATCCTCATCCTAATATGACAGAAGTAATTCGTGAGTTGCTTCTGAAACCAGAGCTTCCCTCGGAACGCTTAGCCTGCCAGATGGCTTCTTGGAGAGCTCTCACTCACTTTTCTCCTTCTGCTATTGCTGCTCATTCATTCCAGCTTTTAAAAATTCATCTTTATCCATGAACCTCGCTTCTAGAAAAGTCATACAGGTGCTTCCAGGAGGCTACATGGGCACCCATATTTTTCTAGCCACATTCATTAGACCAATGCAGCAGAGAAGAAAAGCCTCAATAATTATTATGACATGGCATGTTAGGATACCAAGTAAATTGCATTTGTAAAATGTGATTTTCTGTTGGTGTTCACTTCTGCTCTACTGACATTTGGTAAGTATTATTGACTGACTGACTAACTAATGTGGTCATTAGTCTTCATAAAGAAAGGCTCTCTACAAAAACGGAGGGATGCCCTTTTTCTGGCATTTAATACGTAAGAAATTGCCTCCGACAGAAACCAGAGTTGCCTGATTACTATCAGCACAGGAGAAATGTATTAATGTGCCTTTCTAGTAACAGGTTTTTAGAAAGTCTAATATAAACAAATCTGTCTATTTGTGTGTGTGCATGTGGTAGTGGGGAGGGAAGAAAAAAGGAGGGGGAGAGAAAGAGAAATAAGAACCAAGTTTATTATACTGTATTCAGGGGGAAAAAATTTTCCCAAGGTTCTAACAGAAGAGCAAAGTGCCACTGTCAATAGCCTCAGTAGTGTTAGG GTTGCTtttatttatttatttatttatttatttatttatttatttatttttccttttttttcctttctctttttttcttc-tttttttttcttttctttctttttttttttctttttttggacagagtctcacactgtcgcctgggctggagtgcattggtgcaatcttgactcactgcaacctctgcctcccaggttcaagtgattctcctgcctcagcggcccaagtagctgggattacaggtgtctgccaccatgcctagctaatttttttgtatttttagtagagatgaggtttcactatgttgg-caggctggtctcaaactcctgacctcgtgatccacccaccttggcctcccaaagtgctgggattacaggcgtgagccaccgcccctggccAGGATTGCTTTTATAGCCAGTCTTCAGGTGCCCACTGTAGGAACAATGTCATTTAACCCTCGGGATTATTCTGTGCCAAATATGGATAATGACTAATATTCAACACAGATATTCTCAGCTCAGAAGAGCAATTAGCAAGTTCATAAATTAAGTGCTTGCTTCCTTTTTATTCAAATACAAACGTTTGTTAAAAGATATTATTTTGCTTTACACTTTTTCTCTCAGAAATAAACAGATGCTTGAATTCCCACAGTGCTGCTTGAGCCTCACACCATGTCATCCTGCCAGGCACCCAGATCCAGTTCTAGAGTTTCACATGATCATGAAtgttggttaataagtcaacgtgaactgggaggggagatttttcaggagggacacagggctctccctttaatcACATACACTCCCTGCTTTCATTGGAAAGTGTATAATGATGTCAGAGTGCCCCAGAATGGAGCTAGTTGGAAGACTGCCGTCATAGGGATGCCTTAGTGAATTAATAAGGTTTTAATTTCTGGCTCTCAACTTTGTAGATGTAAAAGTTGATTTATCAATATGTGAGAAAGGATGAATCTTTCTGAAGGTT ATGTCATCACACTCACTAAGCACACAGAGAATAATGTCTAGAATCTGAGTGCCATGTTATCAAATTATACTGAGACTCTTGCAGTCACACGGGCTGACATGTAAGCATCGCCATGCCTAGTACAGACTCTCCCTGTGGATGAAATTATATGGGATGCTAAATTATAATCAGAACAATGTTTGGTGAGCCAAAACTACAACAAGGGAAGCTAATTGGATGAATTTATAAAAATATGCCTCAGCCAAAATAGCTTAATTCAGTCTCCCTTATCATAAGGATAATCTTGCCTAAAGGGACAGTAATATTAAAGACACTAGGAATAACCTCTGTACTTTGGACAGTAGACCTGCATAGCCCATTAGGCCTCAGTGAAGTCTTATGCAAGACCAGAAGCCAATTTGCCATTTTAAGGTGATTCTCCATGTTTCTGCTCTAACTGTGCTTCACAATACTCAAGACACTGAATCAGGATGTTTCCTGGAGTGCAGGGAGCTGTCCGTGTTACTGAGCAGTTCTCAGCAACACAAAGATCCTACTGACTCCTCATCAGACTTCTTTCTCACTGGAATTTTACACCTGGGCTGTTAACACCAGGCCAGGTCAAATTCAAAGGAGAGAAAAAAGCTCATTATGAAGGGTAAAATCCAAAACACTGTGCATAAAGATATGTGTGCACAATTTTTATACATAAAGATTTCATAAAGCCAAAGCATCAGGAAATGAAAAGAGATACAGAAAGAAAAATGATGGTAAATGAGACATTAATTTACCCTTCTAATCTCTATCACAGCAAAAAGATAATTAAAAAATCTATATGAGGACCACAAAATACACAAAAATTATGTAGAAAAGCCTATAGCCTGAAAAAGTATACATTGAAATTTGTGTGTCCATAAAATGTTTACAAAATTCAGTACATATTACACACCCCACCCTAAAAACATCTAAGCAAAGTAGAGAATGTAGAAATGCTACAGATTATATTCTCT GATTATGACACAACAAAACTAGAAATTACAGCATGGAAATTTAAAAGCTTTCTCTTAAATAATTCTATGTCAAAAAGAAATCCAggccgggtacagtggctcatgcctgtaattccagtactttgggaggccaaggtgggcaggtcacttgaggtcaggagttcaagaccagcctcgtcaacatggcgacaccctgtctctactaaaaatacaaaaattagctgggcctagtggcgcatgcctgtaatcccagctacttaggaggctgaggcaggagaattccttgaacccagaaggtggaggttgcagtgagctgagattgcaccactgcactccagcctacgtgacacagcaagactctgtcaaaaaaaaaaaaaaagaaaTCCAAATAAAATTTCCAGAATATGTGGAAAATAGTGACAATAAAAATATTACACATGtgtaatcccagcattttgagatgccaaggtggcaggatcacttgagaccaggagttcgcaaccagcctggacaacatagggagactccatctccacacacgccaaaaaaattttttaaatagccaggtatagtggtacttcttgtaatcccatctacttgggaggctaaggtgggagaatcacccaacctcaggagttcagggcttcagcaagccatgatcatatcactgcactccagcctCAGCA + +a score=160185 +s hg18.chr1 237834 1775 + 247249719 acagagcaagatcctatctcaaaaaaaaaaaaaaaTCACATGTGGGAAATAGCTATAGCACAAtaaaaataaatgtattaagtatgaacaacaaaaaagctagtaaaggttgaacaacaactatccttaggaaagtggaaataatgtattaataaatatgaaagcaggctaggcatggtgactcacatctgtaatcccagcactttgggaggctgaggcaggcagatcacctgaggtcaggagttccagaccagcctggccaacatggtgaaatcttgtctctcctacaaatacaaaaactagccaggcttggttgtgcactcctgtaattcgagctacttgggaggctgaggcaggagaatctcttgaacctgagaggcagaggttgcagtgagccaagatcatgccactgcactccagctggggcaacagagtgacactccatctcaaaataaataaataagaaagcagaaactaataaattagaaaacagaaacatagaactaatttataaatcaaagcactatgccttgaaaagaGGGAGAAAAATTGTGAATTAAGGAAGGGAAGAGATGGTTGGAGAGGAGGTGGGAGAAGGCAGAGATAATTGAAGGAGCAAAAGCATCTGGAGAAGCAAAGCCACTGAAAGATGAACAGGGCTCTGAAAGAGATGCTTGATTGCTATCTTTTCAAATGACTGCAGTTCCCAGTGACATCATTTTTCTCCTCCCTGGAAGTCTGAGGGGCAGTTCACTTATCTCCTCCCCTCCCCTACTCCTCACCCCACACTCAAAACCTGTCTATGCTCCTTTCATTCTCATATGACAGATTTCAGATGGCAGTCTTATTTCCCTGATTTCTTTTTGAGATAGCTTGCATTTCCCTCCTCTATataaagccaccgtttatcaaatgcctacatggaccaagcagtccacaaaggcttc acagacagttttactaaactcatgccaaaactttcaggttttatacctaccttatagataaagaaattgaagcttatagagtttaagtaatgttcccaaagcctcatggctagtaattcaaacctaatttctgcctactccaaagtctatttttccttatgatactatactgcctctcCAtggataaagacagagatcacatattaataaaatttgcacaaagtcggcaaattgttgaaagggaaggctaagatgattaataaaatcaagagccagatgatctcaacaacctgaaataactggctgacaaccaatttgaataactccctgcgggtgaagttcaaagtactattcgggttttttttttaaagtttggctgggtgcagcggctcacgcctgtaatccaagcacttagggaagccaaggtgggcagatcatgaagtcaggagttgaagaccagcccggtcaacatggtgaaaccccatttctactaaaaataaaaaattagccgggcctgctggtggatgcctgtagtcccagctactcgggaggctaaggcaggagaatcgcttgaacccaggaggtggaggttgcagggagccgagatcgcaccactgcactccagcctgggcgacagagcgagattccgtctcaaaaagtaaaataaaataaaataaaaaataaaagtttgatatattcagaatcagggaggtctgctgggtgcagttcatttgaaaaattcctcagcattttagtGATCTGTATGGTCCCTCtatctgtcagggtcctagcaggaaattgttgcactctcaaaggattaagcagaaa +s panTro2.chr1 223998133 1767 + 229974691 acagagcaagatcctatctc--aaaaaaaaaaaaaTCACATGTGGGAAATAGCTATAGCACAAtaaaaataaatgtattaagtatgaacaacaaaaaaactagtaaaggttgaacaacaactatccttaggaaagtggaaataatgtattaataaatatgaaagaaggctaggcacggtgactcacatctgtaatcccagcactttgggaggctgaggcaggcagatcacctgaggtcaggagttccagaccagcctggccaacatggtgaaatcttgtctctcctacaaatacaaaaactagccaggcttggttgcacactcctgtaattccagctacttgggaggctgaggcaggagaatctcttgaacctgggaggcagaggttacagtgagccgagatcatgccactgcactccaactggggcaacagagtgacactccatctcaaaataaataaataagaaagcagaaactaataaattagaaaacagaaacatagaactaattcat-----aaagcactatgccttgaaaagaGGGAGAAAAATTGTGAATTAAGGAAGGGAAGAGATGGTTGGACAGGAGGTGGGAGAAGGCAGAGATAATTGAAGGAGCAAAAGCATCTGGAGAAGCAAAGCCACTGAAAGATGAACAGGGCTCTGAAAGAAATGCTTGATTGCTATCTTTTCAAATGACTGCAGTTCCCAGTGACATCATTTTTCTCCTCCCTGGAAGTCTGAGGGGCAGTTCACTTATCTCCTCCCCTCCCCTACTCCTCACCCCACACTCAAAACCTGTCTATGCTCCTTTCATTCTCATATGACAGATTTCAGATGGCATTCTTATTTCCCTGATTTCTTTTTGAGATAGCTTGCATTTCCCTCCTCTATataaagccaccgtttatcaaatgcctacatggaccaagcagtccaaaagggcttc acagacagttttactaaactcatgccaaaactttcaggttttatacctaccttataggtaaagaaattgaagcttatagagtttaagtaatgtttccaaagcctcgtggctagtaattcaaacctaatttctgcctactccaaagtctatttttcctcatgatactatactgcctctcCAtggataaagacagagatcacatattaataaaatttgcacaaagtcagcaaattgttgaaagggaaggctaagatgattaataagatcaagagccagatgatctcaacaacctgaaataactggctgacaaccaatttgaataattccctgcgggtgaagttcaaagtactatttggg-gtttttcttaaagtttggctgggtgcagcggctcacgcctgtaatccaagcacttagggaagccaacgtaggcggatcatgaagtcaagagttgaagaccagcctggtcaacatggtgaaaccccgtctctactaaaaataaaaaattagccgggcgtgctggtggatgcctgtagtcccagctactcgggaggctaaggcaggagaatcgcttgaacccaggaggtggaggttgcagggagccaagatcgcaccactgcactccagcctgggcgacagagcgagattccgtctcaaaaaattaaataaaataaaataaaaaataaaagtttgatatattcagaatcagggaggtctgttgggtgcagttcatttgaaaaattcctcagcattttagtGATCTGTATGGTCCCTCtatctgtcacggtcctagcaggaaattgttgcactctcaaaggattaagcagaaa + +a score=600826 +s hg18.chr1 239609 6564 + 247249719 gagtttaatgaaggatctctttccagggttaagggaactgctagggtttggatatttgaccactccaaactcatgttgaaatgtgatccccattgttggaggtggggcctaatgggaggtgttttggtcctgagtgtggacctctcacgaatgtcttggtgccatccaagtgagttcttgctcgctcttttttttctttttgcgatgtagtttcactcttgctgcccaggttggaatgtagtggtgcgatcttggctcactgcaacatccacctcacgggttcaacccattctcctgtgtcagcctccagagtagctaggattacaggtgcccaccactatgcccagctaatttttggtatttttagtagagacggggtttcaccatgttggccaggctggtctcaaactcctgacctcaggtgatccacctgcctcggcctcccaaagtgctgggattacaggcgtgagccaccgtgcctacctagttctagctctcttaattcccacaagagctggttgttaacaagagcctggcacaaacccctctctctcgccacgtgatctctgcacatgccagcttcccttccccttctgtcatgagtggaaacagcctaacgccctcaccagaagcaaatggtggcaccatgcttcttgcacaccttcagaactgtgagccaaataaacctctcttctttaaaattattcagcctctggtattcctttataacaacacacacacacacacacacacatacacacacac------------------gcaaaagcagactaaaacaggaactaattagaaatggtgatgcaccgagggattggcaCCGAGGCTCCCCAACAGGAACTGAGGTCATGGATAGAAGGACACATTCATGTTATTTTTTTCTAATGGTTAAGTAATTATTTGctcttactctcaaaattt ctgccaaggcctcccatggaccaaactcaactagaatctaggaagcagagaacctgagtgttgcattcagcagaagtcagcttcctagggaatcttgcaggaagggtgaaggtagagaatctggtggggaagcaagcaaatgcccatcacaTGCACTTTCCTccaacagagcgactcagatgctataaaacttgctaacacagtctcagggtctgatcacagtaacatacaatccaggttttaatcatcagaaatcacagtcctattgtcttctgcacagacccaaacacacttggaggtcatgttcaatatgaatacctcacagagaaggaaatttacacgcgagaagtacatctgcagaaagccagctggcatgtcaaccattcaaaaactcagggtgttctggataaagaagactcaggaagacaagtatgaagcataatctgtgacattccatgcggcagacattagacatatacaagagagttgttggaaagcggaatttatcttcatataaacaacactgagctaaatctcaatatttcagatctctagaactatccatcagtgaaatggattgcaaatacaaagagtaataccatgtcacttaagaatacaatcatggacgaggctgccacctgctgttgggggccactgcagaagaaattccagaacactggactggagagcacctcactttccttacagctctaagtttctgACTCAGTGACCTGATTCACTACCATATACACAAAGACCCACTTACACAAATGACTGTTCTTCACACTAGGCCCATGGAGACAGGGATAAAATTCTGAATTTGCTCAGATACCTTCTCCGCTACTGACATCTAGGCATTACACAATTCATCTCTTCATATTTAACCTTTGAAGTTTGCTACTTCTCAGAGAGACTAATGAGTAGTGAGCAAATATCCTGAAGTTGAGAATGCTTCTACCTCCTCTCAAAACAACGGAATATTCATCAAA ACACAACAGTTCTGCACTTAACTTTAGGCCTTTTCTAACACCTTGTTTCTTGGCAGTAACTGTGGCCAGAATAGCTCTTTCCACAGATAAAGGACCTTTTGAAAGGATAGGGTCTCTAGATAGAAAAGCAAATGCCTCATTCCAGAAGGTCTTCAAGAAGAAAATGTTGTGGTGATAACAAACATAACTGATTATAATCTATTCTGTGAAAAAAGCTTATGAAACAGTAGATGTGTGTATCTAGTACATAAGAGCTGAATGTCAATATATATATA--GATATATACacacactcaaataaataatagttatctctaactagagaaattctagttgccttatattttcttctttttccttactatattttctacaataaacatgtgtttttaacaagaaaaGTCTTTTCTGGTGTGCTTTTTAATTTTCTTTGTTTAAGTGAGAGTGAGGCTACATAACTACATGGCTAGGTAGACTTTTAGAAAACTTGACTGCTCTAGAAAATTGACATATCCTGATTTCTTCCATAGCTTGGATCTTGACCTAGAGGGAAATATAAAAGTGTTGACTTGAACCTGAGGGGTGCCATTTTCACTGCTGAAGTAGTTTCATGGATCATGAATTGGAGAAATGACTTCAGCAACATGGGTGTTAAAAACAGAAAGCACAAGTGACCCACAACAGATGATGGAGAACAAAGAGCAAGCTGGGAAA-GCAGTGGCCTTTAATACAGAAAAGAAGAAGTATAGCCACAATAAATATTAGGCAGACAGCAGTTCAGCAGTTTATACTATTAAGCTGTTGTTTAGGGGAATAGTAAACTGACATGACCCTTGAGGTAGGTATATATAGGTAAATTCTATGTGTCCCTTGAAATAGGTGTATGACACAACTTCTGGCATCTACATGGATTTGGTCACTCTAAAGTAGCCATGAGGCTTAAGATAGTTCAGCTGTTTGGGGATAAGTTAAATCATTTGCCATTGTCT TTCTGCAATTTGCATATCCTACAGTTATCATTGCCATTACTGAATGGCACAGAGAAAAATTCTGGTCTAAAGTGGTTCTCAAACCTGGTTGCTGGAGGGccaccctcagtgatgatgatttaatctgtagaagagtagaacattgatagtttttatatatctccaggtaattttaatatataactggggtgagaatcattgACGTAATTGTAAGAGGATAATATTCAGGAAATATGGAGATAAATAATTTTCTTCTCGACATTAAAAAAATCTAATAAAAAGTTTTATCTTTTCCCCTAACTCAGGGTCATCAGCCTTCAAGCTTCAGTCTCTGTGTGTTCACAGGTGCTGTAAACACACGCATCACTACTAATATCCCACTTCAGTGCTATTGCTGCTCCCAAAACTCCAGGTATTTTTAACCTTATAAACCTCCAGAATAATGAGACCACTGGGTTCAGTAAATTGCTTTGTTTTGAAGCAGTATTAGACAAAGTGGGAGACTAGAAGATAAATCTGTCAATGACATGTCCTTTAAGACTACTTAGATTTTGTTGAATTTGTGGATCATTCCTTACTTGAGCAAATGGTAAATTAACTCTCTCTTTTCTCTCTCTCTCTAGCTGGCACACTTTTTCCAGTAGCCATTCTACTTGGTATGCTTACTTATCAGCTGTCCTCCAGGGGCCTCACATTAGATGTTTCTCT-GACTAACCAAACATGACACACAGCTGAAGTCAGAAAAACCAGATTGATAATTTCACTCAAACTATTTTCCTTCATTCTAACAATTTACTGGAGTACACAATTGTGACTATTTTTAGCCATAGGAACTCATAGAAAGACCAACTTCATTAGACCTACAAAATCGAATTGTGTAACAGTATATGCAGTATGTGTAGGAATAAAAAGCATTTCTCAAATATGCAGTACTGGATTTTGCAAAAGCACCTTACACTTAGCTATAAAGGAGTGGAAAACACAAAGA TGAGTAACTGCACCTTTCAAAAGACTAGAGCTATACCAATAATACAAAGGTGTAAACAAATAATGATGAGATGACAAAGGCTGAGTGTTTTCTATTTGGAAGCTATGTTGTTGAGTTATTTATGTATATAATTTCATGCAATCTTCATGTTATGGGGATGTTctaatccactgtgactctgtccttaaataaaagggagatttggacatagagagaggcacacggggaggatgccatatgagaattgacactgtgctgtcacaagccaaggaactactggaaggagagaaagaggactggaacagttccttccttagcaccttttcaggcagcctagccctgccagcttcttgatctggacttctcacctctagaattgtgaggcaataaatctctgttgcttaagttacccagtttgtggtaccttattacaggagccctaggaaaataattcaTTATATAATctgctaaggtagatctgatcattgtctccaatttccatatgaagaaactatgcctcaggcattgtgtcagttgtccaaaatcatacattcctgactcacttcaatgaattcctcattcagcaaaatttttaaggtaccttaaaaaaattatgttaactcttaaggccttgctttaaagcttcaatgggcttttcctttgcaaagaataaaatcctaatacttaagcatagctctctttcctggctatgtttctgacatcctcttgtaccatgctcctccttaatcattctgaggttacatcttaagtcctttccccttgccattcccacttcttggaatactttcccatcaactcttcaaagaactgccttctttaagtatttggtctcagttcaaatgtcacttccctgtaaaagcttcctggccatcaagccttctttacacactctattttattttttcatggttcctataacaacctaatatattctcaattgattaactgttttgctgactactgccttc cataagaatggaaagaaaacgtggccaggtgcagtggctcacacctgtaatcccaccacttcaggaggctgaggcaacatggcaaaaccttctcttcaaaaaattttttaaaagttagctggatgttgtggaggcaagaggatcacttgaggatcacttgagtccatgaggtcaaggctgcagtgagtcatgtttgcaccactgcactctagcctaggtgacagagctagtccctatcaaaaaaaaaaaaaaaaaaaaaagaatggagagaatgctacatgagagaaaggatcttatctatcacgttcacctcccaagaggtgaacatatcccccaaagcctgatagagagaagatgctcattaatatttaatgcatgaCCATGTGCAGACTTGGGAGGAAAAATATGCCTCAGCCTATCAATATTGGATCCTTAATAAACAAGGATGTTTCTGCATCATTTCCCCACAACACCGAACAAGTGTGGCTCACTGTGGATGTTTAAGCAAATGCATTGTTTTTCCAGTTATATATCTGGTAGAGATTAGGCCATTGATAGGAATGGGAAGACGATCTCCTTTTATTTTGATGACCCAGCATGGCTGAACACTCAGTGACTACCACTGCACTTTGTTGTACTTTCAGCATTAGAGATGCCAGCCCTGTAGGATATAAAACAGGAACATCTAGTCCTCAATTATATTCAGAATTACTCAAGTCTTAGAAGCACCACTTGTCTTTTTTCAAGGGAGAGAAATGCTCAAGTGATGGGCTGAAGTGAAGGGAGGGAGTCACTCACTTGAATGGTTCCCTTAGGCTGTGTGGATGCAAACAGCATTAGACAATGACACTGACAGTGGGAAATGCACTGGAGACGATGATTGGCAAAGCCCTCCTTTTCTCCCCATCCACTATAGATACTGACAGCAAAGGGTTTGTCACAATGACAACTATACACTCCCAATATCACAGAAGAAGGAGGAATAAAAG GGTATATTATGAGTGACTGaaatttagaataaattaataaatattatGTCCCTCATCCATAGAAACCACAAAGGTCTAGTAAGGCTAAGGATATAACAAGAAAATAATATGAATATTTGCTTCCCCTTCCTAGTGTAATAGAGTAAGTTACAAATGGCTTCAGGAAGGGGAGAGAGGAAGAAGAGTGGATGAGATACGTAAGAGTGCTTGAGGGATAATTTTATGAAAGCTTTGGGAAGTTTTAAGAAAAAGAAAAGCTATTTTTCAAGGTACAtgtgtgtatgcgtgtgtgtgtgtatgtgtgtgtgtgtgtgtgtgAAAGACAGAAGAAAGAGGGAGACCTAAGAAGACTATGAGACACTAAGAGAAAAATTAAGGTAAAAAAGACACACACTTAGAAAAACACACATAAGGAGGAGGGAGGAGGTTAAGACATTTTACTATGTGCTGTGAATGGAAACTACAAACCATTTTTGATatatgcaatatatatacatatatacacacatatacatatGTATTTAAATATTTAAATTACAttttctctttttttagagatatggtttcactatgtcactctgcccaggctgcagtacagtggttgttcacagtcatgatcatagcacattatagccttgaactcctgggctcaagcaaccctcctgtattagtctccccagtagttgggattactagcat +s panTro2.chr1_random 7333834 6571 + 9420409 GAGTTTAATGAAGGGTCTCTTTCCAGGGTTAAGGGAACtgctagggtttggatatttgaccactccaaactcatgttgaaatgtgatccccattgttggaggtggggcctaatgggaggtgttttggtcctgagtgtggacctctcacgaatgtcttggtgccatccaagtgagttcttgctcgctcttttttttctttttgagatgtagtttcactcttgctgcccaggttggaatgtagtggtgcgatcttggctcactgcaacatccacctcatgggttcaacccattctcctgtgtcagcctccagagtagctaggattacaggtgcccaccactatgcccagctaatttttggtatttttagtagagatggggtttcaccatgttggccaggctggtctcaaactcctgacctcaggtgatccacctgcctcggcctcccaaagtgctgggattacaggcgtgagccaccgtgcctacctagttctagctctcttaattcccacaagagctggttgttaacaagagcctggcacaaacccctctctctcgccacgtgatctctgcacatgccagcttcccttccccttctgccatgagtggaaacagcctaaagccctcaccagaagcaaatggtggcaccatgcttcttgcacaccttcagaactgtgaaccaaataaacctctcttctttaaaattattcagcctctggtattcctttataacaacacacacacacacacacacacacacacacacacacacacacacacacatatgcaaaagcagactaaaacaGGAAATAATTAGAAATGGTGATGCAACGAGGGATTGGCACCGAGGCTCCCCAACAGGAACTGAGGTCATGGATAGAAGGACACATTCATGTTATTTTTTTCTAATGGTTAAGTAATTATTTGctcttactctcaaaattt ctgccaaggcctcccatggaccaaactcaactagaatctaggaagcagagaacctgagtgttgcattcagcagaagtcagcttcctagggaatcttgcaggaagggtgaaggtagagaatctggtggggaagcaagcaaatgcccatcacaTGCACTTTCCTccaacagagcgactcagatgctataaaacttgctaacgcagtctcagggtctgatcacagtaacatacaatccaggttttaatcatcagaaatcacagtcctattgtcttctgcacagacccaaacacacttggaggtcatgttcaatatgaatacctcacagggaaggaaatttacacacgagaagtacatctgcagaaAGCCAGCTGGCATGTCAACCATTCAAAAATTCAGGGTGTTCGGGATAAAGAAGACTCAGGAAGACAAGTATGAAGCATAATCTGTGACATTCCATGCGGCAGACGTTAGACACATACAAGAGAGTTGTTGGAAAGCGGAATTTATCTTCATATAAACAACACTGAGCTAAATCTCAATACTTCAGATCTCTAGAACTATCCATCAGTGAAATGGAGGGCAAATAGAAAGAGTAATACCATGTAACTTAAGAATACAATCATGGACAAGGCTGCCACCTGCTGTTGGGGGCCACTGCAGAAGAAATTCCAGAACACTGGACTGGAGAGCACCTCACTTTCCTTACAGCTCTAAGTTTGTGACTCAGTGACCTGATTCAGTACCATATACACAAAGACCCACTTACACAAATGACTGTTCTTCACACTAGGCCCATGGAGACAGGGATAAAATTCTGAATTTGCTCAGATACCTTCTCCGCTACTGACATCTAGGCATTACACAATTCATCTCTTCATATTTAACCTTTGAAGTTTGCTACTTCTCAGAGAGACTAATGAGTAGTGAGCAAATATCCTGAAGCTGAGAATGCTTCTACCTCCTCTCAAAACAACGGAATATTCATCAAA ACACAGCAGTTCTGCACTTAACTTTAGGCCTTTTCTTACACCTTGTTACTTGGCAGTAACTGTGGCCAGAATAGCTCTTTCCACAGATAAATGACCTTTTGAAAGGATAGGGTCTCTAGATAGAACAGCAAATGCCTCATTCCAGAAGGTCTTCAAGAAGAAAATGTTGTGGTGATAACAAACATAACTGATTATAATCTATTCTGTGAAAAAAGCTTATGAAACAGTAGATGTGTGTATCTAGTACATAAGAGCTGAATGTCAATATATATATATAGATATATACACACACTCAAATAAATAATAGTTATCTCTAACTAGAGAAATTCTAGTTGCCTTATATTTTCTTCTTTTTCCTTACTATATTTTCTACAATAAACATGTGTTTTTAACAAGAAAAGTCTTTTCTGGTGTGCTTTTTAATTTTCTTTGTTTAAGTGAGAGTGAGGCTACATAACTACATGGCTAGGTAGACTTTTAGAAAACTTGGCTGCTCTAGAAAATTGACATATCCTGATTTCTTCCATAGCTTGGATCTTGACCTAGAGGGAAATATAAAAATGTTGACTTGAACCTGAGGGGTGCCATTTTCACTGCTGAAGTAGTTACATGGATCATGAATTGGAGAAATGACTTCAGCAACACGGGTGTTAAAAACAGAAAGCACAAGTGACCCACAACAGATGATGGAGAACAAAGAGCAAGCTGGGAAAAGCAGTGGCCGTTAATACAGAAAAGAAGAAGTATAGCCACAATAAATATTAGGCAGACAGCAGTTCAGCAGTTTATACTATTAAGCTGTTGTTTAGGGGAATGGTAAACTGACATGACCCTTGAGGTAGGTATATATAGGTAAATTCTATGTGTCCCTTGAAATAGGTGTATGACACAACTTCTGGCGTCTACATGGATTTGGTCACTCTAAAGTAGCCATGAGGCTTAAGATAGTTCAGCTGTTTGGGGATAAGTTAAACCATTTGTCGTTGTCT TTCTGCAATTTGCATATCCTACAGTTATCATTGCCATTACTGAATGGCACAGAGAAAAATTCTGGTCTAAAGTGGTTCTCAAACCTGGTTGCTGGAAGGccaccctcagtgatgatgatttaatctgtagaagagtagaacattgatagtttttatatatctccaggtaattttaatatataactggggtgagaatcattgACGTAATTGTAAGAGGATAATATTCAAGAAATGTGGAGATAAATAATTTTCTTCTCGACATTAAAAAAATCTAATAAAAAGTTTTATCTTTTCCCCTAACTCAGGGTCATCAGCCTTCAAGCTTCAGTCTCTGTGTGTTCACAGGTGCTGTAAACACACACATCATTACTAATATCCCACTTCAGTGCTATTGCTGCTCCCAAAACTCCAGGTATTTTTAACCTTATAAACCTCCAGAATAATGAGACCACTGGGTTCAGTAAATTGCTTTGTTTTGAAGCAGTATTAGACAAAGTGGGAGACTAGAAGATAAATCTGTCAATGACATGTCCTTTAAGACTACTTAGATTTTGTTGAATTTGTGGATCATTCCTTACTTGAGCAAATGGTAAATTAACTCTCTCTTTTCTCTCTCTCTCTAGCTGGCACACTTTTTCCAGTAGCCATTCTACTTGGTATGCTTACTTATCAGCTGTCCTCCACGGGCCTCACATTAGATGTTTCTCTTGACTAACCAAACATGACACACAGCTGAAGTCAGAAAAACCAGATTGATAATTTCACTCAAACTATTTTCCTTCATTCTAACAATTTACTGGAGTACACAATTGTGACTATTTTTAGCCATAGGAACTCATAGAAAGACCAACTTCATTAGACCTACAAAATTGAATTGTGTAACAGTATATGCAGTATGTGTAGGAATAAAAAGCATTTCTCAAATATGCAGTACTGGATTTTGCAAAAGCACCTTACACTTAGCTATAAAGGAGTGGAAAACACAAAGA TGAGTAACTGCACCTTTCAAAAGACTAGAGCTATACCAATAATACAAAGGTGTAAACAAATAATGATGAGATGACAAAGGCTGAGTGTTTTCTATTTGGAAGTTACGTTGTTGAATTATTTATGTATATAATTTCGTGCAATCTTCATGTTATGGgggtgttctaatccactgtgactctgtccttaaataaaagggagatttggacatagagagaggcacacggggaggatgccatatgagaattgacactgtgctgtcacaagtcaaggaactactggaaggagagaaagaggactggaacagttccttccttagcaccttttcaggcagcctagccctgccagcttcttgatctggacttctcacctctagaattgtgaggcaataaatctctgttgcttaagttacccagtttgtggtactctattacaggagccctaggaaaataattcaTTATataatctgctaaggtagatatgatcattgtctccaatttccatatgaagaaactatgcctcaggcattgtgtcggttgtccaaaatcatacaTTCCTGACTCACTTCAATGAATTCTTCATTCAGCAAAATTTTTAAGGTACCTTTAAAAA-TTATGTTAACTCTTAGGTCCTTGCTTTAAAGCTTCAATGGGCTTTTCCTTTGCAAAGAATAAAATCCTAATACTTAAGCATAGCTCTCTTTCCTGGCTATGTTTCTGACATCCTCTTGTACCATGCTCCTCCTTAATCATTCTGAGGTTACATcttaagtcctttccccttgccattcccacttcttgggatactttcccatcaactcttcaaagaactggcttctttaagtatttggtctcagttcaaatgtcacttccctgtaaaagcttcctggccatcaagccttctttacacactctattttattttttcatggttcctataacaacctaatatattctcaattgattaactgttttgctgactactgccttc cataagaatggaaagaaaacatggccagatgcagtggctcacacctgtaatcccaccacttcaggaggctgaggcaacatggcaaaaccttctcttcaaaaaattttttaaaagttagctggatgttgtggaggcaagaggatcacttgaggatcacttgagtccatgaggtcaaggctgcagtgagtcatgtttgcaccactgcactctagcctaggtgacagagctagtccctatcaaaaaaaaaaaaaaaaa-----gaatggagagaatgctacatgagagaaaggatcttatttatcatgttcacctcccaagaggtgaacatatcccccaaagcctgatagagagaagatgctcattaatatttaatgcatgaCCATGTGCAGACTTGGGAGGAAAAATATGCCTCAGCCTATCAAAATTGGATCCTTAATAAACAAGGATGCTTCTGTATCATTTCCCCACAACACCGAACAAGTGTGGCTCACTGTGGATGTTTAAGCAAATGCATTGTTTTTCCAGTTATATATCTGGTAGAGATGAGGCCATTGATAGGAATGGGAAGACGATCTCCTTTTATTTTGATGACCCAGCATGGCTGAACACTCAGTGACTACCACTGCACTTTGTTGTACTTTCAGCATTAGAGATGCCAGCCCTGTAGGATATAAAACAGGAACATCTAGTCCTCAATTATATTCAGAATTACTCAAGTCTTAGAAGCACAACCTGTCTTTTTTCAAGGGAGAGAAATGCTCAAGTGATGGGCTGAAGTGAAGGGAGGGAGTCACTCACTTAAACGGTTCCCTTAGGCTGTGTGGATGCCAACAGCATTAGACAATGACGCTGACAGTGGGAAATGCACTGGAGATGATGATTGGCAAAGCCCTCCTTTTCTCCCCATCCACTATAGATACTGACAGCAAAGGGTTTGTCACAATGACAACTATACACTCCCAATATCACAGAAGAAGGAGGAATAAAAG GGTATATTATGAGTGACTGAAGTTTAGAATAAATTAATAAATATCATGTCCCTCATCCATAGAAACCACAAAGGTCTAGTAATGCTAAGGATATAACAAGAAAATAATATGAATATTTGCTTCCCCTTCCTAGTGTAATAGAGTAAGTTACAAATGGCTTCAGGAAGGGGAGAGAGGAAGAAGAGTGGATGAGATACGTAAGAGTGCCTGAGGGCTAATTTTATGAAAGCTTTGGGAAGTTTTAAGAAAAAGAAAAGCTATTTTTCAAGGTACAtgtgtgtatgcgtgcg--------tgtgtgtgtgtgtgtgtgtgAAAGACAGAAGAAAGAGGGAGACCTAAGAAGACTATGAGACACTAAGAGAAAAATTAAGGTAAAAAAGACACACACTTAGAAAAACACACATAGGGAGGAGGGAGGAGGTTAAGACATTTTACTATGTGCTGTGAATGGAAACTACAAACCATTTTTGATatatgcaatatatatacatatatacacacatatacatatGTATTTAAAGATTTAAATTACAttttctatttttttagagatatggtttcactatgtcactctgcccaggctgcagtacagtggttgttcacagtcatgatcatagcacattataaccttgaactcctgggctcaaggaatcctcctgtattagtctccccagtagct-ggattacTAGCAT + +a score=518950 +s hg18.chr1 246173 3827 + 247249719 atgccaccatgtccACCTTTATGCTTTTTAAAGTGAAAAACCATACTAAGAATGAGGCAGCTCAACTTAATAATAAAAACATTTCAAATGtaaagaaatttacaaaagaaaaacaatcaaccccattaaaattgggcaaagggaatgaacggacacttttcaaaagaatacatgcatgcagccaacaaacatacaaaaaaaaagttcaacatcactgatcattagagaaatgcaaatcaaaaccataatgagataccatttcacaccagtcagaatagctatcattaaaaagtcaaaaactaacagatgctagtgaggctatggagaaaagggaatgcttatacactgttgttgggtgtgcaaatcagttcaatcattgtgcaaggaa-agtgattcctcaaagagctaaaagcagagctaccattcgacccagtaatcccactactgggtatatacccagatgaatataaaccattctaccataaagacacatgcatacaaatgttcattgcagcactgttcacaatagcaaaagtatgggatcaacctaaatgcccatcaatgacagattggataaagaaaatgtggtacatatacaccatggaatactatgccgccattaaaaaatgatatcatgtcttttgctggaatatggatggaccttctattatccttagcaaactaatgcaggaacagaaaaccaaatacagcatactctcagttataagtgggagctaaatgatgagaactcatgaacacaaagaataaaacagacactggggtctacttgagggtggagggtgagaaacggaagagaaacagaaaagataactattgggtactaggtttaatacctgggtgatgaaatgatctgtacaataaccccctgtgacaccagtctacctatgtaacaaatgcccctaaacttaaaataaaagtta aaaaaaaaAGAAAATTAAAATCTCCTTATCATCTACCTGGTAATATGAAAAACACATATCTTTCATtcattcctttcaactgatgaggaaactgaggcattgggagttagtaaAAGTCCACATTGAGATATGAGACCCACCACTggctggacacagtggctcacacctgtaatcccagcactttgggaggccgatgctggtggatcacctaaggtcaggagttcgggaccaggctggccaacatggtgaaacccccatctctactaaaaatacaaaaattagctgggtgtggtggctggcacctgtaataccagctactagggaggctgaggcaggagaatcgcttgaacccaggaggtggagtttacagtgagccaaaatcatgccattgcactccagcctgggcaacaagagcaagactctgtcggggaaaaaaaaaaacaaaaaaaaCCACCACCATCATTTTGCAAGTGTTACCACTATTGTGTGTTAATATTGTAGAAGTATTCCTAATTATGATTTCTTTGTATTCCTAATTGTAATAGCTTTGTATTTGAAAAATTATTGATTCATACTCTATATGTTATTATTTTGTATGCGATGACAACAGAATATATTATCATGCTCCTTTTGTGAATCTCATTCATAATATAAAGTATAAATTTGTGATTTTGCTTTAATTTGAAATATTAATTTCAAATATGTTATCACAATTTGATACAAACTATTGACAGTAAATCTGTGGATTAAGTAATGTCTTAGTAGGTATTGGGAAAATTTGAAACTAGTAACATGGAGGACTATTGTCATTGTTTATTTCAAAGCCAGTTAAAATTCTGCAAAGCAGTGTACATAAAAATAATTTCAAGAAATTTATAAAATACCGAGATTATGGTGTATAAACAACTTTAGATTCTTTGTTTAAGAAATACTGCCAGTTTGTAATATAtgcttcattcaaagtagctaagggctgtacctggctaata gtaggcacctaatatttgttgaaaaggaatACTGAGTAGCTGGGACCTCCTGAGTAGCTGGGACCACACACATTTAACCTGTATTTATAAAATTACTGTTTAGAGAATAACATTTGATGGAatcatgcttttactttctgcttacgactcaattgtttgtactgacattaacatcccaaatccttagcatggcctacaaggccctgagcaatgtggcacctgctgaagcctgctgcctcatttaataactctttgtctctttcccagatccagccactctaacattttttagctcctggaccaagacaagctcttcccagaacctgagctttgtacctgttctttattcctggagtatttttcccctgacaaattacttatcatctatcataattcaggttaaatggcactaactcagggaaggcttccctaactgtctcccttctccaaccaaattaggaacaattatatggccacatagtatcgaatcaagtttataattttaaaataattgggagattttgttgtttaacacttgttttcactataagactgtaattacatgcaagtaagaaccatgcctgtttgttcactcctgccacagtcagaatagtgcctggaatatgcagtaagggctgaacaagcactaaataaatgaaCAAGTGAATAAATGGATATTGTCTCATTTTCAGAACAGAGTACTAAATGGATCATGAACACTATCTGGTATGTCACGTAGGTAATTTACAAGGGCTACAATTTCAGCTCAGATTTACCTTTTCCTGGATACAGGTCTTGATAGGTCTCTTGATGTCATTTCACTTCAGATTCTTCTTTAGAAAACTTGGACAATAGCATTTGCTGTCTTGTCCAAATTGTTACTAAGAATCAAGAGAGATATCTGACATGAAATGACATTGGAAAACATTAAACACGATTGAAATAATGCTAGCCAATATGGTTACTATTAGAAACCAATTACATTTTCA ACTTAAAAATAGTAATACTTATTGCAGACTCAAATGTGCTTATTCTAAAACAAGTAAATGTTTGCCTATGGTCTGAGATTCTAATCCACGGAGTTCATTCTAATCCACATTCAACACTATCATGTACCAGTGGGCCTCATAACCCACCTAGCCCTGTGATTTTTCAGGTTCACTTTTCTAAACTTGTGAATTAAATATTTATTTTCTTAGTTCAGAAGAGGAAAAAAACTCTTGTAATTGTTGCCCATTTCAGGAGAAATCTTGCATATGAAAACAAGAGATAAATATACACAACTGAGGGCTGTGGTTTAAACAAAATCTTGAGAATGTTTTTTGACCTTATACATTTGTGCTTTAGTATAACAAAATGATATAGACAAAGGTAACTTTTAATAGAACCAGTCACTAAATTAAAAAAATGACAAATTCTTCTGCTTAGCTAAGCAACAGAGAAGGTAAAATACTAATTCAATTCATCAATTTAAGCAATACTCATTAAGAGCCAAGTATGTGCTTACTGAATAAGCTGCTAAGGTTTGGTGGTTACAGAGTGTGCGGTGAAATGATGTCTACATCACAGTCCAACATTCACAGAGTTTAAAAGCCTACCAAGAATCAAGACAGACACAAATACCTAACATAGACGTTTGTATATGATAAGAGAGCCAGAGTACAATTTAGGAGAAGAAATTGTATGGAAGGAAGGTTCATTTCCATTAGACCAGAAAAGACAGCACATTTGAAGGCCTGAATAAGAAATATTCTGGATAAGATATTGTggctgctaccagaatggctcttgatgatctctacctcttggtatttatacccttatataatctctttcctatagtgtaagctggtcccaggtacttgtttctattgaatagaatagaacaaaagaaatg +s panTro2.chr1_random 7107868 3820 + 9420409 atgccaccatgtccACCTTTATGCTTTTTAAAGTGAAAAACCATACTAAGAATGAGGCAGCTCAACTTAATAATAAAAACATTTCGCATGtaaagaaatttacaaaagaaaaacaatcaaccccattaaaattgggcaaagggaatgaacagacacttttcaaaggaatacatgcatgcagccaacaaatatac-aaaaaaaagttcaacatcactgatcattagagaaatgcaaatcaaaaccataatgagataccatctcacaccagtcagaatagctatcattaaaaagtcaaaaaataacagatgctagtgagtctatggagaaaagggaatgcttatacactgttggtgggtgtgcaaatcagttcaatcattgtgcaaagaatagtgattcctcaaagagctaaaagcagagctaccattcgacccagtaatcccactactgggtatatacccagatgaatataaaccattctaccataaagacataggcatacaaatgttcattgcagcactgttcacaatagcaaaagtataggatcaacctaaatgcccatcaatgacagattggataaggaaaatgtggtacatatacaccatggaatactatgccgccattaaaaaatgatatcatgtcttttgctggaatat-gatggaccttctattatccttagcaaactaatacaggaacagaaaaccaaatacagcatactctcagttataagtgggagctaaatgatgagaactaatgaacacaaagaataaaacagacactggggtctacttgagggtggagggtgagaaaaggaagagaagcagaaaagataactattgggtactaggtttaatacctgggtgatgaaataatctgtacaataaccccctgtgacaccagtttacgtatgtaacaaatgcccctaaacttaaaataaaagtta aaaaaaaaAGAAAATTAAAATCTCCTTATCATCTACCTGGTAATATGAAAAACACATATCTTTCATtcattcctttcaactgatgaggaaactgaggcatcgggagttagtaaAAGTCCACATTGAGATATGAGACCCACCACTggctggacgcagtggctcacacctgtaatcccagcactttgggaggccgatgctggtggatcacctaaggtcaggagttcgggaccaggctggccaacatggtgaaacccccatctcttctaaaaatacaaaaattagctgggtgtggtggcaggcacctgtaataccagctactagggaggctgaggcaggagaatcgcttgaacccaggaggtggagtttacagtgagccaaaatcacgccattgcactccagcctgggcaacaagagcaagactctgtcgggaaaagaaaaaaa-aaaaaaaaaCACCACCATCATTTTGCAAGTGTTACCACTATTGTGTGTTAATATTGTAGAAGTATTCCTAATTATGATTTCTTTGTATTCCTAATTGTAATAGCTTTGTACTTGAAAAATTATTGATTCATACTCTATATGTTATTATTTTATATGCGATGACAACAGAATATATTATCATGCTCCTTTTGTGAATCTCATTCATAATATAAAGTATAAATTTGTGATTTTGCTTTAATTTGAAATATTAATTTCAAATATGTTATCACAATTTGATACAAACTATTGACAGTAAATCTGTGGATTAAGTAATGTCTTAGTAGGTATTGGGAAAATTTGAAACTAGTAACATGGAGGACTATTGTCATTGTTTATTTCAAAGCCAGTTAAAATTCTGCAAAGCAGTGTAAATAAAAATAATTTCAAGAAATTTATAAAATACCGAGATTATGGTGTATAAACAACTTTAGATTCTTTGTTTAAGAAATTCTGCCAGTTTGTAATATAtgcttcattcaaagtagctaagggctgtacctggctaata gtaggcacctaatatttgttgaaaaggaatACTGAGTAGCTGGGACCTCCTGAATAGCTGGGACCACACACATTTAACCTGTATTTATAAAATTGCTGTTTAGAGAATAACATTTGATGGAatcatgcttttactttctgcttatgactcaattgtttgtactgacattaacatcccaaatccttagcatggcctacaaggccctgagcaatgtggcacctgctgaagcctgctgcctcatttaataactctttgtctctttcccagatccagccactctaacattttttagttcctggaccaagacaagctcttcccagaacctgacctttgtacctgttctttattcctggagtatttttcccctgacaaattacttatcatctatcataaatcaggttaaatggcactaactcagggaaggcttccctaactgcctcccttctctaaccaaattaggaacaattatatggccacatagtatcgaatcaagtttataattttaaaataattgggagattttg----ttaacacttgttttcactataagactgtaattacatgcaagtaagaaccatgcctgtttgtttactcctgccacagtcagaatagtgcctggaatatgcagtaagggctgaacaaacactaaataaataaaCAAGTGAATAAATGGATATTGTCTCATTTTTAGAACAGAGTACTAAATGGATCATGAACACTATCTGGAATGTCACGTAGGTAATTTACAAGGGCTACAATTTCAGCTCAGATTTACCTTTTCCTGGATACAGGTcttgataggtctcttgatgtcatttcacttcagattcttctttagaaaacttggacaatagcatttgctgtcttgtccaaattgttactaagaatcaaaagagatatctgacatgaaatgacattggaaaacattaaacacgattgaaataatgctagccaatatggttatTATTAGAAACCAATTACATTTTCA ACTTAAAAATAGTAATACTTATTGCAGACTCAAATGTGCTCATTCTAAAACAAGTAAATGTTTGCCTGTGGTCTGAGATTCTAATCCACGGAGTTCATTCTAATCCACATTCAACACTATCATGTACCAGTGGGCCTCATAACCCACCTAGCCCTGTGATTTTTCAGGTTCACTTTTCTAAACTTGTGAAGTAAATATTTATTTTCTTAGTTCAGAAGAGGAAAAAAACTCTTGTAATTTTTGCCCATTTCAGGAGAAATCTTGCATATGAAAACAAGAGATAAATATACACAACTGAGGGCTGTGGTTTAAACAAAATCTTGAGAAT-TTTTTTGACCTTATACATTTGTGCTTTAGTATAACAAAATGATATAGACAAAGGTAACTTTTAATAGAACCAGTCACTAAATTAAAAAAATGACAAATTCTTCTGCTTAGCTAAGCAACAGAGAAGGTAAAATACTAATTCAATTCATCAATTTAAGCAATACTCATTAAGAGCCAAGTATGTGCTTACTGAATAAGCTGCTAAGGTTTGGTGGTTACAGAGTGTGCGGTGAAATGATGTCTACATCACAGTCCAACATTCACAGAGTTTAAAAGCCTACCAAGAATCAAGACAGACACAAATACCTAACATAGACGTTTGTATGTGATAAGAGAGCCACAGTACAATTTAGGAGAAGAAATTGTATGGAAGGAAGGTTCATTTCCATTAGACCAGAAAAGACAGCACATTTGAAGGCCTGAATAAGAAATATTCTGGATAAGATATtgtggctgccaccagaatgactcttgatgatctctacctcttggtatttatacccttatataatctctttcctatagtataagctggtcccaggtacttgtttctattgaatagaatcgaacaaaagtaatg + diff -r 447c74d98fe5 -r ad3f61801a82 test-data/ortho_ms.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ortho_ms.tab Wed Sep 24 18:20:39 2008 -0400 @@ -0,0 +1,106 @@ +#Block Seq1_Name Seq1_Start Seq1_End Seq1_Type Seq1_Length Seq1_RepeatNumber Seq1_Unit Seq2_Name Seq2_Start Seq2_End Seq2_Type Seq2_Length Seq2_RepeatNumber Seq2_Unit +5 hg18.chr1 6483 6496 trinucleotide 13 4 GCT panTro2.chr15 100042575 100042588 trinucleotide 13 4 GCT +10 hg18.chr1 16317 16329 dinucleotide 12 6 GT panTro2.chr15 100035910 100035921 dinucleotide 11 5 TG +10 hg18.chr1 18452 18467 mononucleotide 15 15 T panTro2.chr15 100038029 100038042 mononucleotide 13 13 T +12 hg18.chr1 20736 20756 dinucleotide 20 10 TC panTro2.chr15_random 1091184 1091198 dinucleotide 14 7 TC +13 hg18.chr1 20774 20786 dinucleotide 12 6 TC panTro2.chrUn 1510792 1510803 dinucleotide 11 5 TC +13 hg18.chr1 20799 20812 dinucleotide 13 6 TC panTro2.chrUn 1510811 1510831 dinucleotide 20 10 TC +13 hg18.chr1 20774 20786 dinucleotide 12 6 TC panTro2.chrUn 1510792 1510803 dinucleotide 11 5 TC +13 hg18.chr1 20799 20812 dinucleotide 13 6 TC panTro2.chrUn 1510811 1510831 dinucleotide 20 10 TC +14 hg18.chr1 23313 23328 mononucleotide 15 15 A panTro2.chrUn 1508926 1508942 mononucleotide 16 16 A +14 hg18.chr1 23384 23405 mononucleotide 21 21 T panTro2.chrUn 1508999 1509025 mononucleotide 26 26 T +15 hg18.chr1 25352 25371 tetranucleotide 19 4 AAAT panTro2.chr15_random 1087905 1087924 tetranucleotide 19 4 AAAT +16 hg18.chr1 26215 26228 mononucleotide 13 13 A panTro2.chrUn 135175 135189 mononucleotide 14 14 A +16 hg18.chr1 30483 30495 trinucleotide 12 4 TTC panTro2.chrUn 139435 139447 trinucleotide 12 4 TTC +16 hg18.chr1 30503 30522 mononucleotide 19 19 T panTro2.chrUn 139457 139482 mononucleotide 25 25 T +17 hg18.chr1 33660 33676 mononucleotide 16 16 A panTro2.chrUn 9698149 9698162 mononucleotide 13 13 A +17 hg18.chr1 34037 34047 mononucleotide 10 10 A panTro2.chrUn 9698527 9698537 mononucleotide 10 10 A +19 hg18.chr1 37182 37192 mononucleotide 10 10 A panTro2.chrUn 9701917 9701928 mononucleotide 11 11 A +19 hg18.chr1 40345 40377 dinucleotide 32 16 GT panTro2.chrUn 9705094 9705126 dinucleotide 32 16 GT +19 hg18.chr1 41728 41741 mononucleotide 13 13 A panTro2.chrUn 9706479 9706495 mononucleotide 16 16 A +20 hg18.chr1 44576 44638 tetranucleotide 62 15 TTTC panTro2.chrUn 9709825 9709899 tetranucleotide 74 18 TTTC +20 hg18.chr1 44654 44681 tetranucleotide 27 6 TTTC panTro2.chrUn 9709915 9709942 tetranucleotide 27 6 TTTC +22 hg18.chr1 51726 51744 mononucleotide 18 18 T panTro2.chrUn 9717633 9717652 mononucleotide 19 19 T +22 hg18.chr1 52103 52120 dinucleotide 17 8 AC panTro2.chrUn 9718011 9718024 dinucleotide 13 6 AC +25 hg18.chr1 61983 61995 dinucleotide 12 6 TA panTro2.chrUn 9729161 9729173 dinucleotide 12 6 TA +25 hg18.chr1 62004 62027 tetranucleotide 23 5 ATAC panTro2.chrUn 9729184 9729219 tetranucleotide 35 8 ATAC +25 hg18.chr1 63706 63720 mononucleotide 14 14 T panTro2.chrUn 9730896 9730914 mononucleotide 18 18 T +26 hg18.chr1 67038 67059 mononucleotide 21 21 A panTro2.chrUn 9734760 9734777 mononucleotide 17 17 A +27 hg18.chr1 72077 72088 dinucleotide 11 5 AC panTro2.chrUn 9742946 9742957 dinucleotide 11 5 AC +28 hg18.chr1 73838 73906 tetranucleotide 68 17 AAAG panTro2.chr15 99975357 99975380 tetranucleotide 23 5 AAAG +28 hg18.chr1 73838 73906 tetranucleotide 68 17 AAAG panTro2.chr15 99975357 99975380 tetranucleotide 23 5 AAAG +32 hg18.chr1 81064 81077 mononucleotide 13 13 A panTro2.chrUn 1797471 1797489 mononucleotide 18 18 A +35 hg18.chr1 82527 82541 mononucleotide 14 14 A panTro2.chr1_random 7070707 7070721 mononucleotide 14 14 A +40 hg18.chr1 91199 91212 mononucleotide 13 13 A panTro2.chr1_random 7089889 7089900 mononucleotide 11 11 A +41 hg18.chr1 91538 91554 mononucleotide 16 16 A panTro2.chr1 223998154 223998167 mononucleotide 13 13 A +42 hg18.chr1 94024 94060 dinucleotide 36 18 AC panTro2.chr1_random 7090945 7090970 dinucleotide 25 12 AC +42 hg18.chr1 95472 95491 dinucleotide 19 9 AT panTro2.chr1_random 7092383 7092404 dinucleotide 21 10 AT +43 hg18.chr1 96802 96815 dinucleotide 13 6 TC panTro2.chr1 243988 244001 dinucleotide 13 6 TC +44 hg18.chr1 98409 98425 mononucleotide 16 16 A panTro2.chr1_random 7095323 7095342 mononucleotide 19 19 A +45 hg18.chr1 99439 99478 dinucleotide 39 19 GT panTro2.chr1 246661 246696 dinucleotide 35 17 GT +45 hg18.chr1 100799 100809 mononucleotide 10 10 A panTro2.chr1 248017 248028 mononucleotide 11 11 A +45 hg18.chr1 101230 101250 mononucleotide 20 20 A panTro2.chr1 248453 248467 mononucleotide 14 14 A +49 hg18.chr1 111133 111148 mononucleotide 15 15 T panTro2.chr1 260455 260473 mononucleotide 18 18 T +49 hg18.chr1 111503 111515 trinucleotide 12 4 TAA panTro2.chr1 260828 260846 trinucleotide 18 6 TAA +49 hg18.chr1 112927 112938 dinucleotide 11 5 CA panTro2.chr1 262255 262267 dinucleotide 12 6 AC +49 hg18.chr1 112974 112995 dinucleotide 21 10 TA panTro2.chr1 262299 262320 dinucleotide 21 10 TA +55 hg18.chr1 114709 114728 mononucleotide 19 19 A panTro2.chr1 262958 262973 mononucleotide 15 15 A +55 hg18.chr1 114709 114728 mononucleotide 19 19 A panTro2.chr1 262958 262973 mononucleotide 15 15 A +56 hg18.chr1 118460 118475 mononucleotide 15 15 T panTro2.chr1 267602 267617 mononucleotide 15 15 T +56 hg18.chr1 119541 119556 mononucleotide 15 15 T panTro2.chr1 268682 268695 mononucleotide 13 13 T +56 hg18.chr1 120154 120164 mononucleotide 10 10 A panTro2.chr1 269287 269300 mononucleotide 13 13 A +56 hg18.chr1 123929 123958 mononucleotide 29 29 T panTro2.chr1 273095 273130 mononucleotide 35 35 T +56 hg18.chr1 118460 118475 mononucleotide 15 15 T panTro2.chr1 267602 267617 mononucleotide 15 15 T +56 hg18.chr1 119541 119556 mononucleotide 15 15 T panTro2.chr1 268682 268695 mononucleotide 13 13 T +56 hg18.chr1 120154 120164 mononucleotide 10 10 A panTro2.chr1 269287 269300 mononucleotide 13 13 A +72 hg18.chr1 131317 131331 trinucleotide 14 4 TTA panTro2.chr1_random 7185786 7185800 trinucleotide 14 4 TTA +72 hg18.chr1 134751 134763 mononucleotide 12 12 A panTro2.chr1_random 7189181 7189197 mononucleotide 16 16 A +72 hg18.chr1 134994 135006 trinucleotide 12 4 GTG panTro2.chr1_random 7189427 7189439 trinucleotide 12 4 GTG +72 hg18.chr1 136901 136911 mononucleotide 10 10 A panTro2.chr1_random 7191338 7191350 mononucleotide 12 12 A +72 hg18.chr1 137298 137339 trinucleotide 41 13 AAC panTro2.chr1_random 7191741 7191782 trinucleotide 41 13 AAC +72 hg18.chr1 137771 137781 mononucleotide 10 10 A panTro2.chr1_random 7192213 7192224 mononucleotide 11 11 A +72 hg18.chr1 138639 138652 trinucleotide 13 4 AAT panTro2.chr1_random 7193082 7193095 trinucleotide 13 4 AAT +72 hg18.chr1 139543 139563 mononucleotide 20 20 A panTro2.chr1_random 7193986 7194009 mononucleotide 23 23 A +72 hg18.chr1 141348 141361 mononucleotide 13 13 T panTro2.chr1_random 7195790 7195814 mononucleotide 24 24 T +73 hg18.chr1 145718 145733 mononucleotide 15 15 A panTro2.chr1_random 7202121 7202135 mononucleotide 14 14 A +74 hg18.chr1 146143 146155 mononucleotide 12 12 T panTro2.chr1_random 7208622 7208632 mononucleotide 10 10 T +74 hg18.chr1 146971 146985 mononucleotide 14 14 A panTro2.chr1_random 7209449 7209463 mononucleotide 14 14 A +75 hg18.chr1 148861 148895 dinucleotide 34 17 AC panTro2.chr1_random 7211571 7211605 dinucleotide 34 17 AC +75 hg18.chr1 150335 150351 mononucleotide 16 16 T panTro2.chr1_random 7213029 7213047 mononucleotide 18 18 T +75 hg18.chr1 152174 152208 tetranucleotide 34 8 GGAG panTro2.chr1_random 7214870 7214904 tetranucleotide 34 8 GGAG +75 hg18.chr1 153993 154017 pentanucleotide 24 4 AAAAC panTro2.chr1_random 7216686 7216711 pentanucleotide 25 5 AAAAC +75 hg18.chr1 155151 155174 mononucleotide 23 23 A panTro2.chr1_random 7217843 7217867 mononucleotide 24 24 A +75 hg18.chr1 156998 157017 tetranucleotide 19 4 TTTA panTro2.chr1_random 7219691 7219710 tetranucleotide 19 4 TTTA +75 hg18.chr1 148861 148895 dinucleotide 34 17 AC panTro2.chr1_random 7211571 7211605 dinucleotide 34 17 AC +75 hg18.chr1 152174 152208 tetranucleotide 34 8 GGAG panTro2.chr1_random 7214870 7214904 tetranucleotide 34 8 GGAG +75 hg18.chr1 153993 154017 pentanucleotide 24 4 AAAAC panTro2.chr1_random 7216686 7216711 pentanucleotide 25 5 AAAAC +75 hg18.chr1 154537 154559 mononucleotide 22 22 A panTro2.chr1_random 7217231 7217251 mononucleotide 20 20 A +75 hg18.chr1 156998 157017 tetranucleotide 19 4 TTTA panTro2.chr1_random 7219691 7219710 tetranucleotide 19 4 TTTA +76 hg18.chr1 159723 159736 mononucleotide 13 13 T panTro2.chr1 224074251 224074269 mononucleotide 18 18 T +76 hg18.chr1 160798 160818 pentanucleotide 20 4 GTTTT panTro2.chr1 224075335 224075355 pentanucleotide 20 4 GTTTT +77 hg18.chr1 164907 164918 dinucleotide 11 5 CA panTro2.chr1_random 7295345 7295356 dinucleotide 11 5 CA +77 hg18.chr1 165310 165322 mononucleotide 12 12 A panTro2.chr1_random 7295748 7295770 mononucleotide 22 22 A +77 hg18.chr1 164907 164918 dinucleotide 11 5 CA panTro2.chr1_random 7295345 7295356 dinucleotide 11 5 CA +77 hg18.chr1 165310 165322 mononucleotide 12 12 A panTro2.chr1_random 7295748 7295770 mononucleotide 22 22 A +78 hg18.chr1 166066 166095 pentanucleotide 29 5 AAAAC panTro2.chr1 224080667 224080691 pentanucleotide 24 4 AAAAC +83 hg18.chr1 219668 219689 tetranucleotide 21 5 TAAA panTro2.chr3 77587413 77587435 tetranucleotide 22 5 TAAA +87 hg18.chr1 222298 222309 mononucleotide 11 11 T panTro2.chrUn 1781936 1781946 mononucleotide 10 10 T +87 hg18.chr1 222298 222309 mononucleotide 11 11 T panTro2.chrUn 1781936 1781946 mononucleotide 10 10 T +93 hg18.chr1 227392 227408 mononucleotide 16 16 A panTro2.chr1_random 7325593 7325616 mononucleotide 23 23 A +93 hg18.chr1 228854 228869 mononucleotide 15 15 A panTro2.chr1_random 7327066 7327078 mononucleotide 12 12 A +94 hg18.chr1 231193 231209 mononucleotide 16 16 T panTro2.chr1 223990552 223990572 mononucleotide 20 20 T +97 hg18.chr1 235198 235229 tetranucleotide 31 7 TTTA panTro2.chr1_random 7331178 7331221 tetranucleotide 43 10 TTTA +97 hg18.chr1 235279 235294 mononucleotide 15 15 T panTro2.chr1_random 7331271 7331290 mononucleotide 19 19 T +97 hg18.chr1 237516 237529 mononucleotide 13 13 A panTro2.chr1_random 7333512 7333527 mononucleotide 15 15 A +98 hg18.chr1 237855 237870 mononucleotide 15 15 A panTro2.chr1 223998154 223998167 mononucleotide 13 13 A +99 hg18.chr1 240341 240375 dinucleotide 34 17 AC panTro2.chr1_random 7334566 7334615 dinucleotide 49 24 AC +99 hg18.chr1 241787 241806 dinucleotide 19 9 AT panTro2.chr1_random 7336030 7336051 dinucleotide 21 10 AT +99 hg18.chr1 243117 243130 dinucleotide 13 6 TC panTro2.chr1_random 7337363 7337376 dinucleotide 13 6 TC +99 hg18.chr1 244724 244746 mononucleotide 22 22 A panTro2.chr1_random 7338970 7338987 mononucleotide 17 17 A +99 hg18.chr1 240341 240375 dinucleotide 34 17 AC panTro2.chr1_random 7334566 7334615 dinucleotide 49 24 AC +99 hg18.chr1 241787 241806 dinucleotide 19 9 AT panTro2.chr1_random 7336030 7336051 dinucleotide 21 10 AT +99 hg18.chr1 243117 243130 dinucleotide 13 6 TC panTro2.chr1_random 7337363 7337376 dinucleotide 13 6 TC +99 hg18.chr1 244724 244746 mononucleotide 22 22 A panTro2.chr1_random 7338970 7338987 mononucleotide 17 17 A +99 hg18.chr1 245760 245793 dinucleotide 33 16 GT panTro2.chr1_random 7340006 7340026 dinucleotide 20 10 TG +100 hg18.chr1 247114 247124 mononucleotide 10 10 A panTro2.chr1_random 7108808 7108818 mononucleotide 10 10 A +100 hg18.chr1 247545 247565 mononucleotide 20 20 A panTro2.chr1_random 7109243 7109259 mononucleotide 16 16 A diff -r 447c74d98fe5 -r ad3f61801a82 test-data/ortho_ms_mut.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ortho_ms_mut.tab Wed Sep 24 18:20:39 2008 -0400 @@ -0,0 +1,75 @@ +#Window Species_1 Window_Start Window_End Species_2 Groupby_Feature SubGroupby_Feature Mutability Count +5 hg18.chr1 6483 6496 panTro2.chr15 100042575 100042588 trinucleotide GCT 0.00e+00 4 +10 hg18.chr1 18452 18467 panTro2.chr15 100038029 100038042 mononucleotide T 4.00e+00 13 +10 hg18.chr1 18452 18467 panTro2.chr15 100038029 100038042 dinucleotide GT 1.00e+00 5 +12 hg18.chr1 20736 20756 panTro2.chr15_random 1091184 1091198 dinucleotide TC 9.00e+00 7 +13 hg18.chr1 20799 20812 panTro2.chrUn 1510811 1510831 dinucleotide TC 1.10e+01 24 +14 hg18.chr1 23384 23405 panTro2.chrUn 1508999 1509025 mononucleotide A 1.00e+00 15 +14 hg18.chr1 23384 23405 panTro2.chrUn 1508999 1509025 mononucleotide T 1.30e+01 36 +15 hg18.chr1 25352 25371 panTro2.chr15_random 1087905 1087924 tetranucleotide AAAT 0.00e+00 4 +16 hg18.chr1 30503 30522 panTro2.chrUn 139457 139482 trinucleotide TTC 0.00e+00 4 +16 hg18.chr1 30503 30522 panTro2.chrUn 139457 139482 mononucleotide A 1.00e+00 13 +16 hg18.chr1 30503 30522 panTro2.chrUn 139457 139482 mononucleotide T 1.85e+01 32 +17 hg18.chr1 34037 34047 panTro2.chrUn 9698527 9698537 mononucleotide A 4.50e+00 23 +19 hg18.chr1 41728 41741 panTro2.chrUn 9706479 9706495 mononucleotide A 5.00e+00 23 +19 hg18.chr1 41728 41741 panTro2.chrUn 9706479 9706495 dinucleotide GT 0.00e+00 16 +20 hg18.chr1 44654 44681 panTro2.chrUn 9709915 9709942 tetranucleotide TTTC 4.50e+00 21 +22 hg18.chr1 52103 52120 panTro2.chrUn 9718011 9718024 mononucleotide T 1.00e+00 18 +22 hg18.chr1 52103 52120 panTro2.chrUn 9718011 9718024 dinucleotide AC 4.00e+00 6 +25 hg18.chr1 63706 63720 panTro2.chrUn 9730896 9730914 mononucleotide T 1.60e+01 14 +25 hg18.chr1 63706 63720 panTro2.chrUn 9730896 9730914 dinucleotide TA 0.00e+00 6 +25 hg18.chr1 63706 63720 panTro2.chrUn 9730896 9730914 tetranucleotide ATAC 9.00e+00 5 +26 hg18.chr1 67038 67059 panTro2.chrUn 9734760 9734777 mononucleotide A 1.60e+01 17 +27 hg18.chr1 72077 72088 panTro2.chrUn 9742946 9742957 dinucleotide AC 0.00e+00 5 +28 hg18.chr1 73838 73906 panTro2.chr15 99975357 99975380 tetranucleotide AAAG 1.44e+02 10 +32 hg18.chr1 81064 81077 panTro2.chrUn 1797471 1797489 mononucleotide A 2.50e+01 13 +35 hg18.chr1 82527 82541 panTro2.chr1_random 7070707 7070721 mononucleotide A 0.00e+00 14 +40 hg18.chr1 91199 91212 panTro2.chr1_random 7089889 7089900 mononucleotide A 4.00e+00 11 +41 hg18.chr1 91538 91554 panTro2.chr1 223998154 223998167 mononucleotide A 9.00e+00 13 +42 hg18.chr1 95472 95491 panTro2.chr1_random 7092383 7092404 dinucleotide AT 1.85e+01 22 +42 hg18.chr1 95472 95491 panTro2.chr1_random 7092383 7092404 dinucleotide AC 3.60e+01 12 +43 hg18.chr1 96802 96815 panTro2.chr1 243988 244001 dinucleotide TC 0.00e+00 6 +44 hg18.chr1 98409 98425 panTro2.chr1_random 7095323 7095342 mononucleotide A 9.00e+00 16 +45 hg18.chr1 101230 101250 panTro2.chr1 248453 248467 mononucleotide A 1.85e+01 25 +45 hg18.chr1 101230 101250 panTro2.chr1 248453 248467 dinucleotide GT 4.00e+00 17 +49 hg18.chr1 112974 112995 panTro2.chr1 262299 262320 trinucleotide TAA 4.00e+00 4 +49 hg18.chr1 112974 112995 panTro2.chr1 262299 262320 dinucleotide TA 5.00e-01 15 +49 hg18.chr1 112974 112995 panTro2.chr1 262299 262320 mononucleotide T 9.00e+00 15 +49 hg18.chr1 112974 112995 panTro2.chr1 262299 262320 dinucleotide CA 1.00e+00 5 +55 hg18.chr1 114709 114728 panTro2.chr1 262958 262973 mononucleotide A 1.60e+01 30 +56 hg18.chr1 120154 120164 panTro2.chr1 269287 269300 mononucleotide A 8.89e+00 109 +56 hg18.chr1 120154 120164 panTro2.chr1 269287 269300 mononucleotide T 8.80e+00 89 +72 hg18.chr1 141348 141361 panTro2.chr1_random 7195790 7195814 mononucleotide T 3.65e+01 65 +72 hg18.chr1 141348 141361 panTro2.chr1_random 7195790 7195814 trinucleotide GTG 0.00e+00 8 +72 hg18.chr1 141348 141361 panTro2.chr1_random 7195790 7195814 trinucleotide AAC 0.00e+00 21 +72 hg18.chr1 141348 141361 panTro2.chr1_random 7195790 7195814 mononucleotide A 8.33e+00 52 +72 hg18.chr1 141348 141361 panTro2.chr1_random 7195790 7195814 trinucleotide TTA 0.00e+00 4 +72 hg18.chr1 141348 141361 panTro2.chr1_random 7195790 7195814 trinucleotide AAT 0.00e+00 25 +73 hg18.chr1 145718 145733 panTro2.chr1_random 7202121 7202135 mononucleotide A 1.00e+00 14 +74 hg18.chr1 146971 146985 panTro2.chr1_random 7209449 7209463 mononucleotide A 2.00e+00 24 +74 hg18.chr1 146971 146985 panTro2.chr1_random 7209449 7209463 mononucleotide T 4.00e+00 10 +75 hg18.chr1 156998 157017 panTro2.chr1_random 7219691 7219710 mononucleotide T 4.00e+00 16 +75 hg18.chr1 156998 157017 panTro2.chr1_random 7219691 7219710 tetranucleotide GGAG 0.00e+00 16 +75 hg18.chr1 156998 157017 panTro2.chr1_random 7219691 7219710 tetranucleotide TTTA 0.00e+00 24 +75 hg18.chr1 156998 157017 panTro2.chr1_random 7219691 7219710 pentanucleotide AAAAC 1.00e+00 8 +75 hg18.chr1 156998 157017 panTro2.chr1_random 7219691 7219710 mononucleotide A 3.00e+00 61 +75 hg18.chr1 156998 157017 panTro2.chr1_random 7219691 7219710 dinucleotide AC 0.00e+00 34 +76 hg18.chr1 160798 160818 panTro2.chr1 224075335 224075355 mononucleotide T 2.50e+01 13 +76 hg18.chr1 160798 160818 panTro2.chr1 224075335 224075355 pentanucleotide GTTTT 0.00e+00 4 +77 hg18.chr1 165310 165322 panTro2.chr1_random 7295748 7295770 mononucleotide A 1.00e+02 24 +77 hg18.chr1 165310 165322 panTro2.chr1_random 7295748 7295770 dinucleotide CA 0.00e+00 10 +78 hg18.chr1 166066 166095 panTro2.chr1 224080667 224080691 pentanucleotide AAAAC 1.00e+00 4 +83 hg18.chr1 219668 219689 panTro2.chr3 77587413 77587435 tetranucleotide TAAA 0.00e+00 5 +87 hg18.chr1 222298 222309 panTro2.chrUn 1781936 1781946 mononucleotide T 1.00e+00 20 +93 hg18.chr1 228854 228869 panTro2.chr1_random 7327066 7327078 mononucleotide A 2.90e+01 31 +94 hg18.chr1 231193 231209 panTro2.chr1 223990552 223990572 mononucleotide T 1.60e+01 16 +97 hg18.chr1 237516 237529 panTro2.chr1_random 7333512 7333527 mononucleotide A 1.00e+01 28 +97 hg18.chr1 237516 237529 panTro2.chr1_random 7333512 7333527 mononucleotide T 1.60e+01 15 +97 hg18.chr1 237516 237529 panTro2.chr1_random 7333512 7333527 tetranucleotide TTTA 9.00e+00 7 +98 hg18.chr1 237855 237870 panTro2.chr1 223998154 223998167 mononucleotide A 4.00e+00 13 +99 hg18.chr1 245760 245793 panTro2.chr1_random 7340006 7340026 dinucleotide AT 2.50e+01 52 +99 hg18.chr1 245760 245793 panTro2.chr1_random 7340006 7340026 dinucleotide TC 1.67e+01 64 +99 hg18.chr1 245760 245793 panTro2.chr1_random 7340006 7340026 mononucleotide A 2.50e+01 34 +99 hg18.chr1 245760 245793 panTro2.chr1_random 7340006 7340026 dinucleotide GT 2.31e+01 114 +99 hg18.chr1 245760 245793 panTro2.chr1_random 7340006 7340026 dinucleotide AC 4.90e+01 34 +100 hg18.chr1 247545 247565 panTro2.chr1_random 7109243 7109259 mononucleotide A 8.00e+00 26 diff -r 447c74d98fe5 -r ad3f61801a82 tool_conf.xml.sample --- a/tool_conf.xml.sample Wed Sep 24 15:05:38 2008 -0400 +++ b/tool_conf.xml.sample Wed Sep 24 18:20:39 2008 -0400 @@ -134,6 +134,8 @@ <tool file="regVariation/getIndelRates_3way.xml" /> <tool file="regVariation/substitutions.xml" /> <tool file="regVariation/substitution_rates.xml" /> + <tool file="regVariation/microsats_alignment_level.xml" /> + <tool file="regVariation/microsats_mutability.xml" /> </section> <section name="Multiple regression" id="multReg"> <tool file="regVariation/linear_regression.xml" /> diff -r 447c74d98fe5 -r ad3f61801a82 tools/regVariation/getIndelRates_3way.xml --- a/tools/regVariation/getIndelRates_3way.xml Wed Sep 24 15:05:38 2008 -0400 +++ b/tools/regVariation/getIndelRates_3way.xml Wed Sep 24 18:20:39 2008 -0400 @@ -5,7 +5,7 @@ #if $region.type == "align" "None" #else - $region.input2 $input2_dbkey $input2_chromCol,$input2_startCol,$input2_endCol,$input2_strandCol + $region.input2 $input2.dbkey $input2.metadata.chromCol,$input2.metadata.startCol,$input2.metadata.endCol,$input2.metadata.strandCol #end if </command> <inputs> diff -r 447c74d98fe5 -r ad3f61801a82 tools/regVariation/microsats_alignment_level.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/regVariation/microsats_alignment_level.py Wed Sep 24 18:20:39 2008 -0400 @@ -0,0 +1,323 @@ + #!/usr/bin/env python +#Guruprasad Ananda +""" +Uses SPUTNIK to fetch microsatellites and extracts orthologous repeats from the sputnik output. +""" +from galaxy import eggs +import sys, os, tempfile, string, math, re + +def reverse_complement(text): + DNA_COMP = string.maketrans( "ACGTacgt", "TGCAtgca" ) + comp = [ch for ch in text.translate(DNA_COMP)] + comp.reverse() + return "".join(comp) + +def main(): + if len(sys.argv) != 8: + print >>sys.stderr, "Insufficient number of arguments." + sys.exit() + + infile = open(sys.argv[1],'r') + separation = int(sys.argv[2]) + outfile = sys.argv[3] + align_type = sys.argv[4] + if align_type == "2way": + align_type_len = 2 + elif align_type == "3way": + align_type_len = 3 + mono_threshold = int(sys.argv[5]) + non_mono_threshold = int(sys.argv[6]) + allow_different_units = int(sys.argv[7]) + + print "Min distance = %d bp; Min threshold for mono repeats = %d; Min threshold for non-mono repeats = %d; Allow different motifs = %s" %(separation, mono_threshold, non_mono_threshold, allow_different_units==1) + try: + fout = open(outfile, "w") + print >>fout, "#Block\tSeq1_Name\tSeq1_Start\tSeq1_End\tSeq1_Type\tSeq1_Length\tSeq1_RepeatNumber\tSeq1_Unit\tSeq2_Name\tSeq2_Start\tSeq2_End\tSeq2_Type\tSeq2_Length\tSeq2_RepeatNumber\tSeq2_Unit" + #sputnik_cmd = os.path.join(os.path.split(sys.argv[0])[0], "sputnik") + sputnik_cmd = "bx-sputnik" + input = infile.read() + skipped = 0 + block_num = 0 + input = input.replace('\r','\n') + for block in input.split('\n\n'): + block_num += 1 + tmpin = tempfile.NamedTemporaryFile() + tmpout = tempfile.NamedTemporaryFile() + tmpin.write(block.strip()) + blk = tmpin.read() + cmdline = sputnik_cmd + " " + tmpin.name + " > /dev/null 2>&1 >> " + tmpout.name + try: + os.system(cmdline) + except Exception, es: + continue + sputnik_out = tmpout.read() + tmpin.close() + tmpout.close() + if sputnik_out != "": + if len(block.split('>')[1:]) != 2: #len(sputnik_out.split('>')): + skipped += 1 + continue + align_block = block.strip().split('>') + + lendict = {'mononucleotide':1, 'dinucleotide':2, 'trinucleotide':3, 'tetranucleotide':4, 'pentanucleotide':5, 'hexanucleotide':6} + blockdict={} + r=0 + namelist=[] + for k,sput_block in enumerate(sputnik_out.split('>')[1:]): + whole_seq = ''.join(align_block[k+1].split('\n')[1:]).replace('\n','').strip() + p = re.compile('\n(\S*nucleotide)') + repeats = p.split(sput_block.strip()) + repeats_count = len(repeats) + j = 1 + name = repeats[0].strip() + try: + coords = re.search('\d+[-_:]\d+',name).group() + coords = coords.replace('_','-').replace(':','-') + except Exception, e: + coords = '0-0' + pass + r += 1 + blockdict[r]={} + try: + sp_name = name[:name.index('.')] + chr_name = name[name.index('.'):name.index('(')] + namelist.append(sp_name + chr_name) + except: + namelist.append(name[:20]) + while j < repeats_count: + try: + if repeats[j].strip() not in lendict: + j += 2 + continue + + if blockdict[r].has_key('types'): + blockdict[r]['types'].append(repeats[j].strip()) #type of microsat + else: + blockdict[r]['types'] = [repeats[j].strip()] #type of microsat + + sequence = ''.join(align_block[r].split('\n')[1:]).replace('\n','').strip() + start = int(repeats[j+1].split('--')[0].split(':')[0].strip()) + #check to see if there are gaps before the start of the repeat, and change the start accordingly + sgaps = 0 + ch_pos = start - 1 + while ch_pos >= 0: + if whole_seq[ch_pos] == '-': + sgaps += 1 + else: + break #break at the 1st non-gap character + ch_pos -= 1 + if blockdict[r].has_key('starts'): + blockdict[r]['starts'].append(start+sgaps) #start co-ords adjusted with alignment co-ords to include GAPS + else: + blockdict[r]['starts'] = [start+sgaps] + + end = int(repeats[j+1].split('--')[0].split(':')[1].strip()) + #check to see if there are gaps after the end of the repeat, and change the end accordingly + egaps = 0 + for ch in whole_seq[end:]: + if ch == '-': + egaps += 1 + else: + break #break at the 1st non-gap character + if blockdict[r].has_key('ends'): + blockdict[r]['ends'].append(end+egaps) #end co-ords adjusted with alignment co-ords to include GAPS + else: + blockdict[r]['ends'] = [end+egaps] + + repeat_seq = ''.join(repeats[j+1].replace('\r','\n').split('\n')[1:]).strip() #Repeat Sequence + repeat_len = repeats[j+1].split('--')[1].split()[1].strip() + gap_count = repeat_seq.count('-') + #print repeats[j+1].split('--')[1], len(repeat_seq), repeat_len, gap_count + repeat_len = str(int(repeat_len) - gap_count) + + rel_start = blockdict[r]['starts'][-1] + gaps_before_start = whole_seq[:rel_start].count('-') + + if blockdict[r].has_key('gaps_before_start'): + blockdict[r]['gaps_before_start'].append(gaps_before_start) #lengths + else: + blockdict[r]['gaps_before_start'] = [gaps_before_start] #lengths + + whole_seq_start= int(coords.split('-')[0]) + if blockdict[r].has_key('whole_seq_start'): + blockdict[r]['whole_seq_start'].append(whole_seq_start) #lengths + else: + blockdict[r]['whole_seq_start'] = [whole_seq_start] #lengths + + if blockdict[r].has_key('lengths'): + blockdict[r]['lengths'].append(repeat_len) #lengths + else: + blockdict[r]['lengths'] = [repeat_len] #lengths + + if blockdict[r].has_key('counts'): + blockdict[r]['counts'].append(str(int(repeat_len)/lendict[repeats[j].strip()])) #Repeat Unit + else: + blockdict[r]['counts'] = [str(int(repeat_len)/lendict[repeats[j].strip()])] #Repeat Unit + + if blockdict[r].has_key('units'): + blockdict[r]['units'].append(repeat_seq[:lendict[repeats[j].strip()]]) #Repeat Unit + else: + blockdict[r]['units'] = [repeat_seq[:lendict[repeats[j].strip()]]] #Repeat Unit + + except Exception, eh: + pass + j+=2 + #check the co-ords of all repeats corresponding to a sequence and remove adjacent repeats separated by less than the user-specified 'separation'. + delete_index_list = [] + for ind, item in enumerate(blockdict[r]['ends']): + try: + if blockdict[r]['starts'][ind+1]-item < separation: + if ind not in delete_index_list: + delete_index_list.append(ind) + if ind+1 not in delete_index_list: + delete_index_list.append(ind+1) + except Exception, ek: + pass + for index in delete_index_list: #mark them for deletion + try: + blockdict[r]['starts'][index] = 'marked' + blockdict[r]['ends'][index] = 'marked' + blockdict[r]['types'][index] = 'marked' + blockdict[r]['gaps_before_start'][index] = 'marked' + blockdict[r]['whole_seq_start'][index] = 'marked' + blockdict[r]['lengths'][index] = 'marked' + blockdict[r]['counts'][index] = 'marked' + blockdict[r]['units'][index] = 'marked' + except Exception, ej: + pass + #remove 'marked' elements from all the lists + """ + for key in blockdict[r].keys(): + for elem in blockdict[r][key]: + if elem == 'marked': + blockdict[r][key].remove(elem) + """ + #print blockdict + + #make sure that the blockdict has keys for both the species + if (1 not in blockdict) or (2 not in blockdict): + continue + + visited_2 = [0 for x in range(len(blockdict[2]['starts']))] + for ind1,coord_s1 in enumerate(blockdict[1]['starts']): + if coord_s1 == 'marked': + continue + coord_e1 = blockdict[1]['ends'][ind1] + out = [] + for ind2,coord_s2 in enumerate(blockdict[2]['starts']): + if coord_s2 == 'marked': + visited_2[ind2] = 1 + continue + coord_e2 = blockdict[2]['ends'][ind2] + #skip if the 2 repeats are not of the same type or don't have the same repeating unit. + if allow_different_units == 0: + if (blockdict[1]['types'][ind1] != blockdict[2]['types'][ind2]): + continue + else: + if (blockdict[1]['units'][ind1] not in blockdict[2]['units'][ind2]*2) and (reverse_complement(blockdict[1]['units'][ind1]) not in blockdict[2]['units'][ind2]*2): + continue + #print >>sys.stderr, (reverse_complement(blockdict[1]['units'][ind1]) not in blockdict[2]['units'][ind2]*2) + #skip if the repeat number thresholds are not met + if blockdict[1]['types'][ind1] == 'mononucleotide': + if (int(blockdict[1]['counts'][ind1]) < mono_threshold): + continue + else: + if (int(blockdict[1]['counts'][ind1]) < non_mono_threshold): + continue + + if blockdict[2]['types'][ind2] == 'mononucleotide': + if (int(blockdict[2]['counts'][ind2]) < mono_threshold): + continue + else: + if (int(blockdict[2]['counts'][ind2]) < non_mono_threshold): + continue + #print "s1,e1=%s,%s; s2,e2=%s,%s" %(coord_s1,coord_e1,coord_s2,coord_e2) + if (coord_s1 in range(coord_s2,coord_e2)) or (coord_e1 in range(coord_s2,coord_e2)): + out.append(str(block_num)) + out.append(namelist[0]) + rel_start = blockdict[1]['whole_seq_start'][ind1] + coord_s1 - blockdict[1]['gaps_before_start'][ind1] + rel_end = rel_start + int(blockdict[1]['lengths'][ind1]) + out.append(str(rel_start)) + out.append(str(rel_end)) + out.append(blockdict[1]['types'][ind1]) + out.append(blockdict[1]['lengths'][ind1]) + out.append(blockdict[1]['counts'][ind1]) + out.append(blockdict[1]['units'][ind1]) + out.append(namelist[1]) + rel_start = blockdict[2]['whole_seq_start'][ind2] + coord_s2 - blockdict[2]['gaps_before_start'][ind2] + rel_end = rel_start + int(blockdict[2]['lengths'][ind2]) + out.append(str(rel_start)) + out.append(str(rel_end)) + out.append(blockdict[2]['types'][ind2]) + out.append(blockdict[2]['lengths'][ind2]) + out.append(blockdict[2]['counts'][ind2]) + out.append(blockdict[2]['units'][ind2]) + print >>fout, '\t'.join(out) + visited_2[ind2] = 1 + out=[] + + if 0 in visited_2: #there are still some elements in 2nd set which haven't found orthologs yet. + for ind2, coord_s2 in enumerate(blockdict[2]['starts']): + if coord_s2 == 'marked': + continue + if visited_2[ind] != 0: + continue + coord_e2 = blockdict[2]['ends'][ind2] + out = [] + for ind1,coord_s1 in enumerate(blockdict[1]['starts']): + if coord_s1 == 'marked': + continue + coord_e1 = blockdict[1]['ends'][ind1] + #skip if the 2 repeats are not of the same type or don't have the same repeating unit. + if allow_different_units == 0: + if (blockdict[1]['types'][ind1] != blockdict[2]['types'][ind2]): + continue + else: + if (blockdict[1]['units'][ind1] not in blockdict[2]['units'][ind2]*2):# and reverse_complement(blockdict[1]['units'][ind1]) not in blockdict[2]['units'][ind2]*2: + continue + #skip if the repeat number thresholds are not met + if blockdict[1]['types'][ind1] == 'mononucleotide': + if (int(blockdict[1]['counts'][ind1]) < mono_threshold): + continue + else: + if (int(blockdict[1]['counts'][ind1]) < non_mono_threshold): + continue + + if blockdict[2]['types'][ind2] == 'mononucleotide': + if (int(blockdict[2]['counts'][ind2]) < mono_threshold): + continue + else: + if (int(blockdict[2]['counts'][ind2]) < non_mono_threshold): + continue + + if (coord_s2 in range(coord_s1,coord_e1)) or (coord_e2 in range(coord_s1,coord_e1)): + out.append(str(block_num)) + out.append(namelist[0]) + rel_start = blockdict[1]['whole_seq_start'][ind1] + coord_s1 - blockdict[1]['gaps_before_start'][ind1] + rel_end = rel_start + int(blockdict[1]['lengths'][ind1]) + out.append(str(rel_start)) + out.append(str(rel_end)) + out.append(blockdict[1]['types'][ind1]) + out.append(blockdict[1]['lengths'][ind1]) + out.append(blockdict[1]['counts'][ind1]) + out.append(blockdict[1]['units'][ind1]) + out.append(namelist[1]) + rel_start = blockdict[2]['whole_seq_start'][ind2] + coord_s2 - blockdict[2]['gaps_before_start'][ind2] + rel_end = rel_start + int(blockdict[2]['lengths'][ind2]) + out.append(str(rel_start)) + out.append(str(rel_end)) + out.append(blockdict[2]['types'][ind2]) + out.append(blockdict[2]['lengths'][ind2]) + out.append(blockdict[2]['counts'][ind2]) + out.append(blockdict[2]['units'][ind2]) + print >>fout, '\t'.join(out) + visited_2[ind2] = 1 + out=[] + + #print >>fout, blockdict + except Exception, exc: + print >>sys.stderr, "type(exc),args,exc: %s, %s, %s" %(type(exc), exc.args, exc) + +if __name__ == "__main__": + main() + diff -r 447c74d98fe5 -r ad3f61801a82 tools/regVariation/microsats_alignment_level.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/regVariation/microsats_alignment_level.xml Wed Sep 24 18:20:39 2008 -0400 @@ -0,0 +1,61 @@ +<tool id="microsats_align1" name="Extract Orthologous Microsatellites"> + <description> from pair-wise alignments</description> + <command interpreter="python"> + microsats_alignment_level.py $input1 $separation $out_file1 "2way" $mono_threshold $non_mono_threshold $allow_different_units + </command> + <inputs> + <page> + <param format="fasta" name="input1" type="data" label="Select data"/> + <param name="separation" size="10" type="integer" value="10" label="Minimum basepair distance between adjacent microsatellites" + help="A value of 10 means: Adjacent microsatellites separated by less than 10 basepairs will be excluded from the output."/> + <param name="mono_threshold" size="10" type="integer" value="9" label="Minimum Threshold for the number of repeats for mononucleotide microsatellites" + help="A value of 9 means: All mononucleotide microsatellites having fewer than 9 repeats will be excluded from the output."/> + <param name="non_mono_threshold" size="10" type="integer" value="4" label="Minimum Threshold for the number of repeats for non-mononucleotide microsatellites" + help="A value of 4 means: All non-mononucleotide microsatellites having fewer than 4 repeats will be excluded from the output."/> + <param name="allow_different_units" size="5" type="select" label="Allow orthologous positions to have different microsatellite repeat units/motifs?"> + <option value="0" selected="true">No</option> + <option value="1">Yes</option> + </param> + </page> + </inputs> + <outputs> + <data format="tabular" name="out_file1" metadata_source="input1"/> + </outputs> + <requirements> + <requirement type="binary">bx-sputnik</requirement> + </requirements> + <tests> + <test> + <param name="input1" value="2way.maf"/> + <param name="separation" value="10"/> + <param name="mono_threshold" value="9"/> + <param name="non_mono_threshold" value="4"/> + <param name="allow_different_units" value="0"/> + <output name="out_file1" file="ortho_ms.tab"/> + </test> + </tests> + + <help> + +.. class:: infomark + +**What it does** + +This tool uses a modified version of SPUTNIK to fetch microsatellite repeats from the input fasta sequences and extracts orthologous repeats from the sputnik output. The modified version allows detection of mononucleotide microsatellites. More information on SPUTNIK can be found on this website_. The modified version is available here_. + +----- + +.. class:: warningmark + +**Note** + +- Any block/s not containing exactly 2 species will be omitted. + +- This tool will filter out microsatellites based on the user input values for minimum distance and repeat number thresholds. Further, this tool will also filter out microsatellites that have no orthologous microsatellites in one of the species. + +.. _website: http://espressosoftware.com/pages/sputnik.jsp +.. _here: http://www.bx.psu.edu/svn/universe/dependencies/sputnik/ +</help> + + +</tool> \ No newline at end of file diff -r 447c74d98fe5 -r ad3f61801a82 tools/regVariation/microsats_mutability.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/regVariation/microsats_mutability.py Wed Sep 24 18:20:39 2008 -0400 @@ -0,0 +1,504 @@ +#!/usr/bin/env python +#Guruprasad Ananda +""" +This tool computes microsatellite mutability for the orthologous microsatellites fetched from 'Extract Orthologous Microsatellites from pair-wise alignments' tool. +""" +from galaxy import eggs +import sys, string, re, commands, tempfile, os, fileinput +from galaxy.tools.util.galaxyops import * +from bx.intervals.io import * +from bx.intervals.operations import quicksect + +fout = open(sys.argv[2],'w') +p_group = int(sys.argv[3]) #primary "group-by" feature +p_bin_size = int(sys.argv[4]) +s_group = int(sys.argv[5]) #sub-group by feature +s_bin_size = int(sys.argv[6]) +mono_threshold = 9 +non_mono_threshold = 4 +p_group_cols = [p_group, p_group+7] +s_group_cols = [s_group, s_group+7] +num_generations = int(sys.argv[7]) +region = sys.argv[8] +int_file = sys.argv[9] +if int_file != "None": #User has specified an interval file + try: + fint = open(int_file, 'r') + dbkey_i = sys.argv[10] + chr_col_i, start_col_i, end_col_i, strand_col_i = parse_cols_arg( sys.argv[11] ) + except: + stop_err("Unable to open input Interval file") + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit() + +def reverse_complement(text): + DNA_COMP = string.maketrans( "ACGTacgt", "TGCAtgca" ) + comp = [ch for ch in text.translate(DNA_COMP)] + comp.reverse() + return "".join(comp) + +def get_unique_elems(elems): + seen=set() + return[x for x in elems if x not in seen and not seen.add(x)] + +def get_binned_lists(uniqlist, binsize): + binnedlist=[] + uniqlist.sort() + start = int(uniqlist[0]) + bin_ind=0 + l_ind=0 + binnedlist.append([]) + while l_ind < len(uniqlist): + elem = int(uniqlist[l_ind]) + if elem in range(start,start+binsize): + binnedlist[bin_ind].append(elem) + else: + start += binsize + bin_ind += 1 + binnedlist.append([]) + binnedlist[bin_ind].append(elem) + l_ind += 1 + return binnedlist + +def fetch_weight(H,C,t): + if (H-(C-H)) < t: + return 2.0 + else: + return 1.0 + +def mutabilityEstimator(repeats1,repeats2,thresholds): + mut_num = 0.0 #Mutability Numerator + mut_den = 0.0 #Mutability denominator + for ind,H in enumerate(repeats1): + C = repeats2[ind] + t = thresholds[ind] + w = fetch_weight(H,C,t) + mut_num += ((H-C)*(H-C)*w) + mut_den += w + return [mut_num, mut_den] + +def output_writer(blk, blk_lines): + global winspecies, speciesind + all_elems_1=[] + all_elems_2=[] + all_s_elems_1=[] + all_s_elems_2=[] + for bline in blk_lines: + if not(bline): + continue + items = bline.split('\t') + seq1 = items[1] + start1 = items[2] + end1 = items[3] + seq2 = items[8] + start2 = items[9] + end2 = items[10] + if p_group_cols[0] == 6: + items[p_group_cols[0]] = int(items[p_group_cols[0]]) + items[p_group_cols[1]] = int(items[p_group_cols[1]]) + if s_group_cols[0] == 6: + items[s_group_cols[0]] = int(items[s_group_cols[0]]) + items[s_group_cols[1]] = int(items[s_group_cols[1]]) + all_elems_1.append(items[p_group_cols[0]]) #primary col elements for species 1 + all_elems_2.append(items[p_group_cols[1]]) #primary col elements for species 2 + if s_group_cols[0] != -1: #sub-group is not None + all_s_elems_1.append(items[s_group_cols[0]]) #secondary col elements for species 1 + all_s_elems_2.append(items[s_group_cols[1]]) #secondary col elements for species 2 + uniq_elems_1 = get_unique_elems(all_elems_1) + uniq_elems_2 = get_unique_elems(all_elems_2) + if s_group_cols[0] != -1: + uniq_s_elems_1 = get_unique_elems(all_s_elems_1) + uniq_s_elems_2 = get_unique_elems(all_s_elems_2) + mut1={} + mut2={} + count1 = {} + count2 = {} + """ + if p_group_cols[0] == 7: #i.e. the option chosen is group-by unit(AG, GTC, etc) + uniq_elems_1 = get_unique_units(j.sort(lambda x, y: len(x)-len(y))) + """ + if p_group_cols[0] == 6: #i.e. the option chosen is group-by repeat number. + uniq_elems_1 = get_binned_lists(uniq_elems_1,p_bin_size) + uniq_elems_2 = get_binned_lists(uniq_elems_2,p_bin_size) + + if s_group_cols[0] == 6: #i.e. the option chosen is subgroup-by repeat number. + uniq_s_elems_1 = get_binned_lists(uniq_s_elems_1,s_bin_size) + uniq_s_elems_2 = get_binned_lists(uniq_s_elems_2,s_bin_size) + + for pitem1 in uniq_elems_1: + repeats1 = [] + repeats2 = [] + thresholds = [] + if s_group_cols[0] != -1: #Sub-group by feature is not None + for sitem1 in uniq_s_elems_1: + if type(sitem1) == type(''): + sitem1 = sitem1.strip() + for bline in blk_lines: + belems = bline.split('\t') + if type(pitem1) == list: + if p_group_cols[0] == 6: + belems[p_group_cols[0]] = int(belems[p_group_cols[0]]) + if belems[p_group_cols[0]] in pitem1: + if belems[s_group_cols[0]]==sitem1: + repeats1.append(int(belems[6])) + repeats2.append(int(belems[13])) + if belems[4] == 'mononucleotide': + thresholds.append(mono_threshold) + else: + thresholds.append(non_mono_threshold) + mut1[str(pitem1)+'\t'+str(sitem1)]=mutabilityEstimator(repeats1,repeats2,thresholds) + if region == 'align': + count1[str(pitem1)+'\t'+str(sitem1)]=min(sum(repeats1),sum(repeats2)) + else: + if winspecies == 1: + count1["%s\t%s" %(pitem1,sitem1)]=sum(repeats1) + elif winspecies == 2: + count1["%s\t%s" %(pitem1,sitem1)]=sum(repeats2) + else: + if type(sitem1) == list: + if s_group_cols[0] == 6: + belems[s_group_cols[0]] = int(belems[s_group_cols[0]]) + if belems[p_group_cols[0]]==pitem1 and belems[s_group_cols[0]] in sitem1: + repeats1.append(int(belems[6])) + repeats2.append(int(belems[13])) + if belems[4] == 'mononucleotide': + thresholds.append(mono_threshold) + else: + thresholds.append(non_mono_threshold) + mut1["%s\t%s" %(pitem1,sitem1)]=mutabilityEstimator(repeats1,repeats2,thresholds) + if region == 'align': + count1[str(pitem1)+'\t'+str(sitem1)]=min(sum(repeats1),sum(repeats2)) + else: + if winspecies == 1: + count1[str(pitem1)+'\t'+str(sitem1)]=sum(repeats1) + elif winspecies == 2: + count1[str(pitem1)+'\t'+str(sitem1)]=sum(repeats2) + else: + if belems[p_group_cols[0]]==pitem1 and belems[s_group_cols[0]]==sitem1: + repeats1.append(int(belems[6])) + repeats2.append(int(belems[13])) + if belems[4] == 'mononucleotide': + thresholds.append(mono_threshold) + else: + thresholds.append(non_mono_threshold) + mut1["%s\t%s" %(pitem1,sitem1)]=mutabilityEstimator(repeats1,repeats2,thresholds) + if region == 'align': + count1[str(pitem1)+'\t'+str(sitem1)]=min(sum(repeats1),sum(repeats2)) + else: + if winspecies == 1: + count1["%s\t%s" %(pitem1,sitem1)]=sum(repeats1) + elif winspecies == 2: + count1["%s\t%s" %(pitem1,sitem1)]=sum(repeats2) + else: #Sub-group by feature is None + for bline in blk_lines: + belems = bline.split('\t') + if type(pitem1) == list: + #print >>sys.stderr, "item: " + str(item1) + if p_group_cols[0] == 6: + belems[p_group_cols[0]] = int(belems[p_group_cols[0]]) + if belems[p_group_cols[0]] in pitem1: + repeats1.append(int(belems[6])) + repeats2.append(int(belems[13])) + if belems[4] == 'mononucleotide': + thresholds.append(mono_threshold) + else: + thresholds.append(non_mono_threshold) + else: + if belems[p_group_cols[0]]==pitem1: + repeats1.append(int(belems[6])) + repeats2.append(int(belems[13])) + if belems[4] == 'mononucleotide': + thresholds.append(mono_threshold) + else: + thresholds.append(non_mono_threshold) + mut1["%s" %(pitem1)]=mutabilityEstimator(repeats1,repeats2,thresholds) + if region == 'align': + count1["%s" %(pitem1)]=min(sum(repeats1),sum(repeats2)) + else: + if winspecies == 1: + count1[str(pitem1)]=sum(repeats1) + elif winspecies == 2: + count1[str(pitem1)]=sum(repeats2) + + for pitem2 in uniq_elems_2: + repeats1 = [] + repeats2 = [] + thresholds = [] + if s_group_cols[0] != -1: #Sub-group by feature is not None + for sitem2 in uniq_s_elems_2: + if type(sitem2)==type(''): + sitem2 = sitem2.strip() + for bline in blk_lines: + belems = bline.split('\t') + if type(pitem2) == list: + if p_group_cols[0] == 6: + belems[p_group_cols[1]] = int(belems[p_group_cols[1]]) + if belems[p_group_cols[1]] in pitem2 and belems[s_group_cols[1]]==sitem2: + repeats2.append(int(belems[13])) + repeats1.append(int(belems[6])) + if belems[4] == 'mononucleotide': + thresholds.append(mono_threshold) + else: + thresholds.append(non_mono_threshold) + mut2["%s\t%s" %(pitem2,sitem2)]=mutabilityEstimator(repeats2,repeats1,thresholds) + #count2[str(pitem2)+'\t'+str(sitem2)]=len(repeats2) + if region == 'align': + count2["%s\t%s" %(pitem2,sitem2)]=min(sum(repeats1),sum(repeats2)) + else: + if winspecies == 1: + count2["%s\t%s" %(pitem2,sitem2)]=len(repeats2) + elif winspecies == 2: + count2["%s\t%s" %(pitem2,sitem2)]=len(repeats1) + else: + if type(sitem2) == list: + if s_group_cols[0] == 6: + belems[s_group_cols[1]] = int(belems[s_group_cols[1]]) + if belems[p_group_cols[1]]==pitem2 and belems[s_group_cols[1]] in sitem2: + repeats2.append(int(belems[13])) + repeats1.append(int(belems[6])) + if belems[4] == 'mononucleotide': + thresholds.append(mono_threshold) + else: + thresholds.append(non_mono_threshold) + mut2["%s\t%s" %(pitem2,sitem2)]=mutabilityEstimator(repeats2,repeats1,thresholds) + if region == 'align': + count2["%s\t%s" %(pitem2,sitem2)]=min(sum(repeats1),sum(repeats2)) + else: + if winspecies == 1: + count2["%s\t%s" %(pitem2,sitem2)]=len(repeats2) + elif winspecies == 2: + count2["%s\t%s" %(pitem2,sitem2)]=len(repeats1) + else: + if belems[p_group_cols[1]]==pitem2 and belems[s_group_cols[1]]==sitem2: + repeats1.append(int(belems[13])) + repeats2.append(int(belems[6])) + if belems[4] == 'mononucleotide': + thresholds.append(mono_threshold) + else: + thresholds.append(non_mono_threshold) + mut2["%s\t%s" %(pitem2,sitem2)]=mutabilityEstimator(repeats2,repeats1,thresholds) + if region == 'align': + count2["%s\t%s" %(pitem2,sitem2)]=min(sum(repeats1),sum(repeats2)) + else: + if winspecies == 1: + count2["%s\t%s" %(pitem2,sitem2)]=len(repeats2) + elif winspecies == 2: + count2["%s\t%s" %(pitem2,sitem2)]=len(repeats1) + else: #Sub-group by feature is None + for bline in blk_lines: + belems = bline.split('\t') + if type(pitem2) == list: + if p_group_cols[0] == 6: + belems[p_group_cols[1]] = int(belems[p_group_cols[1]]) + if belems[p_group_cols[1]] in pitem2: + repeats2.append(int(belems[13])) + repeats1.append(int(belems[6])) + if belems[4] == 'mononucleotide': + thresholds.append(mono_threshold) + else: + thresholds.append(non_mono_threshold) + else: + if belems[p_group_cols[1]]==pitem2: + repeats2.append(int(belems[13])) + repeats1.append(int(belems[6])) + if belems[4] == 'mononucleotide': + thresholds.append(mono_threshold) + else: + thresholds.append(non_mono_threshold) + mut2["%s" %(pitem2)]=mutabilityEstimator(repeats2,repeats1,thresholds) + if region == 'align': + count2["%s" %(pitem2)]=min(sum(repeats1),sum(repeats2)) + else: + if winspecies == 1: + count2["%s" %(pitem2)]=sum(repeats2) + elif winspecies == 2: + count2["%s" %(pitem2)]=sum(repeats1) + for key in mut1.keys(): + if key in mut2.keys(): + mut = (mut1[key][0]+mut2[key][0])/(mut1[key][1]+mut2[key][1]) + count = count1[key] + del mut2[key] + else: + unit_found = False + if p_group_cols[0] == 7 or s_group_cols[0] == 7: #if it is Repeat Unit (AG, GCT etc.) check for reverse-complements too + if p_group_cols[0] == 7: + this,other = 0,1 + else: + this,other = 1,0 + groups1 = key.split('\t') + mutn = mut1[key][0] + mutd = mut1[key][1] + count = 0 + for key2 in mut2.keys(): + groups2 = key2.split('\t') + if groups1[other] == groups2[other]: + if groups1[this] in groups2[this]*2 or reverse_complement(groups1[this]) in groups2[this]*2: + #mut = (mut1[key][0]+mut2[key2][0])/(mut1[key][1]+mut2[key2][1]) + mutn += mut2[key2][0] + mutd += mut2[key2][1] + count += int(count2[key2]) + unit_found = True + del mut2[key2] + #break + if unit_found: + mut = mutn/mutd + else: + mut = mut1[key][0]/mut1[key][1] + count = count1[key] + mut = "%.2e" %(mut/num_generations) + if region == 'align': + print >>fout, str(blk) + '\t'+seq1 + '\t' + start1+ '\t'+end1+ '\t'+seq2 + '\t'+start2+ '\t'+end2+ '\t'+key.strip()+ '\t'+str(mut) + '\t'+ str(count) + elif region == 'win': + fout.write("%s\t%s\t%s\t%s\n" %(blk,key.strip(),mut,count)) + fout.flush() + #print >>fout, blk + '\t'+key.strip()+ '\t'+str(mut)+ '\t'+ str(count) + + #catch any remaining repeats, for instance if the orthologous position contained different repeat units + for remaining_key in mut2.keys(): + mut = mut2[remaining_key][0]/mut2[remaining_key][1] + mut = "%.2e" %(mut/num_generations) + count = count2[remaining_key] + if region == 'align': + print >>fout, str(blk) + '\t'+seq1 + '\t' + start1+ '\t'+end1+ '\t'+seq2 + '\t'+start2+ '\t'+end2+ '\t'+remaining_key.strip()+ '\t'+str(mut)+ '\t'+ str(count) + elif region == 'win': + fout.write("%s\t%s\t%s\t%s\n" %(blk,remaining_key.strip(),mut,count)) + fout.flush() + #print >>fout, blk + '\t'+remaining_key.strip()+ '\t'+str(mut)+ '\t'+ str(count) + +def counter(node, start, end, report_func): + if start <= node.start < end and start < node.end <= end: + report_func(node) + if node.right: + counter(node.right, start, end, report_func) + if node.left: + counter(node.left, start, end, report_func) + elif node.start < start and node.right: + counter(node.right, start, end, report_func) + elif node.start >= end and node.left and node.left.maxend > start: + counter(node.left, start, end, report_func) + + +def main(): + infile = sys.argv[1] + + for i, line in enumerate( file ( infile )): + line = line.rstrip('\r\n') + if len( line )>0 and not line.startswith( '#' ): + elems = line.split( '\t' ) + break + if i == 30: + break # Hopefully we'll never get here... + + if len( elems ) != 15: + stop_err( "This tool only works on tabular data output by 'Extract Orthologous Microsatellites from pair-wise alignments' tool. The data in your input dataset is either missing or not formatted properly." ) + global winspecies, speciesind + if region == 'win': + if dbkey_i in elems[1]: + winspecies = 1 + speciesind = 1 + elif dbkey_i in elems[8]: + winspecies = 2 + speciesind = 8 + else: + stop_err("The species build corresponding to your interval file is not present in the Microsatellite file.") + + fin = open(infile, 'r') + skipped = 0 + blk=0 + win=0 + linestr="" + ff=open("junkmabc","w") + + if region == 'win': + + """ + sorted_infile = tempfile.NamedTemporaryFile() + if winspecies == 1: + cmdline = "sort -n -k 3"+" -o "+sorted_infile.name+" "+infile + elif winspecies == 2: + cmdline = "sort -n -k 10"+" -o "+sorted_infile.name+" "+infile + os.system(cmdline) + print >>ff, "Finished sorting" + """ + msats = NiceReaderWrapper( fileinput.FileInput( infile ), + chrom_col = speciesind, + start_col = speciesind+1, + end_col = speciesind+2, + strand_col = -1, + fix_strand = True) + msatTree = quicksect.IntervalTree() + for item in msats: + #print >>sys.stderr, item + if type( item ) is GenomicInterval: + msatTree.insert( item, msats.linenum, item.fields ) + """ + result = [] + msatTree.traverse(lambda node: result.append( node )) + for n in result: + print >>sys.stderr,n.other + print >>sys.stderr,msatTree.chroms + #sys.exit() + """ + for iline in fint: + try: + iline = iline.rstrip('\r\n') + if not(iline) or iline == "": + continue + ielems = iline.strip("\r\n").split('\t') + ichr = ielems[chr_col_i] + istart = int(ielems[start_col_i]) + iend = int(ielems[end_col_i]) + isrc = "%s.%s" %(dbkey_i,ichr) + if isrc not in msatTree.chroms: + continue + result = [] + root = msatTree.chroms[isrc] #root node for the chrom + counter(root, istart, iend, lambda node: result.append( node )) + if not(result): + continue + tmpfile1 = tempfile.NamedTemporaryFile('wb+') + for node in result: + tmpfile1.write("%s\n" % "\t".join( node.other )) + + tmpfile1.seek(0) + output_writer(iline, tmpfile1.readlines()) + except: + skipped+=1 + if skipped: + print "Skipped %d intervals as invalid." %(skipped) + elif region == 'align': + if s_group_cols[0] != -1: + print >>fout, "#Window\tSpecies_1\tWindow_Start\tWindow_End\tSpecies_2\tGroupby_Feature\tSubGroupby_Feature\tMutability\tCount" + else: + print >>fout, "#Window\tSpecies_1\tWindow_Start\tWindow_End\tSpecies_2\tGroupby_Feature\tMutability\tCount" + prev_bnum = -1 + try: + for line in fin: + line = line.strip("\r\n") + if not(line) or line == "": + continue + elems = line.split('\t') + try: + assert int(elems[0]) + assert len(elems) == 15 + except: + continue + new_bnum = int(elems[0]) + if new_bnum != prev_bnum: + if prev_bnum != -1: + output_writer(prev_bnum, linestr.strip().replace('\r','\n').split('\n')) + linestr = line + "\n" + else: + linestr += line + linestr += "\n" + prev_bnum = new_bnum + output_writer(prev_bnum, linestr.strip().replace('\r','\n').split('\n')) + except Exception, ea: + print >>sys.stderr, ea + skipped += 1 + if skipped: + print "Skipped %d lines as invalid." %(skipped) +if __name__ == "__main__": + main() \ No newline at end of file diff -r 447c74d98fe5 -r ad3f61801a82 tools/regVariation/microsats_mutability.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/regVariation/microsats_mutability.xml Wed Sep 24 18:20:39 2008 -0400 @@ -0,0 +1,117 @@ +<tool id="microsats_mutability1" name="Estimate microsatellite mutability" version="1.0.0"> + <description>by specified attributes</description> + <command interpreter="python"> + microsats_mutability.py + $input1 + $out_file1 + ${pri_condition.primary_group} + #if $pri_condition.primary_group == "6": + ${pri_condition.binsize} ${pri_condition.subgroup} -1 + #else: + 0 ${pri_condition.sub_condition.subgroup} + #if $pri_condition.sub_condition.subgroup == "6": + ${pri_condition.sub_condition.s_binsize} + #else: + -1 + #end if + #end if + $gens + ${region.type} + #if $region.type == "win": + ${region.input2} $input2.dbkey $input2.metadata.chromCol,$input2.metadata.startCol,$input2.metadata.endCol,$input2.metadata.strandCol + #else: + "None" + #end if + </command> + <inputs> + <page> + <param name="input1" type="data" format="tabular" label="Select dataset containing Orthologous microsatellites"/> + <conditional name="region"> + <param name="type" type="select" label="Estimate rates corresponding to" multiple="false"> + <option value="align">Alignment block</option> + <option value="win">Intervals in your history</option> + </param> + <when value="win"> + <param format="interval" name="input2" type="data" label="Choose intervals"> + <validator type="unspecified_build" /> + </param> + </when> + <when value="align" /> + </conditional> + <param name="gens" size="10" type="integer" value="1" label="Number of generations between the two species in input file"/> + <conditional name="pri_condition"> + <param name="primary_group" type="select" label="Group by" multiple="false"> + <option value="4">Motif type (mono/di/tri etc.)</option> + <option value="7">Repeat Unit (AG, GCT etc.)</option> + <option value="6">Repeat Number </option> + </param> + <when value="6"> + <param name="binsize" size="10" type="integer" value="1" label="Bin-size" help="Bin-size denotes the number of repeat numbers to be considered as a group. Bin-size of 5 will group every 5 consecutive repeat numbers into a group."/> + <param name="subgroup" type="select" label="Sub-group by" multiple="false"> + <option value="-1">None</option> + <option value="4">Motif type (mono/di/tri etc.)</option> + <option value="7">Repeat Unit (AG, GCT etc.)</option> + </param> + </when> + <when value="7"> + <conditional name="sub_condition"> + <param name="subgroup" type="select" label="Sub-group by" multiple="false"> + <option value="-1">None</option> + <option value="4">Motif type (mono/di/tri etc.)</option> + <option value="6">Repeat Number </option> + </param> + <when value="-1"></when> + <when value="4"></when> + <when value="6"> + <param name="s_binsize" size="10" type="integer" value="1" label="Bin size" help="Bin-size denotes the number of repeat numbers to be considered as a group. Bin-size of 5 will group every 5 consecutive repeat numbers into a group."/> + </when> + </conditional> + </when> + <when value="4"> + <conditional name="sub_condition"> + <param name="subgroup" type="select" label="Sub-group by" multiple="false"> + <option value="-1">None</option> + <option value="7">Repeat Unit (AG, GCT etc.)</option> + <option value="6">Repeat Number </option> + </param> + <when value="-1"></when> + <when value="7"></when> + <when value="6"> + <param name="s_binsize" size="10" type="integer" value="1" label="Bin size" help="Bin-size denotes the number of repeat numbers to be considered as a group. Bin-size of 5 will group every 5 consecutive repeat numbers into a group."/> + </when> + </conditional> + </when> + </conditional> + </page> + </inputs> + <outputs> + <data format="tabular" name="out_file1" /> + </outputs> +  +<help> +.. class:: infomark + +**What it does** + +This tool computes microsatellite mutability for the orthologous microsatellites fetched from 'Extract Orthologous Microsatellites from pair-wise alignments' tool. + +----- + +.. class:: warningmark + +**Note** + +The user selected group and subgroup by features, the computed mutability and the count of the number of repeats used to compute that mutability are added as columns to the output. +</help> +</tool>

1 0

[hg] galaxy 1528: Eliminate enable_beta_features ( and the conce...
by greg＠scofield.bx.psu.edu 24 Sep '08

24 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/447c74d98fe5 changeset: 1528:447c74d98fe5 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Sep 24 15:05:38 2008 -0400 description: Eliminate enable_beta_features ( and the concept of 'beta' from the controllers ). 8 file(s) affected in this change: lib/galaxy/config.py lib/galaxy/web/base/controller.py lib/galaxy/web/buildapp.py lib/galaxy/web/controllers/workflow.py lib/galaxy/webapps/reports/base/controller.py lib/galaxy/webapps/reports/buildapp.py templates/history/options.mako templates/root/tool_menu.mako diffs (133 lines): diff -r b6420d2f247c -r 447c74d98fe5 lib/galaxy/config.py --- a/lib/galaxy/config.py Wed Sep 24 13:52:01 2008 -0400 +++ b/lib/galaxy/config.py Wed Sep 24 15:05:38 2008 -0400 @@ -23,7 +23,6 @@ def __init__( self, **kwargs ): self.config_dict = kwargs self.root = kwargs.get( 'root_dir', '.' ) - self.enable_beta_features = kwargs.get( "enable_beta_features", False ) # Database related configuration self.database = resolve_path( kwargs.get( "database_file", "database/universe.d" ), self.root ) self.database_connection = kwargs.get( "database_connection", False ) diff -r b6420d2f247c -r 447c74d98fe5 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py Wed Sep 24 13:52:01 2008 -0400 +++ b/lib/galaxy/web/base/controller.py Wed Sep 24 15:05:38 2008 -0400 @@ -16,8 +16,6 @@ """ Base class for Galaxy web application controllers. """ - - beta = False def __init__( self, app ): """Initialize an interface for application 'app'""" diff -r b6420d2f247c -r 447c74d98fe5 lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py Wed Sep 24 13:52:01 2008 -0400 +++ b/lib/galaxy/web/buildapp.py Wed Sep 24 15:05:38 2008 -0400 @@ -41,8 +41,7 @@ for key in dir( module ): T = getattr( module, key ) if isclass( T ) and T is not BaseController and issubclass( T, BaseController ): - if app.config.enable_beta_features or not ( T.beta ): - webapp.add_controller( name, T( app ) ) + webapp.add_controller( name, T( app ) ) def app_factory( global_conf, **kwargs ): """ diff -r b6420d2f247c -r 447c74d98fe5 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Wed Sep 24 13:52:01 2008 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Wed Sep 24 15:05:38 2008 -0400 @@ -13,7 +13,6 @@ from galaxy.model.mapping import desc class WorkflowController( BaseController ): - beta = True @web.expose @web.require_login( "use Galaxy workflows" ) diff -r b6420d2f247c -r 447c74d98fe5 lib/galaxy/webapps/reports/base/controller.py --- a/lib/galaxy/webapps/reports/base/controller.py Wed Sep 24 13:52:01 2008 -0400 +++ b/lib/galaxy/webapps/reports/base/controller.py Wed Sep 24 15:05:38 2008 -0400 @@ -8,7 +8,6 @@ class BaseController( object ): """Base class for Galaxy webapp application controllers.""" - beta = False def __init__( self, app ): """Initialize an interface for application 'app'""" self.app = app \ No newline at end of file diff -r b6420d2f247c -r 447c74d98fe5 lib/galaxy/webapps/reports/buildapp.py --- a/lib/galaxy/webapps/reports/buildapp.py Wed Sep 24 13:52:01 2008 -0400 +++ b/lib/galaxy/webapps/reports/buildapp.py Wed Sep 24 15:05:38 2008 -0400 @@ -40,7 +40,6 @@ for key in dir( module ): T = getattr( module, key ) if isclass( T ) and T is not BaseController and issubclass( T, BaseController ): - #if app.config.enable_beta_features or not ( T.beta ): webapp.add_controller( name, T( app ) ) def app_factory( global_conf, **kwargs ): diff -r b6420d2f247c -r 447c74d98fe5 templates/history/options.mako --- a/templates/history/options.mako Wed Sep 24 13:52:01 2008 -0400 +++ b/templates/history/options.mako Wed Sep 24 15:05:38 2008 -0400 @@ -16,9 +16,7 @@ %if len( history.active_datasets ) > 0: <li><a href="${h.url_for('/history_new')}">Create</a> a new empty history</li> %endif - %if app.config.enable_beta_features: <li><a href="${h.url_for( controller='workflow', action='build_from_current_history' )}">Construct workflow</a> from the current history</li> - %endif <li><a href="${h.url_for( action='history_share' )}" target="galaxy_main">Share</a> current history</div> %endif <li><a href="${h.url_for( action='history_delete', id=history.id )}" confirm="Are you sure you want to delete the current history?">Delete</a> current history</div> diff -r b6420d2f247c -r 447c74d98fe5 templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako Wed Sep 24 13:52:01 2008 -0400 +++ b/templates/root/tool_menu.mako Wed Sep 24 15:05:38 2008 -0400 @@ -82,27 +82,25 @@ ## at least some workflows will appear here (the user should be able to ## configure which of their stored workflows appear in the tools menu). -%if app.config.enable_beta_features: - <div class="toolSectionPad"></div> - <div class="toolSectionPad"></div> - <div class="toolSectionTitle" id="title_XXinternalXXworkflow"> - <span>Workflow <i>(beta)</i></span> - </div> - <div id="XXinternalXXworkflow" class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"> - <a href="${h.url_for( controller='workflow', action='index' )}" target="galaxy_main">Manage</a> workflows - </div> - %if t.user: - %for m in t.user.stored_workflow_menu_entries: - <div class="toolTitle"> - <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(m.stored_workflow_id) )}" target="galaxy_main">${m.stored_workflow.name}</a> - </div> - %endfor - %endif - </div> - </div> -%endif +<div class="toolSectionPad"></div> +<div class="toolSectionPad"></div> +<div class="toolSectionTitle" id="title_XXinternalXXworkflow"> + <span>Workflow <i>(beta)</i></span> +</div> +<div id="XXinternalXXworkflow" class="toolSectionBody"> + <div class="toolSectionBg"> + <div class="toolTitle"> + <a href="${h.url_for( controller='workflow', action='index' )}" target="galaxy_main">Manage</a> workflows + </div> + %if t.user: + %for m in t.user.stored_workflow_menu_entries: + <div class="toolTitle"> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(m.stored_workflow_id) )}" target="galaxy_main">${m.stored_workflow.name}</a> + </div> + %endfor + %endif + </div> +</div> </div>

1 0

[hg] galaxy 1524: Integrate with intermine ( data source ) and e...
by greg＠scofield.bx.psu.edu 24 Sep '08

24 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/aae4754d6828 changeset: 1524:aae4754d6828 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Sep 22 10:36:34 2008 -0400 description: Integrate with intermine ( data source ) and epigraph ( data destination ). Receiving data from epigraph coming soon. Data is sent to epigraph using a combination of DATA_URL and REDIRECT_URL tool params. This tool creates jobs, but does not queue them for execution. 12 file(s) affected in this change: lib/galaxy/tools/__init__.py lib/galaxy/tools/actions/__init__.py lib/galaxy/tools/parameters/basic.py lib/galaxy/web/controllers/async.py lib/galaxy/web/controllers/tool_runner.py templates/root/redirect.mako templates/tool_form.tmpl tool_conf.xml.sample tools/data_destination/epigraph.xml tools/data_source/flymine.xml tools/data_source/flymine_filter_code.py tools/data_source/intermine.py diffs (429 lines): diff -r dabed25dfbaf -r aae4754d6828 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Sun Sep 21 17:36:28 2008 -0400 +++ b/lib/galaxy/tools/__init__.py Mon Sep 22 10:36:34 2008 -0400 @@ -239,6 +239,16 @@ self.command = interpreter + " " + self.command else: self.command = '' + # Parameters used to build URL for redirection to external app + redirect_url_params = root.find( "redirect_url_params" ) + if redirect_url_params is not None and redirect_url_params.text is not None: + # get rid of leading / trailing white space + redirect_url_params = redirect_url_params.text.strip() + # Replace remaining white space with something we can safely split on later + # when we are building the params + self.redirect_url_params = redirect_url_params.replace( ' ', '**^**' ) + else: + self.redirect_url_params = '' # Short description of the tool self.description = util.xml_text(root, "description") # Job runner @@ -677,7 +687,7 @@ return "tool_form.tmpl", dict( errors=errors, tool_state=state, incoming=incoming, error_message=error_message ) # If we've completed the last page we can execute the tool elif state.page == self.last_page: - out_data = self.execute( trans, params ) + out_data = self.execute( trans, incoming=params ) return 'tool_executed.tmpl', dict( out_data=out_data ) # Otherwise move on to the next page else: @@ -689,8 +699,8 @@ # Just a refresh, render the form with updated state and errors. return 'tool_form.tmpl', dict( errors=errors, tool_state=state ) - def update_state( self, trans, inputs, state, incoming, - prefix="", context=None, update_only=False, old_errors={}, changed_dependencies={} ): + def update_state( self, trans, inputs, state, incoming, prefix="", context=None, + update_only=False, old_errors={}, changed_dependencies={} ): """ Update the tool state in `state` using the user input in `incoming`. This is designed to be called recursively: `inputs` contains the @@ -877,14 +887,14 @@ raise Exception( "Unexpected parameter type" ) return args - def execute( self, trans, incoming={}, set_output_hid = True ): + def execute( self, trans, incoming={}, set_output_hid=True ): """ Execute the tool using parameter values in `incoming`. This just dispatches to the `ToolAction` instance specified by `self.tool_action`. In general this will create a `Job` that when run will build the tool's outputs, e.g. `DefaultToolAction`. """ - return self.tool_action.execute( self, trans, incoming, set_output_hid = set_output_hid ) + return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid ) def params_to_strings( self, params, app ): return params_to_strings( self.inputs, params, app ) @@ -1045,7 +1055,54 @@ #e.args = ( 'Error substituting into command line. Params: %r, Command: %s' % ( param_dict, self.command ) ) raise return command_line - + + def build_redirect_url_params( self, param_dict ): + """Substitute parameter values into self.redirect_url_params""" + if not self.redirect_url_params: + return + redirect_url_params = None + # Substituting parameter values into the url params + redirect_url_params = fill_template( self.redirect_url_params, context=param_dict ) + # Remove newlines + redirect_url_params = redirect_url_params.replace( "\n", " " ).replace( "\r", " " ) + return redirect_url_params + + def parse_redirect_url( self, inp_data, param_dict ): + """Parse the REDIRECT_URL tool param""" + # Tools that send data to an external application via a redirect must include the following 3 + # tool params: + # REDIRECT_URL - the url to which the data is being sent + # DATA_URL - the url to which the receiving application will send an http post to retrieve the Galaxy data + # GALAXY_URL - the to which the external application may post data as a response + redirect_url = param_dict.get( 'REDIRECT_URL' ) + redirect_url_params = self.build_redirect_url_params( param_dict ) + # Add the parameters to the redirect url. We're splitting the param string on '**^**' + # because the self.parse() method replaced white space with that separator. + params = redirect_url_params.split( '**^**' ) + rup_dict = {} + for param in params: + p_list = param.split( '=' ) + p_name = p_list[0] + p_val = p_list[1] + rup_dict[ p_name ] = p_val + DATA_URL = param_dict.get( 'DATA_URL', None ) + assert DATA_URL is not None, "DATA_URL parameter missing in tool config." + # Get the dataset - there should only be 1 + for name in inp_data.keys(): + data = inp_data[ name ] + DATA_URL += "/%s/display" % str( data.id ) + redirect_url += "?DATA_URL=%s" % DATA_URL + # Add the redirect_url_params to redirect_url + for p_name in rup_dict: + redirect_url += "&%s=%s" % ( p_name, rup_dict[ p_name ] ) + # Add the current user email to redirect_url + if data.history.user: + USERNAME = str( data.history.user.email ) + else: + USERNAME = 'Anonymous' + redirect_url += "&USERNAME=%s" % USERNAME + return redirect_url + def call_hook( self, hook_name, *args, **kwargs ): """ Call the custom code hook function identified by 'hook_name' if any, diff -r dabed25dfbaf -r aae4754d6828 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Sun Sep 21 17:36:28 2008 -0400 +++ b/lib/galaxy/tools/actions/__init__.py Mon Sep 22 10:36:34 2008 -0400 @@ -2,6 +2,8 @@ from galaxy.tools.parameters import * from galaxy.util.template import fill_template from galaxy.util.none_like import NoneDataset +from galaxy.web import url_for +from galaxy.jobs import JOB_OK import logging log = logging.getLogger( __name__ ) @@ -63,7 +65,7 @@ tool.visit_inputs( param_values, visitor ) return input_datasets - def execute(self, tool, trans, incoming={}, set_output_hid = True ): + def execute(self, tool, trans, incoming={}, set_output_hid=True ): out_data = {} # Collect any input datasets from the incoming parameters inp_data = self.collect_input_datasets( tool, incoming, trans ) @@ -90,15 +92,12 @@ on_text = '%s, %s, and others' % tuple(input_names[0:2]) else: on_text = "" - # Add the dbkey to the incoming parameters incoming[ "dbkey" ] = input_dbkey - # Keep track of parent / child relationships, we'll create all the # datasets first, then create the associations parent_to_child_pairs = [] child_dataset_names = set() - for name, output in tool.outputs.items(): if output.parent: parent_to_child_pairs.append( ( output.parent, name ) ) @@ -149,23 +148,19 @@ out_data[ name ] = data # Store all changes to database trans.app.model.flush() - # Add all the top-level (non-child) datasets to the history for name in out_data.keys(): if name not in child_dataset_names and name not in incoming: #don't add children; or already existing datasets, i.e. async created data = out_data[ name ] trans.history.add_dataset( data, set_hid = set_output_hid ) data.flush() - # Add all the children to their parents for parent_name, child_name in parent_to_child_pairs: parent_dataset = out_data[ parent_name ] child_dataset = out_data[ child_name ] parent_dataset.children.append( child_dataset ) - # Store data after custom code runs trans.app.model.flush() - # Create the job object job = trans.app.model.Job() job.session_id = trans.get_galaxy_session( create=True ).id @@ -189,8 +184,19 @@ for name, dataset in out_data.iteritems(): job.add_output_dataset( name, dataset ) trans.app.model.flush() - - # Queue the job for execution - trans.app.job_queue.put( job.id, tool ) - trans.log_event( "Added job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) - return out_data + # Some tools are not really executable, but jobs are still created for them ( for record keeping ). + # Examples include tools that redirect to other applications ( epigraph ). These special tools must + # include something that can be retrieved from the params ( e.g., REDIRECT_URL ) to keep the job + # from being queued. + if 'REDIRECT_URL' in incoming: + redirect_url = tool.parse_redirect_url( inp_data, incoming ) + # Job should not be queued, so set state to ok + job.state = JOB_OK + job.info = "Redirected to: %s" % redirect_url + job.flush() + trans.response.send_redirect( url_for( controller='tool_runner', action='redirect', redirect_url=redirect_url ) ) + else: + # Queue the job for execution + trans.app.job_queue.put( job.id, tool ) + trans.log_event( "Added job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) + return out_data diff -r dabed25dfbaf -r aae4754d6828 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Sun Sep 21 17:36:28 2008 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Mon Sep 22 10:36:34 2008 -0400 @@ -332,6 +332,8 @@ return form_builder.HiddenField( self.name, self.value ) def get_initial_value( self, trans, context ): return self.value + def get_label( self ): + return None ## This is clearly a HACK, parameters should only be used for things the user ## can change, there needs to be a different way to specify this. I'm leaving @@ -354,6 +356,9 @@ return form_builder.HiddenField( self.name, self.get_value( trans ) ) def get_initial_value( self, trans, context ): return self.value + def get_label( self ): + # BaseURLToolParameters are ultimately "hidden" parameters + return None class SelectToolParameter( ToolParameter ): """ diff -r dabed25dfbaf -r aae4754d6828 lib/galaxy/web/controllers/async.py --- a/lib/galaxy/web/controllers/async.py Sun Sep 21 17:36:28 2008 -0400 +++ b/lib/galaxy/web/controllers/async.py Mon Sep 22 10:36:34 2008 -0400 @@ -68,8 +68,8 @@ galaxy_url = trans.request.base + '/async/%s/%s/%s' % ( tool_id, data.id, key ) galaxy_url = params.get("GALAXY_URL",galaxy_url) params = dict( url=URL, GALAXY_URL=galaxy_url ) - params[tool.outputs.keys()[0]] = data.id #assume there is exactly one output file possible - #tool.execute( app=self.app, history=history, incoming=params ) + # Assume there is exactly one output file possible + params[tool.outputs.keys()[0]] = data.id tool.execute( trans, incoming=params ) else: log.debug('async error -> %s' % STATUS) diff -r dabed25dfbaf -r aae4754d6828 lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py Sun Sep 21 17:36:28 2008 -0400 +++ b/lib/galaxy/web/controllers/tool_runner.py Mon Sep 22 10:36:34 2008 -0400 @@ -51,3 +51,10 @@ add_frame.wiki_url = trans.app.config.wiki_url add_frame.from_noframe = True return trans.fill_template( template, history=history, toolbox=toolbox, tool=tool, util=util, add_frame=add_frame, **vars ) + + @web.expose + def redirect( self, trans, redirect_url=None, **kwd ): + if not redirect_url: + return trans.show_error_message( "Required URL for redirection missing" ) + trans.log_event( "Redirecting to: %s" % redirect_url ) + return trans.fill_template( 'root/redirect.mako', redirect_url=redirect_url ) diff -r dabed25dfbaf -r aae4754d6828 templates/root/redirect.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/root/redirect.mako Mon Sep 22 10:36:34 2008 -0400 @@ -0,0 +1,5 @@ +<%inherit file="/base.mako"/> + +<script type="text/javascript"> + top.location.href = '${redirect_url}'; +</script> \ No newline at end of file diff -r dabed25dfbaf -r aae4754d6828 templates/tool_form.tmpl --- a/templates/tool_form.tmpl Sun Sep 21 17:36:28 2008 -0400 +++ b/templates/tool_form.tmpl Mon Sep 22 10:36:34 2008 -0400 @@ -73,10 +73,12 @@ #set cls = "form-row" #end if <div class="$cls"> - <label> - ${param.get_label()}: - </label> - + #set label = $param.get_label() + #if $label: + <label> + $label: + </label> + #end if #set field = $param.get_html_field( $caller, $parent_state[ $param.name ], $context ) #set $field.refresh_on_change = $param.refresh_on_change <div style="float: left; width: 250px; margin-right: 10px;">$field.get_html( $prefix )</div> diff -r dabed25dfbaf -r aae4754d6828 tool_conf.xml.sample --- a/tool_conf.xml.sample Sun Sep 21 17:36:28 2008 -0400 +++ b/tool_conf.xml.sample Mon Sep 22 10:36:34 2008 -0400 @@ -9,6 +9,7 @@ <tool file="data_source/biomart.xml" /> <tool file="data_source/biomart_test.xml" /> <tool file="data_source/gbrowse_elegans.xml" /> + <tool file="data_source/flymine.xml" /> <tool file="data_source/encode_db.xml" /> <tool file="data_source/hbvar.xml" /> <tool file="validation/fix_errors.xml" /> @@ -20,6 +21,9 @@ <tool file="data_source/encode_import_transcription_regulation.xml"/> <tool file="data_source/encode_import_all_latest_datasets.xml" /> <tool file="data_source/encode_import_gencode.xml" /> + </section> + <section name="Send Data" id="send"> + <tool file="data_destination/epigraph.xml" /> </section> <section name="ENCODE Tools" id="EncodeTools"> <tool file="encode/gencode_partition.xml" /> diff -r dabed25dfbaf -r aae4754d6828 tools/data_destination/epigraph.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_destination/epigraph.xml Mon Sep 22 10:36:34 2008 -0400 @@ -0,0 +1,21 @@ +<?xml version="1.0"?> +<tool name="Perform EpiGRAPH" id="epigraph"> + <description> Genome analysis and prediction</description> + <redirect_url_params>GENOME=${input1.dbkey} NAME=${input1.name} INFO=${input1.info}</redirect_url_params> + <inputs> + <param format="bed" name="input1" type="data" label="Send this dataset to EpiGRAPH"> + <validator type="unspecified_build" /> + </param> + <param name="REDIRECT_URL" type="hidden" value="http://epigraph.mpi-inf.mpg.de/WebGRAPH_Public_Test/faces/DataImport.jsp" /> + <param name="DATA_URL" type="baseurl" value="/datasets" /> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=epigraph_import" /> + </inputs> + <outputs/> + <help> +**What it does** + +This tool sends the selected dataset to EpiGRAPH for in-depth analysis and prediction. + + </help> +</tool> + diff -r dabed25dfbaf -r aae4754d6828 tools/data_source/flymine.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/flymine.xml Mon Sep 22 10:36:34 2008 -0400 @@ -0,0 +1,16 @@ +<?xml version="1.0"?> +<tool name="Flymine" id="flymine"> + <description>server</description> + <command interpreter="python">intermine.py $output</command> + <inputs action="http://preview.flymine.org/preview/begin.do" check_values="false" method="get" target="_top"> + <display>go to Flymine server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" /> + </inputs> + <uihints minwidth="800"/> + <code file="flymine_filter_code.py"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> + diff -r dabed25dfbaf -r aae4754d6828 tools/data_source/flymine_filter_code.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/flymine_filter_code.py Mon Sep 22 10:36:34 2008 -0400 @@ -0,0 +1,31 @@ +# Code for direct connection to flymine +from galaxy.datatypes import sniff +import urllib + +import logging +log = logging.getLogger( __name__ ) + +def exec_before_job( app, inp_data, out_data, param_dict, tool=None ): + """Sets the attributes of the data""" + items = out_data.items() + for name, data in items: + data.dbkey = param_dict.get( 'dbkey', '?' ) + # Store flymine parameters temporarily in output file + out = open( data.file_name, 'w' ) + for key, value in param_dict.items(): + out.write( "%s\t%s\n" % ( key, value ) ) + out.close() + out_data[ name ] = data + +def exec_after_process( app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None ): + """Verifies the data after the run""" + name, data = out_data.items()[0] + if data.state == data.states.OK: + data.info = data.name + if data.extension == 'txt': + data_type = sniff.guess_ext( data.file_name, sniff_order=app.datatypes_registry.sniff_order ) + data = app.datatypes_registry.change_datatype( data, data_type ) + data.set_peek() + data.set_size() + data.flush() + diff -r dabed25dfbaf -r aae4754d6828 tools/data_source/intermine.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/intermine.py Mon Sep 22 10:36:34 2008 -0400 @@ -0,0 +1,45 @@ +#!/usr/bin/env python +#Retreives data from intermine and stores in a file. Intermine parameters are provided in the input/output file. +import urllib, sys, os, gzip, tempfile, shutil +from galaxy import eggs +from galaxy.datatypes import data + +assert sys.version_info[:2] >= ( 2, 4 ) + +def stop_err( msg ): + sys.stderr.write( msg ) + sys.exit() + +def __main__(): + filename = sys.argv[1] + params = {} + + for line in open( filename, 'r' ): + try: + line = line.strip() + fields = line.split( '\t' ) + params[ fields[0] ] = fields[1] + except: + continue + + URL = params.get( 'URL', None ) + if not URL: + open( filename, 'w' ).write( "" ) + stop_err( 'Datasource has not sent back a URL parameter.' ) + + CHUNK_SIZE = 2**20 # 1Mb + try: + page = urllib.urlopen( URL ) + except Exception, exc: + raise Exception( 'Problems connecting to %s (%s)' % ( URL, exc ) ) + sys.exit( 1 ) + + fp = open( filename, 'wb' ) + while 1: + chunk = page.read( CHUNK_SIZE ) + if not chunk: + break + fp.write( chunk ) + fp.close() + +if __name__ == "__main__": __main__()

1 0

[hg] galaxy 1525: Modified INDEL tools under Regional variation ...
by greg＠scofield.bx.psu.edu 24 Sep '08

24 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/675ad84ae008 changeset: 1525:675ad84ae008 user: guru date: Mon Sep 22 12:02:35 2008 -0400 description: Modified INDEL tools under Regional variation section. 6 file(s) affected in this change: test-data/indelrates_3way.tabular test-data/indels_3way.tabular tools/regVariation/getIndelRates_3way.py tools/regVariation/getIndelRates_3way.xml tools/regVariation/getIndels_3way.xml tools/regVariation/parseMAF_smallIndels.pl diffs (908 lines): diff -r aae4754d6828 -r 675ad84ae008 test-data/indelrates_3way.tabular --- a/test-data/indelrates_3way.tabular Mon Sep 22 10:36:34 2008 -0400 +++ b/test-data/indelrates_3way.tabular Mon Sep 22 12:02:35 2008 -0400 @@ -1,13 +1,15 @@ -#Window Species Window_Start Window_End Insertion_Rate Deletion_Rate -1 canFam2 3356001 3357001 3.80e-03 2.17e-03 -2 canFam2 3357001 3358001 2.46e-03 1.85e-03 -3 canFam2 3358001 3359001 1.23e-03 3.08e-03 -4 canFam2 3359001 3360001 6.76e-03 8.39e-03 -5 canFam2 3360001 3361001 8.41e-03 1.12e-02 -6 canFam2 3361001 3362001 9.27e-03 1.85e-02 -7 canFam2 3362001 3363001 1.17e-02 6.67e-03 -8 canFam2 3363001 3364001 1.97e-02 5.62e-03 -9 canFam2 3364001 3365001 5.92e-03 9.65e-03 -10 canFam2 3366001 3367001 3.69e-03 2.63e-03 -11 canFam2 3367001 3368001 9.89e-03 4.95e-03 -12 canFam2 3368001 3369001 6.90e-03 1.38e-02 +#Block hg18_InsRate panTro2_InsRate canFam2_InsRate hg18_DelRate panTro2_DelRate canFam2_DelRate +1 0.00e+00 6.90e-03 6.90e-03 0.00e+00 0.00e+00 1.38e-02 +2 0.00e+00 0.00e+00 1.27e-02 7.25e-04 0.00e+00 6.36e-03 +3 0.00e+00 0.00e+00 6.21e-03 0.00e+00 0.00e+00 6.21e-03 +4 0.00e+00 0.00e+00 2.07e-02 0.00e+00 0.00e+00 5.18e-03 +5 0.00e+00 0.00e+00 2.54e-02 0.00e+00 0.00e+00 1.69e-02 +6 0.00e+00 0.00e+00 9.61e-04 0.00e+00 0.00e+00 0.00e+00 +7 0.00e+00 0.00e+00 1.97e-02 0.00e+00 0.00e+00 5.62e-03 +8 0.00e+00 1.71e-03 1.17e-02 0.00e+00 1.71e-03 6.67e-03 +9 0.00e+00 0.00e+00 1.05e-02 2.72e-03 0.00e+00 1.83e-02 +10 0.00e+00 3.26e-03 1.51e-02 0.00e+00 0.00e+00 1.89e-02 +12 1.25e-03 0.00e+00 8.70e-03 0.00e+00 0.00e+00 1.24e-02 +13 0.00e+00 0.00e+00 6.76e-03 0.00e+00 0.00e+00 4.73e-02 +14 0.00e+00 0.00e+00 4.93e-03 1.23e-03 1.23e-03 5.55e-03 +15 0.00e+00 0.00e+00 2.29e-02 0.00e+00 0.00e+00 1.38e-02 diff -r aae4754d6828 -r 675ad84ae008 test-data/indels_3way.tabular --- a/test-data/indels_3way.tabular Mon Sep 22 10:36:34 2008 -0400 +++ b/test-data/indels_3way.tabular Mon Sep 22 12:02:35 2008 -0400 @@ -1,149 +1,149 @@ -#block indel_type indel_length ingroup1 ingroup1_start ingroup1_end ingroup1_orient ingroup2 ingroup2_start ingroup2_end ingroup2_orient outgroup outgroup_start outgroup_end outgroup_orient -12 hg18.chr1:802_insert 1 hg18.chr1:802 57213 57213 + panTro2.chrUn:801 9724391 9724392 + canFam2.chr30:805 3360548 3360549 - -2 hg18.chr1:1380_delete 4 hg18.chr1:1380 48103 48104 + panTro2.chrUn:1384 9713713 9713716 + canFam2.chr30:1415 3367755 3367758 - -9 hg18.chr1:367_delete 35 hg18.chr1:367 55389 55390 + panTro2.chrUn:402 9721584 9721618 + canFam2.chr30:382 3361661 3361695 - -14 hg18.chr1:1628_delete 1 hg18.chr1:1628 58770 58771 + panTro2.chrUn:1631 9725949 9725949 + canFam2.chr30:1623 3357056 3357056 - -14 hg18.chr1:1628_delete 4 hg18.chr1:1628 58770 58771 + panTro2.chrUn:1631 9725950 9725953 + canFam2.chr30:1623 3357058 3357061 - -1 panTro2.chrUn:145_insert 2 hg18.chr1:143 46857 46858 + panTro2.chrUn:145 9712465 9712466 + canFam2.chr30:145 3368190 3368191 - -8 panTro2.chrUn:585_insert 4 hg18.chr1:582 54744 54745 + panTro2.chrUn:585 9720936 9720939 + canFam2.chr30:600 3362635 3362636 - -10 panTro2.chrUn:307_insert 35 hg18.chr1:272 55984 55985 + panTro2.chrUn:307 9721981 9722015 + canFam2.chr30:265 3361105 3361106 - -8 panTro2.chrUn:585_delete 1 hg18.chr1:582 54979 54979 + panTro2.chrUn:585 9721173 9721174 + canFam2.chr30:600 3362890 3362890 - -14 panTro2.chrUn:1631_delete 1 hg18.chr1:1628 59015 59015 + panTro2.chrUn:1631 9726197 9726198 + canFam2.chr30:1623 3357328 3357328 - -14 panTro2.chrUn:1631_delete 1 hg18.chr1:1628 60211 60211 + panTro2.chrUn:1631 9727392 9727393 + canFam2.chr30:1623 3358490 3358490 - -1 canFam2.chr30:145_insert 4 hg18.chr1:143 46796 46797 + panTro2.chrUn:145 9712403 9712404 + canFam2.chr30:145 3368127 3368130 - -2 canFam2.chr30:1415_insert 8 hg18.chr1:1380 47138 47139 + panTro2.chrUn:1384 9712747 9712748 + canFam2.chr30:1415 3366730 3366737 - -2 canFam2.chr30:1415_insert 3 hg18.chr1:1380 47263 47264 + panTro2.chrUn:1384 9712872 9712873 + canFam2.chr30:1415 3366862 3366864 - -2 canFam2.chr30:1415_insert 1 hg18.chr1:1380 47293 47294 + panTro2.chrUn:1384 9712902 9712903 + canFam2.chr30:1415 3366895 3366895 - -2 canFam2.chr30:1415_insert 1 hg18.chr1:1380 47312 47313 + panTro2.chrUn:1384 9712921 9712922 + canFam2.chr30:1415 3366915 3366915 - -2 canFam2.chr30:1415_insert 7 hg18.chr1:1380 47440 47441 + panTro2.chrUn:1384 9713049 9713050 + canFam2.chr30:1415 3367044 3367050 - -2 canFam2.chr30:1415_insert 1 hg18.chr1:1380 47528 47529 + panTro2.chrUn:1384 9713137 9713138 + canFam2.chr30:1415 3367138 3367138 - -2 canFam2.chr30:1415_insert 10 hg18.chr1:1380 47546 47547 + panTro2.chrUn:1384 9713155 9713156 + canFam2.chr30:1415 3367157 3367166 - -2 canFam2.chr30:1415_insert 4 hg18.chr1:1380 47562 47563 + panTro2.chrUn:1384 9713171 9713172 + canFam2.chr30:1415 3367183 3367186 - -2 canFam2.chr30:1415_insert 1 hg18.chr1:1380 47648 47649 + panTro2.chrUn:1384 9713257 9713258 + canFam2.chr30:1415 3367273 3367273 - -2 canFam2.chr30:1415_insert 3 hg18.chr1:1380 47672 47673 + panTro2.chrUn:1384 9713281 9713282 + canFam2.chr30:1415 3367298 3367300 - -2 canFam2.chr30:1415_insert 5 hg18.chr1:1380 47734 47735 + panTro2.chrUn:1384 9713343 9713344 + canFam2.chr30:1415 3367361 3367365 - -2 canFam2.chr30:1415_insert 2 hg18.chr1:1380 47759 47760 + panTro2.chrUn:1384 9713368 9713369 + canFam2.chr30:1415 3367391 3367392 - -2 canFam2.chr30:1415_insert 2 hg18.chr1:1380 47835 47836 + panTro2.chrUn:1384 9713444 9713445 + canFam2.chr30:1415 3367469 3367470 - -2 canFam2.chr30:1415_insert 1 hg18.chr1:1380 48017 48018 + panTro2.chrUn:1384 9713626 9713627 + canFam2.chr30:1415 3367653 3367653 - -2 canFam2.chr30:1415_insert 1 hg18.chr1:1380 48035 48036 + panTro2.chrUn:1384 9713644 9713645 + canFam2.chr30:1415 3367672 3367672 - -2 canFam2.chr30:1415_insert 4 hg18.chr1:1380 48091 48092 + panTro2.chrUn:1384 9713700 9713701 + canFam2.chr30:1415 3367729 3367732 - -2 canFam2.chr30:1415_insert 10 hg18.chr1:1380 48103 48104 + panTro2.chrUn:1384 9713712 9713713 + canFam2.chr30:1415 3367745 3367754 - -2 canFam2.chr30:1415_insert 1 hg18.chr1:1380 48232 48233 + panTro2.chrUn:1384 9713845 9713846 + canFam2.chr30:1415 3367870 3367870 - -3 canFam2.chr30:483_insert 15 hg18.chr1:455 48379 48380 + panTro2.chrUn:455 9714289 9714290 + canFam2.chr30:483 3366038 3366052 - -3 canFam2.chr30:483_insert 21 hg18.chr1:455 48426 48427 + panTro2.chrUn:455 9714336 9714337 + canFam2.chr30:483 3366096 3366116 - -3 canFam2.chr30:483_insert 1 hg18.chr1:455 48523 48524 + panTro2.chrUn:455 9714433 9714434 + canFam2.chr30:483 3366213 3366213 - -4 canFam2.chr30:193_insert 8 hg18.chr1:183 52535 52536 + panTro2.chrUn:183 9718438 9718439 + canFam2.chr30:193 3364655 3364662 - -4 canFam2.chr30:193_insert 1 hg18.chr1:183 52555 52556 + panTro2.chrUn:183 9718458 9718459 + canFam2.chr30:193 3364683 3364683 - -4 canFam2.chr30:193_insert 1 hg18.chr1:183 52588 52589 + panTro2.chrUn:183 9718491 9718492 + canFam2.chr30:193 3364717 3364717 - -4 canFam2.chr30:193_insert 4 hg18.chr1:183 52691 52692 + panTro2.chrUn:183 9718594 9718595 + canFam2.chr30:193 3364817 3364820 - -5 canFam2.chr30:118_insert 3 hg18.chr1:115 52709 52710 + panTro2.chrUn:115 9718612 9718613 + canFam2.chr30:118 3364525 3364527 - -5 canFam2.chr30:118_insert 1 hg18.chr1:115 52754 52755 + panTro2.chrUn:115 9718657 9718658 + canFam2.chr30:118 3364571 3364571 - -5 canFam2.chr30:118_insert 4 hg18.chr1:115 52763 52764 + panTro2.chrUn:115 9718666 9718667 + canFam2.chr30:118 3364581 3364584 - -6 canFam2.chr30:1041_insert 1 hg18.chr1:1040 53848 53849 + panTro2.chrUn:1040 9719751 9719752 + canFam2.chr30:1041 3364511 3364511 - -7 canFam2.chr30:356_insert 4 hg18.chr1:335 53869 53870 + panTro2.chrUn:335 9719772 9719773 + canFam2.chr30:356 3363136 3363139 - -7 canFam2.chr30:356_insert 1 hg18.chr1:335 53899 53900 + panTro2.chrUn:335 9719802 9719803 + canFam2.chr30:356 3363168 3363168 - -7 canFam2.chr30:356_insert 1 hg18.chr1:335 53921 53922 + panTro2.chrUn:335 9719824 9719825 + canFam2.chr30:356 3363191 3363191 - -7 canFam2.chr30:356_insert 8 hg18.chr1:335 53938 53939 + panTro2.chrUn:335 9719841 9719842 + canFam2.chr30:356 3363209 3363216 - -7 canFam2.chr30:356_insert 7 hg18.chr1:335 53970 53971 + panTro2.chrUn:335 9719873 9719874 + canFam2.chr30:356 3363249 3363255 - -7 canFam2.chr30:356_insert 5 hg18.chr1:335 54101 54102 + panTro2.chrUn:335 9720004 9720005 + canFam2.chr30:356 3363383 3363387 - -7 canFam2.chr30:356_insert 1 hg18.chr1:335 54164 54165 + panTro2.chrUn:335 9720067 9720068 + canFam2.chr30:356 3363451 3363451 - -8 canFam2.chr30:600_insert 1 hg18.chr1:582 54579 54580 + panTro2.chrUn:585 9720770 9720771 + canFam2.chr30:600 3362472 3362472 - -8 canFam2.chr30:600_insert 1 hg18.chr1:582 54654 54655 + panTro2.chrUn:585 9720845 9720846 + canFam2.chr30:600 3362547 3362547 - -8 canFam2.chr30:600_insert 1 hg18.chr1:582 54691 54692 + panTro2.chrUn:585 9720882 9720883 + canFam2.chr30:600 3362585 3362585 - -8 canFam2.chr30:600_insert 18 hg18.chr1:582 54775 54776 + panTro2.chrUn:585 9720970 9720971 + canFam2.chr30:600 3362667 3362684 - -8 canFam2.chr30:600_insert 1 hg18.chr1:582 54799 54800 + panTro2.chrUn:585 9720994 9720995 + canFam2.chr30:600 3362709 3362709 - -8 canFam2.chr30:600_insert 4 hg18.chr1:582 54944 54945 + panTro2.chrUn:585 9721139 9721140 + canFam2.chr30:600 3362851 3362854 - -8 canFam2.chr30:600_insert 1 hg18.chr1:582 54969 54970 + panTro2.chrUn:585 9721164 9721165 + canFam2.chr30:600 3362880 3362880 - -9 canFam2.chr30:382_insert 1 hg18.chr1:367 55360 55361 + panTro2.chrUn:402 9721554 9721555 + canFam2.chr30:382 3361632 3361632 - -9 canFam2.chr30:382_insert 1 hg18.chr1:367 55378 55379 + panTro2.chrUn:402 9721572 9721573 + canFam2.chr30:382 3361651 3361651 - -9 canFam2.chr30:382_insert 1 hg18.chr1:367 55396 55397 + panTro2.chrUn:402 9721625 9721626 + canFam2.chr30:382 3361703 3361703 - -9 canFam2.chr30:382_insert 2 hg18.chr1:367 55444 55445 + panTro2.chrUn:402 9721673 9721674 + canFam2.chr30:382 3361752 3361753 - -10 canFam2.chr30:265_insert 1 hg18.chr1:272 55776 55777 + panTro2.chrUn:307 9721772 9721773 + canFam2.chr30:265 3360902 3360902 - -10 canFam2.chr30:265_insert 5 hg18.chr1:272 55864 55865 + panTro2.chrUn:307 9721860 9721861 + canFam2.chr30:265 3360991 3360995 - -10 canFam2.chr30:265_insert 2 hg18.chr1:272 55969 55970 + panTro2.chrUn:307 9721965 9721966 + canFam2.chr30:265 3361087 3361088 - -10 canFam2.chr30:265_insert 2 hg18.chr1:272 55980 55981 + panTro2.chrUn:307 9721976 9721977 + canFam2.chr30:265 3361100 3361101 - -12 canFam2.chr30:805_insert 33 hg18.chr1:802 56722 56723 + panTro2.chrUn:801 9723901 9723902 + canFam2.chr30:805 3360035 3360067 - -12 canFam2.chr30:805_insert 1 hg18.chr1:802 56746 56747 + panTro2.chrUn:801 9723925 9723926 + canFam2.chr30:805 3360092 3360092 - -12 canFam2.chr30:805_insert 1 hg18.chr1:802 56836 56837 + panTro2.chrUn:801 9724015 9724016 + canFam2.chr30:805 3360183 3360183 - -12 canFam2.chr30:805_insert 1 hg18.chr1:802 56864 56865 + panTro2.chrUn:801 9724043 9724044 + canFam2.chr30:805 3360212 3360212 - -12 canFam2.chr30:805_insert 1 hg18.chr1:802 56894 56895 + panTro2.chrUn:801 9724073 9724074 + canFam2.chr30:805 3360243 3360243 - -12 canFam2.chr30:805_insert 2 hg18.chr1:802 57161 57162 + panTro2.chrUn:801 9724340 9724341 + canFam2.chr30:805 3360496 3360497 - -12 canFam2.chr30:805_insert 1 hg18.chr1:802 57352 57353 + panTro2.chrUn:801 9724530 9724531 + canFam2.chr30:805 3360680 3360680 - -13 canFam2.chr30:148_insert 2 hg18.chr1:176 58529 58530 + panTro2.chrUn:176 9725707 9725708 + canFam2.chr30:148 3359565 3359566 - -14 canFam2.chr30:1623_insert 1 hg18.chr1:1628 58700 58701 + panTro2.chrUn:1631 9725878 9725879 + canFam2.chr30:1623 3356984 3356984 - -14 canFam2.chr30:1623_insert 1 hg18.chr1:1628 58709 58710 + panTro2.chrUn:1631 9725887 9725888 + canFam2.chr30:1623 3356994 3356994 - -14 canFam2.chr30:1623_insert 1 hg18.chr1:1628 58770 58771 + panTro2.chrUn:1631 9725949 9725950 + canFam2.chr30:1623 3357057 3357057 - -14 canFam2.chr30:1623_insert 1 hg18.chr1:1628 58772 58773 + panTro2.chrUn:1631 9725955 9725956 + canFam2.chr30:1623 3357064 3357064 - -14 canFam2.chr30:1623_insert 15 hg18.chr1:1628 58800 58801 + panTro2.chrUn:1631 9725983 9725984 + canFam2.chr30:1623 3357093 3357107 - -14 canFam2.chr30:1623_insert 9 hg18.chr1:1628 58808 58809 + panTro2.chrUn:1631 9725991 9725992 + canFam2.chr30:1623 3357116 3357124 - -14 canFam2.chr30:1623_insert 1 hg18.chr1:1628 60032 60033 + panTro2.chrUn:1631 9727214 9727215 + canFam2.chr30:1623 3358319 3358319 - -14 canFam2.chr30:1623_insert 4 hg18.chr1:1628 60148 60149 + panTro2.chrUn:1631 9727330 9727331 + canFam2.chr30:1623 3358426 3358429 - -15 canFam2.chr30:218_insert 1 hg18.chr1:230 60326 60327 + panTro2.chrUn:230 9727507 9727508 + canFam2.chr30:218 3356643 3356643 - -15 canFam2.chr30:218_insert 2 hg18.chr1:230 60353 60354 + panTro2.chrUn:230 9727534 9727535 + canFam2.chr30:218 3356671 3356672 - -15 canFam2.chr30:218_insert 1 hg18.chr1:230 60391 60392 + panTro2.chrUn:230 9727572 9727573 + canFam2.chr30:218 3356711 3356711 - -15 canFam2.chr30:218_insert 1 hg18.chr1:230 60466 60467 + panTro2.chrUn:230 9727647 9727648 + canFam2.chr30:218 3356783 3356783 - -15 canFam2.chr30:218_insert 5 hg18.chr1:230 60476 60477 + panTro2.chrUn:230 9727657 9727658 + canFam2.chr30:218 3356794 3356798 - -1 canFam2.chr30:145_delete 1 hg18.chr1:143 46857 46857 + panTro2.chrUn:145 9712464 9712464 + canFam2.chr30:145 3368190 3368191 - -1 canFam2.chr30:145_delete 1 hg18.chr1:143 46900 46900 + panTro2.chrUn:145 9712509 9712509 + canFam2.chr30:145 3368232 3368233 - -2 canFam2.chr30:1415_delete 7 hg18.chr1:1380 47080 47086 + panTro2.chrUn:1384 9712689 9712695 + canFam2.chr30:1415 3366677 3366678 - -2 canFam2.chr30:1415_delete 1 hg18.chr1:1380 47168 47168 + panTro2.chrUn:1384 9712777 9712777 + canFam2.chr30:1415 3366766 3366767 - -2 canFam2.chr30:1415_delete 1 hg18.chr1:1380 47482 47482 + panTro2.chrUn:1384 9713091 9713091 + canFam2.chr30:1415 3367091 3367092 - -2 canFam2.chr30:1415_delete 2 hg18.chr1:1380 47703 47704 + panTro2.chrUn:1384 9713312 9713313 + canFam2.chr30:1415 3367330 3367331 - -2 canFam2.chr30:1415_delete 15 hg18.chr1:1380 48139 48153 + panTro2.chrUn:1384 9713752 9713766 + canFam2.chr30:1415 3367793 3367794 - -2 canFam2.chr30:1415_delete 1 hg18.chr1:1380 48160 48160 + panTro2.chrUn:1384 9713773 9713773 + canFam2.chr30:1415 3367799 3367800 - -2 canFam2.chr30:1415_delete 1 hg18.chr1:1380 48174 48174 + panTro2.chrUn:1384 9713787 9713787 + canFam2.chr30:1415 3367812 3367813 - -2 canFam2.chr30:1415_delete 1 hg18.chr1:1380 48197 48197 + panTro2.chrUn:1384 9713810 9713810 + canFam2.chr30:1415 3367834 3367835 - -2 canFam2.chr30:1415_delete 5 hg18.chr1:1380 48280 48284 + panTro2.chrUn:1384 9713893 9713897 + canFam2.chr30:1415 3367917 3367918 - -3 canFam2.chr30:483_delete 4 hg18.chr1:455 48344 48347 + panTro2.chrUn:455 9714254 9714257 + canFam2.chr30:483 3366005 3366006 - -3 canFam2.chr30:483_delete 4 hg18.chr1:455 48410 48413 + panTro2.chrUn:455 9714320 9714323 + canFam2.chr30:483 3366082 3366083 - -3 canFam2.chr30:483_delete 1 hg18.chr1:455 48470 48470 + panTro2.chrUn:455 9714380 9714380 + canFam2.chr30:483 3366159 3366160 - -4 canFam2.chr30:193_delete 4 hg18.chr1:183 52639 52642 + panTro2.chrUn:183 9718542 9718545 + canFam2.chr30:193 3364767 3364768 - -5 canFam2.chr30:118_delete 3 hg18.chr1:115 52707 52709 + panTro2.chrUn:115 9718610 9718612 + canFam2.chr30:118 3364524 3364525 - -5 canFam2.chr30:118_delete 2 hg18.chr1:115 52743 52744 + panTro2.chrUn:115 9718646 9718647 + canFam2.chr30:118 3364560 3364561 - -7 canFam2.chr30:356_delete 2 hg18.chr1:335 53879 53880 + panTro2.chrUn:335 9719782 9719783 + canFam2.chr30:356 3363148 3363149 - -7 canFam2.chr30:356_delete 4 hg18.chr1:335 54052 54055 + panTro2.chrUn:335 9719955 9719958 + canFam2.chr30:356 3363336 3363337 - -8 canFam2.chr30:600_delete 1 hg18.chr1:582 54634 54634 + panTro2.chrUn:585 9720825 9720825 + canFam2.chr30:600 3362526 3362527 - -8 canFam2.chr30:600_delete 3 hg18.chr1:582 54710 54712 + panTro2.chrUn:585 9720901 9720903 + canFam2.chr30:600 3362603 3362604 - -8 canFam2.chr30:600_delete 4 hg18.chr1:582 54876 54879 + panTro2.chrUn:585 9721071 9721074 + canFam2.chr30:600 3362785 3362786 - -8 canFam2.chr30:600_delete 1 hg18.chr1:582 54984 54984 + panTro2.chrUn:585 9721178 9721178 + canFam2.chr30:600 3362894 3362895 - -9 canFam2.chr30:382_delete 1 hg18.chr1:367 55131 55131 + panTro2.chrUn:402 9721325 9721325 + canFam2.chr30:382 3361420 3361421 - -9 canFam2.chr30:382_delete 6 hg18.chr1:367 55213 55218 + panTro2.chrUn:402 9721407 9721412 + canFam2.chr30:382 3361501 3361502 - -9 canFam2.chr30:382_delete 1 hg18.chr1:367 55308 55308 + panTro2.chrUn:402 9721502 9721502 + canFam2.chr30:382 3361590 3361591 - -9 canFam2.chr30:382_delete 4 hg18.chr1:367 55324 55327 + panTro2.chrUn:402 9721518 9721521 + canFam2.chr30:382 3361605 3361606 - -9 canFam2.chr30:382_delete 7 hg18.chr1:367 55340 55346 + panTro2.chrUn:402 9721534 9721540 + canFam2.chr30:382 3361617 3361618 - -9 canFam2.chr30:382_delete 2 hg18.chr1:367 55386 55387 + panTro2.chrUn:402 9721580 9721581 + canFam2.chr30:382 3361658 3361659 - -9 canFam2.chr30:382_delete 4 hg18.chr1:367 55457 55460 + panTro2.chrUn:402 9721686 9721689 + canFam2.chr30:382 3361765 3361766 - -10 canFam2.chr30:265_delete 11 hg18.chr1:272 55893 55903 + panTro2.chrUn:307 9721889 9721899 + canFam2.chr30:265 3361023 3361024 - -10 canFam2.chr30:265_delete 1 hg18.chr1:272 55924 55924 + panTro2.chrUn:307 9721920 9721920 + canFam2.chr30:265 3361043 3361044 - -10 canFam2.chr30:265_delete 1 hg18.chr1:272 55939 55939 + panTro2.chrUn:307 9721935 9721935 + canFam2.chr30:265 3361057 3361058 - -10 canFam2.chr30:265_delete 1 hg18.chr1:272 55959 55959 + panTro2.chrUn:307 9721955 9721955 + canFam2.chr30:265 3361076 3361077 - -10 canFam2.chr30:265_delete 3 hg18.chr1:272 56001 56003 + panTro2.chrUn:307 9722032 9722034 + canFam2.chr30:265 3361121 3361122 - -12 canFam2.chr30:805_delete 6 hg18.chr1:802 56611 56616 + panTro2.chrUn:801 9723790 9723795 + canFam2.chr30:805 3359929 3359930 - -12 canFam2.chr30:805_delete 1 hg18.chr1:802 56696 56696 + panTro2.chrUn:801 9723875 9723875 + canFam2.chr30:805 3360008 3360009 - -12 canFam2.chr30:805_delete 7 hg18.chr1:802 56911 56917 + panTro2.chrUn:801 9724090 9724096 + canFam2.chr30:805 3360259 3360260 - -12 canFam2.chr30:805_delete 3 hg18.chr1:802 56991 56993 + panTro2.chrUn:801 9724170 9724172 + canFam2.chr30:805 3360332 3360333 - -12 canFam2.chr30:805_delete 5 hg18.chr1:802 57110 57114 + panTro2.chrUn:801 9724289 9724293 + canFam2.chr30:805 3360448 3360449 - -12 canFam2.chr30:805_delete 1 hg18.chr1:802 57217 57217 + panTro2.chrUn:801 9724395 9724395 + canFam2.chr30:805 3360551 3360552 - -12 canFam2.chr30:805_delete 5 hg18.chr1:802 57247 57251 + panTro2.chrUn:801 9724425 9724429 + canFam2.chr30:805 3360580 3360581 - -12 canFam2.chr30:805_delete 2 hg18.chr1:802 57310 57311 + panTro2.chrUn:801 9724488 9724489 + canFam2.chr30:805 3360638 3360639 - -12 canFam2.chr30:805_delete 2 hg18.chr1:802 57379 57380 + panTro2.chrUn:801 9724557 9724558 + canFam2.chr30:805 3360706 3360707 - -12 canFam2.chr30:805_delete 4 hg18.chr1:802 57387 57390 + panTro2.chrUn:801 9724565 9724568 + canFam2.chr30:805 3360712 3360713 - -13 canFam2.chr30:148_delete 3 hg18.chr1:176 58409 58411 + panTro2.chrUn:176 9725587 9725589 + canFam2.chr30:148 3359468 3359469 - -13 canFam2.chr30:148_delete 1 hg18.chr1:176 58434 58434 + panTro2.chrUn:176 9725612 9725612 + canFam2.chr30:148 3359490 3359491 - -13 canFam2.chr30:148_delete 2 hg18.chr1:176 58446 58447 + panTro2.chrUn:176 9725624 9725625 + canFam2.chr30:148 3359501 3359502 - -13 canFam2.chr30:148_delete 8 hg18.chr1:176 58470 58477 + panTro2.chrUn:176 9725648 9725655 + canFam2.chr30:148 3359523 3359524 - -13 canFam2.chr30:148_delete 5 hg18.chr1:176 58488 58492 + panTro2.chrUn:176 9725666 9725670 + canFam2.chr30:148 3359533 3359534 - -13 canFam2.chr30:148_delete 6 hg18.chr1:176 58510 58515 + panTro2.chrUn:176 9725688 9725693 + canFam2.chr30:148 3359550 3359551 - -13 canFam2.chr30:148_delete 5 hg18.chr1:176 58565 58569 + panTro2.chrUn:176 9725743 9725747 + canFam2.chr30:148 3359601 3359602 - -14 canFam2.chr30:1623_delete 1 hg18.chr1:1628 58669 58669 + panTro2.chrUn:1631 9725847 9725847 + canFam2.chr30:1623 3356952 3356953 - -14 canFam2.chr30:1623_delete 3 hg18.chr1:1628 58849 58851 + panTro2.chrUn:1631 9726032 9726034 + canFam2.chr30:1623 3357164 3357165 - -14 canFam2.chr30:1623_delete 10 hg18.chr1:1628 59342 59351 + panTro2.chrUn:1631 9726524 9726533 + canFam2.chr30:1623 3357654 3357655 - -14 canFam2.chr30:1623_delete 1 hg18.chr1:1628 59561 59561 + panTro2.chrUn:1631 9726743 9726743 + canFam2.chr30:1623 3357863 3357864 - -14 canFam2.chr30:1623_delete 11 hg18.chr1:1628 59887 59897 + panTro2.chrUn:1631 9727069 9727079 + canFam2.chr30:1623 3358188 3358189 - -14 canFam2.chr30:1623_delete 5 hg18.chr1:1628 59908 59912 + panTro2.chrUn:1631 9727090 9727094 + canFam2.chr30:1623 3358198 3358199 - -14 canFam2.chr30:1623_delete 6 hg18.chr1:1628 60052 60057 + panTro2.chrUn:1631 9727234 9727239 + canFam2.chr30:1623 3358338 3358339 - -14 canFam2.chr30:1623_delete 4 hg18.chr1:1628 60111 60114 + panTro2.chrUn:1631 9727293 9727296 + canFam2.chr30:1623 3358391 3358392 - -14 canFam2.chr30:1623_delete 2 hg18.chr1:1628 60183 60184 + panTro2.chrUn:1631 9727365 9727366 + canFam2.chr30:1623 3358463 3358464 - -15 canFam2.chr30:218_delete 4 hg18.chr1:230 60400 60403 + panTro2.chrUn:230 9727581 9727584 + canFam2.chr30:218 3356719 3356720 - -15 canFam2.chr30:218_delete 8 hg18.chr1:230 60506 60513 + panTro2.chrUn:230 9727687 9727694 + canFam2.chr30:218 3356827 3356828 - -15 canFam2.chr30:218_delete 10 hg18.chr1:230 60520 60529 + panTro2.chrUn:230 9727701 9727710 + canFam2.chr30:218 3356833 3356834 - +#block indel_type indel_length ingroup1 ingroup1_start ingroup1_end ingroup1_alignSize ingroup1_orient ingroup2 ingroup2_start ingroup2_end ingroup2_alignSize ingroup2_orient outgroup outgroup_start outgroup_end outgroup_alignSize outgroup_orient +12 hg18.chr1_insert 1 hg18.chr1 57213 57213 802 + panTro2.chrUn 9724391 9724392 801 + canFam2.chr30 3360548 3360549 805 - +2 hg18.chr1_delete 4 hg18.chr1 48103 48104 1380 + panTro2.chrUn 9713713 9713716 1384 + canFam2.chr30 3367755 3367758 1415 - +9 hg18.chr1_delete 35 hg18.chr1 55389 55390 367 + panTro2.chrUn 9721584 9721618 402 + canFam2.chr30 3361661 3361695 382 - +14 hg18.chr1_delete 1 hg18.chr1 58770 58771 1628 + panTro2.chrUn 9725949 9725949 1631 + canFam2.chr30 3357056 3357056 1623 - +14 hg18.chr1_delete 4 hg18.chr1 58770 58771 1628 + panTro2.chrUn 9725950 9725953 1631 + canFam2.chr30 3357058 3357061 1623 - +1 panTro2.chrUn_insert 2 hg18.chr1 46857 46858 143 + panTro2.chrUn 9712465 9712466 145 + canFam2.chr30 3368190 3368191 145 - +8 panTro2.chrUn_insert 4 hg18.chr1 54744 54745 582 + panTro2.chrUn 9720936 9720939 585 + canFam2.chr30 3362635 3362636 600 - +10 panTro2.chrUn_insert 35 hg18.chr1 55984 55985 272 + panTro2.chrUn 9721981 9722015 307 + canFam2.chr30 3361105 3361106 265 - +8 panTro2.chrUn_delete 1 hg18.chr1 54979 54979 582 + panTro2.chrUn 9721173 9721174 585 + canFam2.chr30 3362890 3362890 600 - +14 panTro2.chrUn_delete 1 hg18.chr1 59015 59015 1628 + panTro2.chrUn 9726197 9726198 1631 + canFam2.chr30 3357328 3357328 1623 - +14 panTro2.chrUn_delete 1 hg18.chr1 60211 60211 1628 + panTro2.chrUn 9727392 9727393 1631 + canFam2.chr30 3358490 3358490 1623 - +1 canFam2.chr30_insert 4 hg18.chr1 46796 46797 143 + panTro2.chrUn 9712403 9712404 145 + canFam2.chr30 3368127 3368130 145 - +2 canFam2.chr30_insert 8 hg18.chr1 47138 47139 1380 + panTro2.chrUn 9712747 9712748 1384 + canFam2.chr30 3366730 3366737 1415 - +2 canFam2.chr30_insert 3 hg18.chr1 47263 47264 1380 + panTro2.chrUn 9712872 9712873 1384 + canFam2.chr30 3366862 3366864 1415 - +2 canFam2.chr30_insert 1 hg18.chr1 47293 47294 1380 + panTro2.chrUn 9712902 9712903 1384 + canFam2.chr30 3366895 3366895 1415 - +2 canFam2.chr30_insert 1 hg18.chr1 47312 47313 1380 + panTro2.chrUn 9712921 9712922 1384 + canFam2.chr30 3366915 3366915 1415 - +2 canFam2.chr30_insert 7 hg18.chr1 47440 47441 1380 + panTro2.chrUn 9713049 9713050 1384 + canFam2.chr30 3367044 3367050 1415 - +2 canFam2.chr30_insert 1 hg18.chr1 47528 47529 1380 + panTro2.chrUn 9713137 9713138 1384 + canFam2.chr30 3367138 3367138 1415 - +2 canFam2.chr30_insert 10 hg18.chr1 47546 47547 1380 + panTro2.chrUn 9713155 9713156 1384 + canFam2.chr30 3367157 3367166 1415 - +2 canFam2.chr30_insert 4 hg18.chr1 47562 47563 1380 + panTro2.chrUn 9713171 9713172 1384 + canFam2.chr30 3367183 3367186 1415 - +2 canFam2.chr30_insert 1 hg18.chr1 47648 47649 1380 + panTro2.chrUn 9713257 9713258 1384 + canFam2.chr30 3367273 3367273 1415 - +2 canFam2.chr30_insert 3 hg18.chr1 47672 47673 1380 + panTro2.chrUn 9713281 9713282 1384 + canFam2.chr30 3367298 3367300 1415 - +2 canFam2.chr30_insert 5 hg18.chr1 47734 47735 1380 + panTro2.chrUn 9713343 9713344 1384 + canFam2.chr30 3367361 3367365 1415 - +2 canFam2.chr30_insert 2 hg18.chr1 47759 47760 1380 + panTro2.chrUn 9713368 9713369 1384 + canFam2.chr30 3367391 3367392 1415 - +2 canFam2.chr30_insert 2 hg18.chr1 47835 47836 1380 + panTro2.chrUn 9713444 9713445 1384 + canFam2.chr30 3367469 3367470 1415 - +2 canFam2.chr30_insert 1 hg18.chr1 48017 48018 1380 + panTro2.chrUn 9713626 9713627 1384 + canFam2.chr30 3367653 3367653 1415 - +2 canFam2.chr30_insert 1 hg18.chr1 48035 48036 1380 + panTro2.chrUn 9713644 9713645 1384 + canFam2.chr30 3367672 3367672 1415 - +2 canFam2.chr30_insert 4 hg18.chr1 48091 48092 1380 + panTro2.chrUn 9713700 9713701 1384 + canFam2.chr30 3367729 3367732 1415 - +2 canFam2.chr30_insert 10 hg18.chr1 48103 48104 1380 + panTro2.chrUn 9713712 9713713 1384 + canFam2.chr30 3367745 3367754 1415 - +2 canFam2.chr30_insert 1 hg18.chr1 48232 48233 1380 + panTro2.chrUn 9713845 9713846 1384 + canFam2.chr30 3367870 3367870 1415 - +3 canFam2.chr30_insert 15 hg18.chr1 48379 48380 455 + panTro2.chrUn 9714289 9714290 455 + canFam2.chr30 3366038 3366052 483 - +3 canFam2.chr30_insert 21 hg18.chr1 48426 48427 455 + panTro2.chrUn 9714336 9714337 455 + canFam2.chr30 3366096 3366116 483 - +3 canFam2.chr30_insert 1 hg18.chr1 48523 48524 455 + panTro2.chrUn 9714433 9714434 455 + canFam2.chr30 3366213 3366213 483 - +4 canFam2.chr30_insert 8 hg18.chr1 52535 52536 183 + panTro2.chrUn 9718438 9718439 183 + canFam2.chr30 3364655 3364662 193 - +4 canFam2.chr30_insert 1 hg18.chr1 52555 52556 183 + panTro2.chrUn 9718458 9718459 183 + canFam2.chr30 3364683 3364683 193 - +4 canFam2.chr30_insert 1 hg18.chr1 52588 52589 183 + panTro2.chrUn 9718491 9718492 183 + canFam2.chr30 3364717 3364717 193 - +4 canFam2.chr30_insert 4 hg18.chr1 52691 52692 183 + panTro2.chrUn 9718594 9718595 183 + canFam2.chr30 3364817 3364820 193 - +5 canFam2.chr30_insert 3 hg18.chr1 52709 52710 115 + panTro2.chrUn 9718612 9718613 115 + canFam2.chr30 3364525 3364527 118 - +5 canFam2.chr30_insert 1 hg18.chr1 52754 52755 115 + panTro2.chrUn 9718657 9718658 115 + canFam2.chr30 3364571 3364571 118 - +5 canFam2.chr30_insert 4 hg18.chr1 52763 52764 115 + panTro2.chrUn 9718666 9718667 115 + canFam2.chr30 3364581 3364584 118 - +6 canFam2.chr30_insert 1 hg18.chr1 53848 53849 1040 + panTro2.chrUn 9719751 9719752 1040 + canFam2.chr30 3364511 3364511 1041 - +7 canFam2.chr30_insert 4 hg18.chr1 53869 53870 335 + panTro2.chrUn 9719772 9719773 335 + canFam2.chr30 3363136 3363139 356 - +7 canFam2.chr30_insert 1 hg18.chr1 53899 53900 335 + panTro2.chrUn 9719802 9719803 335 + canFam2.chr30 3363168 3363168 356 - +7 canFam2.chr30_insert 1 hg18.chr1 53921 53922 335 + panTro2.chrUn 9719824 9719825 335 + canFam2.chr30 3363191 3363191 356 - +7 canFam2.chr30_insert 8 hg18.chr1 53938 53939 335 + panTro2.chrUn 9719841 9719842 335 + canFam2.chr30 3363209 3363216 356 - +7 canFam2.chr30_insert 7 hg18.chr1 53970 53971 335 + panTro2.chrUn 9719873 9719874 335 + canFam2.chr30 3363249 3363255 356 - +7 canFam2.chr30_insert 5 hg18.chr1 54101 54102 335 + panTro2.chrUn 9720004 9720005 335 + canFam2.chr30 3363383 3363387 356 - +7 canFam2.chr30_insert 1 hg18.chr1 54164 54165 335 + panTro2.chrUn 9720067 9720068 335 + canFam2.chr30 3363451 3363451 356 - +8 canFam2.chr30_insert 1 hg18.chr1 54579 54580 582 + panTro2.chrUn 9720770 9720771 585 + canFam2.chr30 3362472 3362472 600 - +8 canFam2.chr30_insert 1 hg18.chr1 54654 54655 582 + panTro2.chrUn 9720845 9720846 585 + canFam2.chr30 3362547 3362547 600 - +8 canFam2.chr30_insert 1 hg18.chr1 54691 54692 582 + panTro2.chrUn 9720882 9720883 585 + canFam2.chr30 3362585 3362585 600 - +8 canFam2.chr30_insert 18 hg18.chr1 54775 54776 582 + panTro2.chrUn 9720970 9720971 585 + canFam2.chr30 3362667 3362684 600 - +8 canFam2.chr30_insert 1 hg18.chr1 54799 54800 582 + panTro2.chrUn 9720994 9720995 585 + canFam2.chr30 3362709 3362709 600 - +8 canFam2.chr30_insert 4 hg18.chr1 54944 54945 582 + panTro2.chrUn 9721139 9721140 585 + canFam2.chr30 3362851 3362854 600 - +8 canFam2.chr30_insert 1 hg18.chr1 54969 54970 582 + panTro2.chrUn 9721164 9721165 585 + canFam2.chr30 3362880 3362880 600 - +9 canFam2.chr30_insert 1 hg18.chr1 55360 55361 367 + panTro2.chrUn 9721554 9721555 402 + canFam2.chr30 3361632 3361632 382 - +9 canFam2.chr30_insert 1 hg18.chr1 55378 55379 367 + panTro2.chrUn 9721572 9721573 402 + canFam2.chr30 3361651 3361651 382 - +9 canFam2.chr30_insert 1 hg18.chr1 55396 55397 367 + panTro2.chrUn 9721625 9721626 402 + canFam2.chr30 3361703 3361703 382 - +9 canFam2.chr30_insert 2 hg18.chr1 55444 55445 367 + panTro2.chrUn 9721673 9721674 402 + canFam2.chr30 3361752 3361753 382 - +10 canFam2.chr30_insert 1 hg18.chr1 55776 55777 272 + panTro2.chrUn 9721772 9721773 307 + canFam2.chr30 3360902 3360902 265 - +10 canFam2.chr30_insert 5 hg18.chr1 55864 55865 272 + panTro2.chrUn 9721860 9721861 307 + canFam2.chr30 3360991 3360995 265 - +10 canFam2.chr30_insert 2 hg18.chr1 55969 55970 272 + panTro2.chrUn 9721965 9721966 307 + canFam2.chr30 3361087 3361088 265 - +10 canFam2.chr30_insert 2 hg18.chr1 55980 55981 272 + panTro2.chrUn 9721976 9721977 307 + canFam2.chr30 3361100 3361101 265 - +12 canFam2.chr30_insert 33 hg18.chr1 56722 56723 802 + panTro2.chrUn 9723901 9723902 801 + canFam2.chr30 3360035 3360067 805 - +12 canFam2.chr30_insert 1 hg18.chr1 56746 56747 802 + panTro2.chrUn 9723925 9723926 801 + canFam2.chr30 3360092 3360092 805 - +12 canFam2.chr30_insert 1 hg18.chr1 56836 56837 802 + panTro2.chrUn 9724015 9724016 801 + canFam2.chr30 3360183 3360183 805 - +12 canFam2.chr30_insert 1 hg18.chr1 56864 56865 802 + panTro2.chrUn 9724043 9724044 801 + canFam2.chr30 3360212 3360212 805 - +12 canFam2.chr30_insert 1 hg18.chr1 56894 56895 802 + panTro2.chrUn 9724073 9724074 801 + canFam2.chr30 3360243 3360243 805 - +12 canFam2.chr30_insert 2 hg18.chr1 57161 57162 802 + panTro2.chrUn 9724340 9724341 801 + canFam2.chr30 3360496 3360497 805 - +12 canFam2.chr30_insert 1 hg18.chr1 57352 57353 802 + panTro2.chrUn 9724530 9724531 801 + canFam2.chr30 3360680 3360680 805 - +13 canFam2.chr30_insert 2 hg18.chr1 58529 58530 176 + panTro2.chrUn 9725707 9725708 176 + canFam2.chr30 3359565 3359566 148 - +14 canFam2.chr30_insert 1 hg18.chr1 58700 58701 1628 + panTro2.chrUn 9725878 9725879 1631 + canFam2.chr30 3356984 3356984 1623 - +14 canFam2.chr30_insert 1 hg18.chr1 58709 58710 1628 + panTro2.chrUn 9725887 9725888 1631 + canFam2.chr30 3356994 3356994 1623 - +14 canFam2.chr30_insert 1 hg18.chr1 58770 58771 1628 + panTro2.chrUn 9725949 9725950 1631 + canFam2.chr30 3357057 3357057 1623 - +14 canFam2.chr30_insert 1 hg18.chr1 58772 58773 1628 + panTro2.chrUn 9725955 9725956 1631 + canFam2.chr30 3357064 3357064 1623 - +14 canFam2.chr30_insert 15 hg18.chr1 58800 58801 1628 + panTro2.chrUn 9725983 9725984 1631 + canFam2.chr30 3357093 3357107 1623 - +14 canFam2.chr30_insert 9 hg18.chr1 58808 58809 1628 + panTro2.chrUn 9725991 9725992 1631 + canFam2.chr30 3357116 3357124 1623 - +14 canFam2.chr30_insert 1 hg18.chr1 60032 60033 1628 + panTro2.chrUn 9727214 9727215 1631 + canFam2.chr30 3358319 3358319 1623 - +14 canFam2.chr30_insert 4 hg18.chr1 60148 60149 1628 + panTro2.chrUn 9727330 9727331 1631 + canFam2.chr30 3358426 3358429 1623 - +15 canFam2.chr30_insert 1 hg18.chr1 60326 60327 230 + panTro2.chrUn 9727507 9727508 230 + canFam2.chr30 3356643 3356643 218 - +15 canFam2.chr30_insert 2 hg18.chr1 60353 60354 230 + panTro2.chrUn 9727534 9727535 230 + canFam2.chr30 3356671 3356672 218 - +15 canFam2.chr30_insert 1 hg18.chr1 60391 60392 230 + panTro2.chrUn 9727572 9727573 230 + canFam2.chr30 3356711 3356711 218 - +15 canFam2.chr30_insert 1 hg18.chr1 60466 60467 230 + panTro2.chrUn 9727647 9727648 230 + canFam2.chr30 3356783 3356783 218 - +15 canFam2.chr30_insert 5 hg18.chr1 60476 60477 230 + panTro2.chrUn 9727657 9727658 230 + canFam2.chr30 3356794 3356798 218 - +1 canFam2.chr30_delete 1 hg18.chr1 46857 46857 143 + panTro2.chrUn 9712464 9712464 145 + canFam2.chr30 3368190 3368191 145 - +1 canFam2.chr30_delete 1 hg18.chr1 46900 46900 143 + panTro2.chrUn 9712509 9712509 145 + canFam2.chr30 3368232 3368233 145 - +2 canFam2.chr30_delete 7 hg18.chr1 47080 47086 1380 + panTro2.chrUn 9712689 9712695 1384 + canFam2.chr30 3366677 3366678 1415 - +2 canFam2.chr30_delete 1 hg18.chr1 47168 47168 1380 + panTro2.chrUn 9712777 9712777 1384 + canFam2.chr30 3366766 3366767 1415 - +2 canFam2.chr30_delete 1 hg18.chr1 47482 47482 1380 + panTro2.chrUn 9713091 9713091 1384 + canFam2.chr30 3367091 3367092 1415 - +2 canFam2.chr30_delete 2 hg18.chr1 47703 47704 1380 + panTro2.chrUn 9713312 9713313 1384 + canFam2.chr30 3367330 3367331 1415 - +2 canFam2.chr30_delete 15 hg18.chr1 48139 48153 1380 + panTro2.chrUn 9713752 9713766 1384 + canFam2.chr30 3367793 3367794 1415 - +2 canFam2.chr30_delete 1 hg18.chr1 48160 48160 1380 + panTro2.chrUn 9713773 9713773 1384 + canFam2.chr30 3367799 3367800 1415 - +2 canFam2.chr30_delete 1 hg18.chr1 48174 48174 1380 + panTro2.chrUn 9713787 9713787 1384 + canFam2.chr30 3367812 3367813 1415 - +2 canFam2.chr30_delete 1 hg18.chr1 48197 48197 1380 + panTro2.chrUn 9713810 9713810 1384 + canFam2.chr30 3367834 3367835 1415 - +2 canFam2.chr30_delete 5 hg18.chr1 48280 48284 1380 + panTro2.chrUn 9713893 9713897 1384 + canFam2.chr30 3367917 3367918 1415 - +3 canFam2.chr30_delete 4 hg18.chr1 48344 48347 455 + panTro2.chrUn 9714254 9714257 455 + canFam2.chr30 3366005 3366006 483 - +3 canFam2.chr30_delete 4 hg18.chr1 48410 48413 455 + panTro2.chrUn 9714320 9714323 455 + canFam2.chr30 3366082 3366083 483 - +3 canFam2.chr30_delete 1 hg18.chr1 48470 48470 455 + panTro2.chrUn 9714380 9714380 455 + canFam2.chr30 3366159 3366160 483 - +4 canFam2.chr30_delete 4 hg18.chr1 52639 52642 183 + panTro2.chrUn 9718542 9718545 183 + canFam2.chr30 3364767 3364768 193 - +5 canFam2.chr30_delete 3 hg18.chr1 52707 52709 115 + panTro2.chrUn 9718610 9718612 115 + canFam2.chr30 3364524 3364525 118 - +5 canFam2.chr30_delete 2 hg18.chr1 52743 52744 115 + panTro2.chrUn 9718646 9718647 115 + canFam2.chr30 3364560 3364561 118 - +7 canFam2.chr30_delete 2 hg18.chr1 53879 53880 335 + panTro2.chrUn 9719782 9719783 335 + canFam2.chr30 3363148 3363149 356 - +7 canFam2.chr30_delete 4 hg18.chr1 54052 54055 335 + panTro2.chrUn 9719955 9719958 335 + canFam2.chr30 3363336 3363337 356 - +8 canFam2.chr30_delete 1 hg18.chr1 54634 54634 582 + panTro2.chrUn 9720825 9720825 585 + canFam2.chr30 3362526 3362527 600 - +8 canFam2.chr30_delete 3 hg18.chr1 54710 54712 582 + panTro2.chrUn 9720901 9720903 585 + canFam2.chr30 3362603 3362604 600 - +8 canFam2.chr30_delete 4 hg18.chr1 54876 54879 582 + panTro2.chrUn 9721071 9721074 585 + canFam2.chr30 3362785 3362786 600 - +8 canFam2.chr30_delete 1 hg18.chr1 54984 54984 582 + panTro2.chrUn 9721178 9721178 585 + canFam2.chr30 3362894 3362895 600 - +9 canFam2.chr30_delete 1 hg18.chr1 55131 55131 367 + panTro2.chrUn 9721325 9721325 402 + canFam2.chr30 3361420 3361421 382 - +9 canFam2.chr30_delete 6 hg18.chr1 55213 55218 367 + panTro2.chrUn 9721407 9721412 402 + canFam2.chr30 3361501 3361502 382 - +9 canFam2.chr30_delete 1 hg18.chr1 55308 55308 367 + panTro2.chrUn 9721502 9721502 402 + canFam2.chr30 3361590 3361591 382 - +9 canFam2.chr30_delete 4 hg18.chr1 55324 55327 367 + panTro2.chrUn 9721518 9721521 402 + canFam2.chr30 3361605 3361606 382 - +9 canFam2.chr30_delete 7 hg18.chr1 55340 55346 367 + panTro2.chrUn 9721534 9721540 402 + canFam2.chr30 3361617 3361618 382 - +9 canFam2.chr30_delete 2 hg18.chr1 55386 55387 367 + panTro2.chrUn 9721580 9721581 402 + canFam2.chr30 3361658 3361659 382 - +9 canFam2.chr30_delete 4 hg18.chr1 55457 55460 367 + panTro2.chrUn 9721686 9721689 402 + canFam2.chr30 3361765 3361766 382 - +10 canFam2.chr30_delete 11 hg18.chr1 55893 55903 272 + panTro2.chrUn 9721889 9721899 307 + canFam2.chr30 3361023 3361024 265 - +10 canFam2.chr30_delete 1 hg18.chr1 55924 55924 272 + panTro2.chrUn 9721920 9721920 307 + canFam2.chr30 3361043 3361044 265 - +10 canFam2.chr30_delete 1 hg18.chr1 55939 55939 272 + panTro2.chrUn 9721935 9721935 307 + canFam2.chr30 3361057 3361058 265 - +10 canFam2.chr30_delete 1 hg18.chr1 55959 55959 272 + panTro2.chrUn 9721955 9721955 307 + canFam2.chr30 3361076 3361077 265 - +10 canFam2.chr30_delete 3 hg18.chr1 56001 56003 272 + panTro2.chrUn 9722032 9722034 307 + canFam2.chr30 3361121 3361122 265 - +12 canFam2.chr30_delete 6 hg18.chr1 56611 56616 802 + panTro2.chrUn 9723790 9723795 801 + canFam2.chr30 3359929 3359930 805 - +12 canFam2.chr30_delete 1 hg18.chr1 56696 56696 802 + panTro2.chrUn 9723875 9723875 801 + canFam2.chr30 3360008 3360009 805 - +12 canFam2.chr30_delete 7 hg18.chr1 56911 56917 802 + panTro2.chrUn 9724090 9724096 801 + canFam2.chr30 3360259 3360260 805 - +12 canFam2.chr30_delete 3 hg18.chr1 56991 56993 802 + panTro2.chrUn 9724170 9724172 801 + canFam2.chr30 3360332 3360333 805 - +12 canFam2.chr30_delete 5 hg18.chr1 57110 57114 802 + panTro2.chrUn 9724289 9724293 801 + canFam2.chr30 3360448 3360449 805 - +12 canFam2.chr30_delete 1 hg18.chr1 57217 57217 802 + panTro2.chrUn 9724395 9724395 801 + canFam2.chr30 3360551 3360552 805 - +12 canFam2.chr30_delete 5 hg18.chr1 57247 57251 802 + panTro2.chrUn 9724425 9724429 801 + canFam2.chr30 3360580 3360581 805 - +12 canFam2.chr30_delete 2 hg18.chr1 57310 57311 802 + panTro2.chrUn 9724488 9724489 801 + canFam2.chr30 3360638 3360639 805 - +12 canFam2.chr30_delete 2 hg18.chr1 57379 57380 802 + panTro2.chrUn 9724557 9724558 801 + canFam2.chr30 3360706 3360707 805 - +12 canFam2.chr30_delete 4 hg18.chr1 57387 57390 802 + panTro2.chrUn 9724565 9724568 801 + canFam2.chr30 3360712 3360713 805 - +13 canFam2.chr30_delete 3 hg18.chr1 58409 58411 176 + panTro2.chrUn 9725587 9725589 176 + canFam2.chr30 3359468 3359469 148 - +13 canFam2.chr30_delete 1 hg18.chr1 58434 58434 176 + panTro2.chrUn 9725612 9725612 176 + canFam2.chr30 3359490 3359491 148 - +13 canFam2.chr30_delete 2 hg18.chr1 58446 58447 176 + panTro2.chrUn 9725624 9725625 176 + canFam2.chr30 3359501 3359502 148 - +13 canFam2.chr30_delete 8 hg18.chr1 58470 58477 176 + panTro2.chrUn 9725648 9725655 176 + canFam2.chr30 3359523 3359524 148 - +13 canFam2.chr30_delete 5 hg18.chr1 58488 58492 176 + panTro2.chrUn 9725666 9725670 176 + canFam2.chr30 3359533 3359534 148 - +13 canFam2.chr30_delete 6 hg18.chr1 58510 58515 176 + panTro2.chrUn 9725688 9725693 176 + canFam2.chr30 3359550 3359551 148 - +13 canFam2.chr30_delete 5 hg18.chr1 58565 58569 176 + panTro2.chrUn 9725743 9725747 176 + canFam2.chr30 3359601 3359602 148 - +14 canFam2.chr30_delete 1 hg18.chr1 58669 58669 1628 + panTro2.chrUn 9725847 9725847 1631 + canFam2.chr30 3356952 3356953 1623 - +14 canFam2.chr30_delete 3 hg18.chr1 58849 58851 1628 + panTro2.chrUn 9726032 9726034 1631 + canFam2.chr30 3357164 3357165 1623 - +14 canFam2.chr30_delete 10 hg18.chr1 59342 59351 1628 + panTro2.chrUn 9726524 9726533 1631 + canFam2.chr30 3357654 3357655 1623 - +14 canFam2.chr30_delete 1 hg18.chr1 59561 59561 1628 + panTro2.chrUn 9726743 9726743 1631 + canFam2.chr30 3357863 3357864 1623 - +14 canFam2.chr30_delete 11 hg18.chr1 59887 59897 1628 + panTro2.chrUn 9727069 9727079 1631 + canFam2.chr30 3358188 3358189 1623 - +14 canFam2.chr30_delete 5 hg18.chr1 59908 59912 1628 + panTro2.chrUn 9727090 9727094 1631 + canFam2.chr30 3358198 3358199 1623 - +14 canFam2.chr30_delete 6 hg18.chr1 60052 60057 1628 + panTro2.chrUn 9727234 9727239 1631 + canFam2.chr30 3358338 3358339 1623 - +14 canFam2.chr30_delete 4 hg18.chr1 60111 60114 1628 + panTro2.chrUn 9727293 9727296 1631 + canFam2.chr30 3358391 3358392 1623 - +14 canFam2.chr30_delete 2 hg18.chr1 60183 60184 1628 + panTro2.chrUn 9727365 9727366 1631 + canFam2.chr30 3358463 3358464 1623 - +15 canFam2.chr30_delete 4 hg18.chr1 60400 60403 230 + panTro2.chrUn 9727581 9727584 230 + canFam2.chr30 3356719 3356720 218 - +15 canFam2.chr30_delete 8 hg18.chr1 60506 60513 230 + panTro2.chrUn 9727687 9727694 230 + canFam2.chr30 3356827 3356828 218 - +15 canFam2.chr30_delete 10 hg18.chr1 60520 60529 230 + panTro2.chrUn 9727701 9727710 230 + canFam2.chr30 3356833 3356834 218 - diff -r aae4754d6828 -r 675ad84ae008 tools/regVariation/getIndelRates_3way.py --- a/tools/regVariation/getIndelRates_3way.py Mon Sep 22 10:36:34 2008 -0400 +++ b/tools/regVariation/getIndelRates_3way.py Mon Sep 22 12:02:35 2008 -0400 @@ -1,56 +1,56 @@ #!/usr/bin/env python #Guruprasad Ananda -import sys, os, tempfile, string +from galaxy import eggs +import pkg_resources +pkg_resources.require( "bx-python" ) -assert sys.version_info[:2] >= ( 2, 4 ) +import sys, os, tempfile +import traceback +import fileinput +from warnings import warn -fout = open(sys.argv[2],'w') -winsize = int(sys.argv[3]) -species_ind = int(sys.argv[4]) +from galaxy.tools.util.galaxyops import * +from bx.intervals.io import * + +from bx.intervals.operations import quicksect def stop_err(msg): sys.stderr.write(msg) sys.exit() + +def counter(node, start, end, sort_col): + global full, blk_len, blk_list + if node.start < start: + if node.right: + counter(node.right, start, end, sort_col) + elif start <= node.start <= end and start <= node.end <= end: + full += 1 + if node.other[0] not in blk_list: + blk_list.append(node.other[0]) + blk_len += int(node.other[sort_col+2]) + if node.left and node.left.maxend > start: + counter(node.left, start, end, sort_col) + if node.right: + counter(node.right, start, end, sort_col) + elif node.start > end: + if node.left: + counter(node.left, start, end, sort_col) + -def rate_estimator(win, blk_lines, wstart, wend, wspecies): - inserts = 0.0 - deletes = 0.0 - ilengths = {} #dict containing lengths of blocks(without gaps) having insertion in wspecies - dlengths = {} #dict containing lengths of blocks(without gaps) having deletion in wspecies - prev_bnum = -1 - for bline in blk_lines: - items = bline.split('\t') - bnum = int(items[0]) - bevent = items[1] - if not(bevent.startswith(wspecies)): - continue - if bevent.endswith('insert'): - inserts += 1 - #Add lengths only if the insert belongs to a new alignment block - if not(ilengths.has_key(bnum)): - ilengths[bnum] = int(items[species_ind].split(':')[1]) - #prev_bnum = bnum - elif bevent.endswith('delete'): - deletes += 1 - #Add lengths only if the delete belongs to a new alignment block - if not(dlengths.has_key(bnum)): - dlengths[bnum] = int(items[species_ind].split(':')[1]) - #prev_bnum = bnum +infile = sys.argv[1] +fout = open(sys.argv[2],'w') +int_file = sys.argv[3] +if int_file != "None": #User has specified an interval file try: - total_ilength = sum(ilengths.values()) - irate = inserts/total_ilength + fint = open(int_file, 'r') + dbkey_i = sys.argv[4] + chr_col_i, start_col_i, end_col_i, strand_col_i = parse_cols_arg( sys.argv[5] ) except: - irate = 0 - try: - total_dlength = sum(dlengths.values()) - drate = deletes/total_dlength - except: - drate = 0 - print >>fout, "%s\t%s\t%s\t%s\t%.2e\t%.2e" %(win, wspecies, wstart, wend, irate , drate) - + stop_err("Unable to open input Interval file") + def main(): - infile = sys.argv[1] + for i, line in enumerate( file ( infile )): line = line.rstrip('\r\n') if len( line )>0 and not line.startswith( '#' ): @@ -58,71 +58,192 @@ break if i == 30: break # Hopefully we'll never get here... - - if len( elems ) != 15: + + if len( elems ) != 18: stop_err( "This tool only works on tabular data output by 'Fetch Indels from 3-way alignments' tool. The data in your input dataset is either missing or not formatted properly." ) - wspecies = elems[species_ind].split(':')[0].split('.')[0] - fin = open(infile, 'r') - skipped = 0 - blk=0 - win=0 - linestr="" - sorted_infile = tempfile.NamedTemporaryFile() - cmdline = "sort -n -k"+str(species_ind+2)+" -o "+sorted_infile.name+" "+infile - try: - os.system(cmdline) - except: - stop_err("Encountered error while sorting the input file.") - - print >>fout, "#Window\tSpecies\tWindow_Start\tWindow_End\tInsertion_Rate\tDeletion_Rate" - - for line in sorted_infile.readlines(): - line = line.strip("\r\n") - if not(line) or line == "": - continue + for i, line in enumerate( file ( infile )): + line = line.rstrip('\r\n') elems = line.split('\t') try: assert int(elems[0]) - assert len(elems) == 15 - except Exception, eon: + assert len(elems) == 18 + if int_file != "None": + if dbkey_i not in elems[3] and dbkey_i not in elems[8] and dbkey_i not in elems[13]: + stop_err("The species build corresponding to your interval file is not present in the Indel file.") + if dbkey_i in elems[3]: + sort_col = 4 + elif dbkey_i in elems[8]: + sort_col = 9 + elif dbkey_i in elems[13]: + sort_col = 14 + else: + species = [] + species.append( elems[3].split('.')[0] ) + species.append( elems[8].split('.')[0] ) + species.append( elems[13].split('.')[0] ) + sort_col = 0 #Based on block numbers + break + except: continue - if not(elems[1].startswith(wspecies)): #Event doesn't belong to the selected species + + fin = open(infile, 'r') + skipped = 0 + + if int_file == "None": + sorted_infile = tempfile.NamedTemporaryFile() + cmdline = "sort -n -k"+str(1)+" -o "+sorted_infile.name+" "+infile + try: + os.system(cmdline) + except: + stop_err("Encountered error while sorting the input file.") + print >>fout, "#Block\t%s_InsRate\t%s_InsRate\t%s_InsRate\t%s_DelRate\t%s_DelRate\t%s_DelRate" %(species[0],species[1],species[2],species[0],species[1],species[2]) + prev_bnum = -1 + sorted_infile.seek(0) + for line in sorted_infile.readlines(): + line = line.rstrip('\r\n') + elems = line.split('\t') + try: + assert int(elems[0]) + assert len(elems) == 18 + new_bnum = int(elems[0]) + if new_bnum != prev_bnum: + if prev_bnum != -1: + irate = [] + drate = [] + for i,elem in enumerate(inserts): + try: + irate.append(str("%.2e" %(inserts[i]/blen[i]))) + except: + irate.append('0') + try: + drate.append(str("%.2e" %(deletes[i]/blen[i]))) + except: + drate.append('0') + print >>fout, "%s\t%s\t%s" %(prev_bnum, '\t'.join(irate) , '\t'.join(drate)) + inserts = [0.0, 0.0, 0.0] + deletes = [0.0, 0.0, 0.0] + blen = [] + blen.append( int(elems[6]) ) + blen.append( int(elems[11]) ) + blen.append( int(elems[16]) ) + line_sp = elems[1].split('.')[0] + sp_ind = species.index(line_sp) + if elems[1].endswith('insert'): + inserts[sp_ind] += 1 + elif elems[1].endswith('delete'): + deletes[sp_ind] += 1 + prev_bnum = new_bnum + except Exception, ei: + #print >>sys.stderr, ei + continue + irate = [] + drate = [] + for i,elem in enumerate(inserts): + try: + irate.append(str("%.2e" %(inserts[i]/blen[i]))) + except: + irate.append('0') + try: + drate.append(str("%.2e" %(deletes[i]/blen[i]))) + except: + drate.append('0') + print >>fout, "%s\t%s\t%s" %(prev_bnum, '\t'.join(irate) , '\t'.join(drate)) + sys.exit() + + + inf = open(infile, 'r') + start_met = False + end_met = False + sp_file = tempfile.NamedTemporaryFile() + for n, line in enumerate(inf): + line = line.rstrip('\r\n') + elems = line.split('\t') + try: + assert int(elems[0]) + assert len(elems) == 18 + if dbkey_i not in elems[1]: + if not(start_met): + continue + else: + sp_end = n + break + else: + print >>sp_file, line + if not(start_met): + start_met = True + sp_start = n + except: continue - - try: - assert wstart - except NameError: - wstart = int(elems[species_ind+1]) - int(elems[species_ind+1])%winsize + 1 - wend = wstart + winsize - lstart = int(elems[species_ind + 1]) - - if lstart in range(wstart,wend+1): - linestr += line.strip() - linestr += "\n" - else: - try: - win += 1 - blk_lines = linestr.strip().split("\n") - rate_estimator(str(win), blk_lines, str(wstart), str(wend), wspecies) - linestr = "" - except: - skipped += 1 - pass - linestr=line.strip()+"\n" - wstart = int(elems[species_ind+1]) - int(elems[species_ind+1])%winsize + 1 - wend = wstart + winsize - if linestr != "": - try: - win += 1 - blk_lines = linestr.strip().split("\n") - rate_estimator(str(win), blk_lines, str(wstart), str(wend), wspecies) - except: - skipped += 1 + + try: + assert sp_end + except: + sp_end = n+1 + + sp_file.seek(0) + win = NiceReaderWrapper( fileinput.FileInput( int_file ), + chrom_col=chr_col_i, + start_col=start_col_i, + end_col=end_col_i, + strand_col=strand_col_i, + fix_strand=True) + + indel = NiceReaderWrapper( fileinput.FileInput( sp_file.name ), + chrom_col=1, + start_col=sort_col, + end_col=sort_col+1, + strand_col=-1, + fix_strand=True) + + indelTree = quicksect.IntervalTree() + for item in indel: + if type( item ) is GenomicInterval: + indelTree.insert( item, indel.linenum, item.fields ) + result=[] + + global full, blk_len, blk_list + for interval in win: + if type( interval ) is Header: pass - if skipped: - print "Skipped %s windows as invalid." %(skipped) + if type( interval ) is Comment: + pass + elif type( interval ) == GenomicInterval: + chrom = interval.chrom + start = int(interval.start) + end = int(interval.end) + if start > end: + warn( "Interval start after end!" ) + ins_chr = "%s.%s_insert" %(dbkey_i,chrom) + del_chr = "%s.%s_delete" %(dbkey_i,chrom) + irate = 0 + drate = 0 + if ins_chr not in indelTree.chroms and del_chr not in indelTree.chroms: + pass + else: + if ins_chr in indelTree.chroms: + full = 0.0 + blk_len = 0 + blk_list = [] + root = indelTree.chroms[ins_chr] #root node for the chrom insertion tree + counter(root, start, end, sort_col) + if blk_len: + irate = full/blk_len + + if del_chr in indelTree.chroms: + full = 0.0 + blk_len = 0 + blk_list = [] + root = indelTree.chroms[del_chr] #root node for the chrom insertion tree + counter(root, start, end, sort_col) + if blk_len: + drate = full/blk_len + + interval.fields.append(str("%.2e" %irate)) + interval.fields.append(str("%.2e" %drate)) + print >>fout, "\t".join(interval.fields) + fout.flush() + if __name__ == "__main__": - main() - \ No newline at end of file + main() \ No newline at end of file diff -r aae4754d6828 -r 675ad84ae008 tools/regVariation/getIndelRates_3way.xml --- a/tools/regVariation/getIndelRates_3way.xml Mon Sep 22 10:36:34 2008 -0400 +++ b/tools/regVariation/getIndelRates_3way.xml Mon Sep 22 12:02:35 2008 -0400 @@ -1,30 +1,30 @@ -<tool id="getIndelRates_3way" name="Estimate Indel Rates" version="1.0.0"> +<tool id="indelRates_3way" name="Estimate Indel Rates" version="1.0.0"> <description> for 3-way alignments</description> <command interpreter="python"> - getIndelRates_3way.py $input1 $out_file1 $winsize $species + getIndelRates_3way.py $input1 $out_file1 + #if $region.type == "align" + "None" + #else + $region.input2 $input2_dbkey $input2_chromCol,$input2_startCol,$input2_endCol,$input2_strandCol + #end if </command> <inputs> <page> - <param format="tabular" name="input1" type="data" label="Select data"/> - <param name="winsize" size="10" type="integer" value="1000" label="Estimate rates in windows of size" /> - <param name="species" type="select" label="and corresponding to co-ordinates of" multiple="false"> - <option value="3">Species 1 (Ingroup 1)</option> - <option value="7">Species 2 (Ingroup 2)</option> - <option value="11">Species 3 (Outgroup)</option> - </param> -  + </page> </inputs> <outputs> @@ -34,8 +34,7 @@ <tests> <test> <param name="input1" value="indels_3way.tabular"/> - <param name="winsize" value="1000"/> - <param name="species" value="11"/> + <param name="type" value="align"/> <output name="out_file1" file="indelrates_3way.tabular"/> </test> </tests> @@ -54,8 +53,8 @@ **Note** -Any block/s not containing exactly 3 species will be omitted. - +This tool only works on the output of the 'Estimate Indel Rates for 3-way alignments' tool. + </help> diff -r aae4754d6828 -r 675ad84ae008 tools/regVariation/getIndels_3way.xml --- a/tools/regVariation/getIndels_3way.xml Mon Sep 22 10:36:34 2008 -0400 +++ b/tools/regVariation/getIndels_3way.xml Mon Sep 22 12:02:35 2008 -0400 @@ -1,4 +1,4 @@ -<tool id="getIndels_3way" name="Fetch Indels" version="1.0.1"> +<tool id="indels_3way" name="Fetch Indels" version="1.0.1"> <description> from 3-way alignments</description> <command interpreter="perl"> parseMAF_smallIndels.pl $input1 $out_file1 $outgroup diff -r aae4754d6828 -r 675ad84ae008 tools/regVariation/parseMAF_smallIndels.pl --- a/tools/regVariation/parseMAF_smallIndels.pl Mon Sep 22 10:36:34 2008 -0400 +++ b/tools/regVariation/parseMAF_smallIndels.pl Mon Sep 22 12:02:35 2008 -0400 @@ -58,7 +58,7 @@ #print OFILE "#align\tingroup1\tingroup1_coord\tingroup1_orient\tingroup2\tingroup2_coord\tingroup2_orient\toutgroup\toutgroup_coord\toutgroup_orient\tindel_type\n"; #print OFILE2 "# small indels summary, parsed from MAF 3-way alignment file, coords are translated from (-) to (+) if necessary\n"; -print OFILE2 "#block\tindel_type\tindel_length\tingroup1\tingroup1_start\tingroup1_end\tingroup1_orient\tingroup2\tingroup2_start\tingroup2_end\tingroup2_orient\toutgroup\toutgroup_start\toutgroup_end\toutgroup_orient\n"; +print OFILE2 "#block\tindel_type\tindel_length\tingroup1\tingroup1_start\tingroup1_end\tingroup1_alignSize\tingroup1_orient\tingroup2\tingroup2_start\tingroup2_end\tingroup2_alignSize\tingroup2_orient\toutgroup\toutgroup_start\toutgroup_end\toutgroup_alignSize\toutgroup_orient\n"; # main body of program while ($record = get_next_record($fh) ){ @@ -348,7 +348,8 @@ && (substr($sequence2,$position,1) !~ m/[-*\#$?^@]/) && (substr($sequence3,$position,1) !~ m/[-*\#$?^@]/)){ $ABC = join("",($ABC,"X")); - $indelType = $seq1."_delete"; + my @s = split(/:/, $seq1); + $indelType = $s[0]."_delete"; #print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n"; $indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType)); @@ -361,7 +362,8 @@ && (substr($sequence2,$position,1) eq "-") && (substr($sequence3,$position,1) !~ m/[-*\$?^]/)){ $ABC = join("",($ABC,"Y")); - $indelType = $seq2."_delete"; + my @s = split(/:/, $seq2); + $indelType = $s[0]."_delete"; #print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n"; $indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType)); push (@indels,$indel_line); @@ -375,7 +377,8 @@ && (substr($sequence2,$position,1) eq "-") && (substr($sequence3,$position,1) eq "-")){ $ABC = join("",($ABC,"Z")); - $indelType = $seq1."_insert"; + my @s = split(/:/, $seq1); + $indelType = $s[0]."_insert"; #print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n"; $indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType)); push (@indels,$indel_line); @@ -387,7 +390,8 @@ && (substr($sequence2,$position,1) !~ m/[-*\#$?^@]/) && (substr($sequence3,$position,1) eq "-")){ $ABC = join("",($ABC,"W")); - $indelType = $seq2."_insert"; + my @s = split(/:/, $seq2); + $indelType = $s[0]."_insert"; #print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n"; $indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType)); push (@indels,$indel_line); @@ -399,7 +403,8 @@ && (substr($sequence2,$position,1) !~ m/[-*\#$?^@]/) && (substr($sequence3,$position,1) eq "-")){ $ABC = join("",($ABC,"S")); - $indelType = $seq3."_delete"; + my @s = split(/:/, $seq3); + $indelType = $s[0]."_delete"; #print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n"; $indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType)); push (@indels,$indel_line); @@ -411,7 +416,8 @@ && (substr($sequence2,$position,1) eq "-") && (substr($sequence3,$position,1) !~ m/[-*\#$?^@]/)){ $ABC = join("",($ABC,"T")); - $indelType = $seq3."_insert"; + my @s = split(/:/, $seq3); + $indelType = $s[0]."_insert"; #print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n"; $indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType)); push (@indels,$indel_line); @@ -622,6 +628,9 @@ my $event_line = $_; my @events = split(/\t/, $event_line); my $event_type = $events[10]; + my @name_align1 = split(/:/, $events[1]); + my @name_align2 = split(/:/, $events[4]); + my @name_align3 = split(/:/, $events[7]); my $seq1_event_start = my $seq1_event_end = my $seq2_event_start = my $seq2_event_end = my $seq3_event_start = my $seq3_event_end = 0; my $final_event_line = ""; # seq1_insert @@ -634,7 +643,7 @@ $seq2_event_end = ($events[5]); $seq3_event_start = ($events[8]-1); $seq3_event_end = ($events[8]); - $final_event_line = join("\t",($events[0],$event_type,$events[11],$events[1],$seq1_event_start,$seq1_event_end,$events[3],$events[4],$seq2_event_start,$seq2_event_end,$events[6],$events[7],$seq3_event_start,$seq3_event_end,$events[9])); + $final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9])); } # seq1_delete elsif ($event_type =~ m/$ingroup1/ && $event_type =~ m/delete/){ @@ -646,7 +655,7 @@ $seq2_event_end = ($events[5]+$events[11]-1); $seq3_event_start = ($events[8]); $seq3_event_end = ($events[8]+$events[11]-1); - $final_event_line = join("\t",($events[0],$event_type,$events[11],$events[1],$seq1_event_start,$seq1_event_end,$events[3],$events[4],$seq2_event_start,$seq2_event_end,$events[6],$events[7],$seq3_event_start,$seq3_event_end,$events[9])); + $final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9])); } # seq2_insert elsif ($event_type =~ m/$ingroup2/ && $event_type =~ m/insert/){ @@ -658,7 +667,7 @@ $seq2_event_end = ($events[5]+$events[11]-1); $seq3_event_start = ($events[8]-1); $seq3_event_end = ($events[8]); - $final_event_line = join("\t",($events[0],$event_type,$events[11],$events[1],$seq1_event_start,$seq1_event_end,$events[3],$events[4],$seq2_event_start,$seq2_event_end,$events[6],$events[7],$seq3_event_start,$seq3_event_end,$events[9])); + $final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9])); } # seq2_delete elsif ($event_type =~ m/$ingroup2/ && $event_type =~ m/delete/){ @@ -670,7 +679,7 @@ $seq2_event_end = ($events[5]); $seq3_event_start = ($events[8]); $seq3_event_end = ($events[8]+$events[11]-1); - $final_event_line = join("\t",($events[0],$event_type,$events[11],$events[1],$seq1_event_start,$seq1_event_end,$events[3],$events[4],$seq2_event_start,$seq2_event_end,$events[6],$events[7],$seq3_event_start,$seq3_event_end,$events[9])); + $final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9])); } # start testing w/seq3_insert elsif ($event_type =~ m/$outgroup/ && $event_type =~ m/insert/){ @@ -682,7 +691,7 @@ $seq2_event_end = ($events[5]); $seq3_event_start = ($events[8]); $seq3_event_end = ($events[8]+$events[11]-1); - $final_event_line = join("\t",($events[0],$event_type,$events[11],$events[1],$seq1_event_start,$seq1_event_end,$events[3],$events[4],$seq2_event_start,$seq2_event_end,$events[6],$events[7],$seq3_event_start,$seq3_event_end,$events[9])); + $final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9])); } # seq3_delete elsif ($event_type =~ m/$outgroup/ && $event_type =~ m/delete/){ @@ -694,7 +703,7 @@ $seq2_event_end = ($events[5]+$events[11]-1); $seq3_event_start = ($events[8]-1); $seq3_event_end = ($events[8]); - $final_event_line = join("\t",($events[0],$event_type,$events[11],$events[1],$seq1_event_start,$seq1_event_end,$events[3],$events[4],$seq2_event_start,$seq2_event_end,$events[6],$events[7],$seq3_event_start,$seq3_event_end,$events[9])); + $final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9])); }

1 0

[hg] galaxy 1526: Convert metadata unicode strings to ascii ( pr...
by greg＠scofield.bx.psu.edu 24 Sep '08

24 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/38e533287df4 changeset: 1526:38e533287df4 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Sep 24 11:14:44 2008 -0400 description: Convert metadata unicode strings to ascii ( previous code doesn't seem to do anything, am I missing something? ). Add no_value metadata attribute to columns and column_types metadata. Fix for column_maker and filter tools. 4 file(s) affected in this change: lib/galaxy/datatypes/metadata.py lib/galaxy/datatypes/tabular.py tools/stats/column_maker.py tools/stats/filtering.py diffs (79 lines): diff -r 675ad84ae008 -r 38e533287df4 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py Mon Sep 22 12:02:35 2008 -0400 +++ b/lib/galaxy/datatypes/metadata.py Wed Sep 24 11:14:44 2008 -0400 @@ -60,10 +60,10 @@ if isinstance( value, ListType ): for i, elem in enumerate( value ): if type ( elem ) == unicode: - value[i] = str( elem ) + value[i] = elem.decode( 'ascii' ) elif isinstance ( value, basestring ): if type( value ) == unicode: - value = str( value ) + value = value.decode( 'ascii' ) self.value = value self.context = context self.display = True @@ -76,7 +76,7 @@ @classmethod def marshal( cls, value ): ''' - This method should/can be overridden to convert the incomming + This method should/can be overridden to convert the incoming value to whatever type it is supposed to be. ''' return value @@ -273,7 +273,6 @@ class ColumnTypesParameter( MetadataParameter ): def __init__( self, spec, value, context ): MetadataParameter.__init__( self, spec, value, context ) - def __str__(self): return ",".join( map( str, self.value ) ) diff -r 675ad84ae008 -r 38e533287df4 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py Mon Sep 22 12:02:35 2008 -0400 +++ b/lib/galaxy/datatypes/tabular.py Wed Sep 24 11:14:44 2008 -0400 @@ -19,8 +19,8 @@ """Tab delimited data""" """Add metadata elements""" - MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=False ) - MetadataElement( name="column_types", default=[], desc="Column types", param=metadata.ColumnTypesParameter, readonly=True, visible=False ) + MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=False, no_value=0 ) + MetadataElement( name="column_types", default=[], desc="Column types", param=metadata.ColumnTypesParameter, readonly=True, visible=False, no_value=[] ) def init_meta( self, dataset, copy_from=None ): data.Text.init_meta( self, dataset, copy_from=copy_from ) diff -r 675ad84ae008 -r 38e533287df4 tools/stats/column_maker.py --- a/tools/stats/column_maker.py Mon Sep 22 12:02:35 2008 -0400 +++ b/tools/stats/column_maker.py Wed Sep 24 11:14:44 2008 -0400 @@ -19,12 +19,10 @@ round = sys.argv[4] try: in_columns = int( sys.argv[5] ) - # in_column_types is passed as a string that looks something like: - # "[u'str', u'int', u'int', u'str', u'int', u'str']" - in_column_types = sys.argv[6].strip( '[' ).strip( ']' ).replace( 'u', '' ).replace( "'", '' ).split( ',' ) + in_column_types = sys.argv[6].split( ',' ) except: stop_err( "Data does not appear to be tabular. This tool can only be used with tab-delimited data." ) - + # Unescape if input has been escaped mapped_str = { '__lt__': '<', diff -r 675ad84ae008 -r 38e533287df4 tools/stats/filtering.py --- a/tools/stats/filtering.py Mon Sep 22 12:02:35 2008 -0400 +++ b/tools/stats/filtering.py Wed Sep 24 11:14:44 2008 -0400 @@ -26,9 +26,7 @@ cond_text = sys.argv[3] try: in_columns = int( sys.argv[4] ) - # in_column_types is passed as a string that looks something like: - # "[u'str', u'int', u'int', u'str', u'int', u'str']" - in_column_types = sys.argv[5].strip( '[' ).strip( ']' ).replace( 'u', '' ).replace( "'", '' ).split( ',' ) + in_column_types = sys.argv[5].split( ',' ) except: stop_err( "Data does not appear to be tabular. This tool can only be used with tab-delimited data." )

1 0

[svn] [2773] Added locally modified sputnik source to svn
by nate＠bx.psu.edu 24 Sep '08

24 Sep '08

Revision: 2773 Author: nate Date: 2008-09-24 10:26:07 -0400 (Wed, 24 Sep 2008) Log Message: ----------- Added locally modified sputnik source to svn Added Paths: ----------- dependencies/sputnik/ dependencies/sputnik/README dependencies/sputnik/sputnik.c Added: dependencies/sputnik/README =================================================================== --- dependencies/sputnik/README (rev 0) +++ dependencies/sputnik/README 2008-09-24 14:26:07 UTC (rev 2773) @@ -0,0 +1,12 @@ +Sputnik's original source is available from: + +http://espressosoftware.com/pages/sputnik.jsp + +The version available from bx.psu.edu contains modifications to include +mononucleotide microsatellites in the output. + +Build with: + +gcc -g -o bx-sputnik sputnik.c + +And ensure that it can be found in your Galaxy user's path. Added: dependencies/sputnik/sputnik.c =================================================================== --- dependencies/sputnik/sputnik.c (rev 0) +++ dependencies/sputnik/sputnik.c 2008-09-24 14:26:07 UTC (rev 2773) @@ -0,0 +1,599 @@ +/* #define DEBUG_SPUTNIK 1 */ + + +/* + find repeats in fasta format seq file + allows for indels, returns score. + + beta version. caveat emptor. + + chrisa 29-Jul-94 + + chris abajian + University of Washington + Dept. of Molecular Biotechnology FJ-20 + Fluke Hall, Mason Road + Seattle WA 98195 +*/ + +#include <stdio.h> +#include <fcntl.h> +#include <unistd.h> +#include <string.h> +#include <errno.h> +#include <sys/types.h> + +/* trivial defs */ +#ifndef True +#define True 1 +#endif +#ifndef False +#define False 0 +#endif + +typedef int Boolean; + +/* size of buffer for reads. */ +#define BUF_SIZE 1024*10 /* 10K */ +/* max size of description line (begins with ">") */ +#define MAX_DESCRIPTION_LEN 1024 +/* max sequence length */ +#define MAX_SEQUENCE_LEN 1024*800 /* 800K */ +/* max number of sequence chars dumped to line */ +#define MAX_OUT_LINE_CHARS 60 + +/* for debugging only */ +#define MAX_ERRCODES 1024 + +/* search params and definitions */ +#define MIN_UNIT_LENGTH 1 /* start search with dinucleotide repeats */ +/* will search for di, tri, tetra ... <n>nucleotide repeats up to + this value for n */ +#define MAX_UNIT_LENGTH 5 /* up to and including pentanucleotides */ +/* this is the point score for each exact match */ +#define EXACT_MATCH_POINTS 1 +/* this is the point score for a mismatch, insertion or deletion */ +#define ERROR_MATCH_POINTS -6 +/* this is the minimum score required to be considered a match */ +#define MATCH_MIN_SCORE 8 +/* this is the low score at which we stop trying */ +#define MATCH_FAIL_SCORE -1 +/* this is the max recursion depth we try to recover errors */ +#define MAX_RECURSION 5 + + +char *repeatName[MAX_UNIT_LENGTH+1] = +{ + "***ERROR***", /* bad programmer! no latte! */ + "mononucleotide", + "dinucleotide", + "trinucleotide", + "tetranucleotide", + "pentanucleotide" +}; + + +char readBuf[BUF_SIZE]; +Boolean endOfFile; +int curBufLen; +int curBufPos; +int fd; +Boolean havePutBack; +char putBack; + +/* struct for indiv sequence in a file */ +typedef struct ss +{ + char descStr[MAX_DESCRIPTION_LEN]; + char seqStr[MAX_SEQUENCE_LEN]; + unsigned int seqLen; +} SeqStruct, *SeqStructPtr; + + +/* + * this structure describes the current state of a comparison. + * it gets passed down to recursive calls of the find repeat + * call so it can know when to bail out of an unsuccessful + * search, or return the size/state of a successful hit, etc. + */ +typedef struct ms +{ + int curPos; /* putative pattern starts here */ + int testPos; /* start testing here */ + int testLen; /* di, tri, tetra, etc. */ + int testCtr; /* # chars in testLen already tested. mod counter */ + int curScore; /* current score */ + int missense; /* keep track of ins, del, err */ + int insertions; + int deletions; + int depth; /* how deep is recursion for this match */ + char errCodes[MAX_ERRCODES]; +} MatchStruct, *MatchStructPtr; +/* a utility macro to copy one testStruct to another */ +#define copyMSPtr(dest,source) memcpy((char *)dest,(char *)source,sizeof(MatchStruct)) +/* a utility macro to increment the modular testCtr */ +#define bumpTestCtr(msp) (msp)->testCtr++; if ((msp)->testCtr==(msp)->testLen) (msp)->testCtr=0; + + +/* + ************************************************************ + * these routines are used to read and parse the fasta format + * sequence file + ************************************************************ + */ + +void fillBuf() +{ + size_t result; + + result = read(fd, (void *)readBuf, BUF_SIZE); + if (result == -1) + { + fprintf(stderr,"error reading file! errno = %d\n",errno); + exit(1); + } + else if (result == 0) + endOfFile = True; + else + { + curBufLen = result; + curBufPos = 0; + } +} /* readBuf */ + + +/* returns True on success */ +Boolean getChar(char *achar) +{ + if (havePutBack) + { + *achar = putBack; + havePutBack = False; + return(True); + } + + if (curBufPos == curBufLen) + fillBuf(); + + if (endOfFile) + return (False); + + *achar = readBuf[curBufPos++]; + return (True); +} + + +void putCharBack(char c) +{ + havePutBack = True; + putBack = c; +} + + +void openFile(char *fn) +{ + /* open the specified file */ + fd = open(fn, O_RDONLY); + if (fd == -1) + { + fprintf(stderr,"unable to open file %s\n", fn); + exit(1); + } +} + +/* should call this once for each file read */ +void initBuffer() +{ + /* initialize length and pointer */ + curBufPos = 0; + curBufLen = 0; + havePutBack = False; + endOfFile = False; +} + +void addCharToLine(char c, char *line, int *lineLen) +{ + if (*lineLen < MAX_DESCRIPTION_LEN) + line[(*lineLen)++] = c; + else + fprintf(stderr,"warning: description line truncated\n"); +} + + +/* + ********************************************************************* + * these routines are (more) specific to reading the fasta file format + ********************************************************************* + */ + + +/* + * pick up a non-blank line from the file, presumably description. + * truncates all leading blanks and/or blank lines + */ +Boolean getNonBlankLine(char *line) +{ + Boolean stop, nonBlank; + char c; + int lineLen; + + lineLen = 0; + stop = False; + nonBlank = False; /* will be set by any non whitespace char */ + while ((! endOfFile) && (! stop)) + if (getChar(&c)) + if (c == '\n') + stop = nonBlank; /* stop if have anything. don't save eol char. */ + else + if (nonBlank) + /* add it to line no matter what */ + addCharToLine(c,line,&lineLen); + else if ((c != ' ') && (c != '\t')) + { + /* only non whitespace will start the line */ + nonBlank = True; + addCharToLine(c,line,&lineLen); + } +} + + +/* load the sequence struct with comment line and bases */ +SeqStructPtr getSeq(char *fname) +{ + SeqStructPtr newSeqP; + Boolean endOfSeq; + char c; + + if (endOfFile) return ((SeqStructPtr )0); /* bombproofing */ + + /* malloc a new seq */ + if (! (newSeqP = (SeqStructPtr )malloc(sizeof(SeqStruct)) ) ) + { + fprintf(stderr,"unable to malloc() memory for sequence.\n"); + exit(1); + } + /* clear mem */ + memset( (void *)newSeqP, '\0', sizeof(SeqStruct)); + + /* pick up description line */ + if (! getNonBlankLine(newSeqP->descStr) ) + { + free(newSeqP); + return ((SeqStructPtr )0); + } + + /* did it start correctly ? */ + if (newSeqP->descStr[0] != '>') + { + fprintf(stderr,"format error in input file: missing '>'\n"); + exit(1); + } + + endOfSeq = False; + while ((!endOfFile) && (!endOfSeq)) + { + if (getChar(&c)) + { + if (c == '>') + { + /* hit new sequence */ + endOfSeq = True; + putCharBack(c); + } + else if (((c >= 'A') && (c <= 'Z')) || + ((c >= 'a') && (c <= 'z')) || (c == '-'))/* bogus test, chris */ + /* have nucleotide */ + newSeqP->seqStr[newSeqP->seqLen++] = toupper(c); + else if ((c != '\n') && (c != ' ') && (c != '\t') && (c != '#') && (c != '$') && (c != '*') && (c != '?') && (c != '^')) + { + /* wierd shit in file. bail. */ + fprintf(stderr,">bad char in sequence, %c\n",c); + exit(1); + } + } + } + + if (! newSeqP->seqLen) + { + fprintf(stderr,"? Null sequence encountered in file %s (ignored)\n",fname); + fprintf(stderr," %s\n", newSeqP->descStr); + free(newSeqP); + return ((SeqStructPtr )0); + } + + return(newSeqP); +} /* getSeq */ + + +/* for debugging. dump entire seq to stdout. */ +#ifdef DEBUG_SPUTNIK +void dumpSeq(SeqStructPtr seqP) +{ + int i, charsOnLine; + + fprintf(stdout,"%s\n", seqP->descStr); + fprintf(stdout,"Sequence (length = %d):\n", seqP->seqLen); + i = 0; + charsOnLine = 0; + while (i < seqP->seqLen) + { + if (charsOnLine == MAX_OUT_LINE_CHARS) + { + fprintf(stdout,"\n"); + charsOnLine = 1; + } + else + charsOnLine++; + fprintf(stdout,"%c", seqP->seqStr[i++]); + } + fprintf(stdout,"\n"); +} /* dumpSeq */ +#endif /* DEBUG_SPUTNIK */ + +/* dump the matched seq & stats to stdout */ +void dumpMatch(SeqStructPtr seqP, + MatchStructPtr matchP, + Boolean anyMatchThisSeq) +{ + int i, charsOnLine; + + if (! anyMatchThisSeq) + fprintf(stdout,"%s\n", seqP->descStr); + + fprintf(stdout,"%s %d : %d -- length %d score %d\n", + repeatName[matchP->testLen], + matchP->curPos+1, + matchP->testPos, + matchP->testPos - matchP->curPos, + matchP->curScore); + +#ifdef DEBUG_SPUTNIK + fprintf(stdout,"mis = %d, del = %d, ins = %d\n", + matchP->missense, + matchP->deletions, + matchP->insertions); +#endif + + i = matchP->curPos; + charsOnLine = 0; + while (i < matchP->testPos) + { + if (charsOnLine == MAX_OUT_LINE_CHARS) + { + fprintf(stdout,"\n"); + charsOnLine = 1; + } + else + charsOnLine++; + fprintf(stdout,"%c", seqP->seqStr[i++]); + } + fprintf(stdout,"\n"); + +#ifdef DEBUG_SPUTNIK + i = 0; + charsOnLine = 0; + while (i < (matchP->testPos - matchP->curPos)) + { + if (charsOnLine == MAX_OUT_LINE_CHARS) + { + fprintf(stdout,"\n"); + charsOnLine = 1; + } + else + charsOnLine++; + if (matchP->errCodes[i] == '\0') + fprintf(stdout," "); + else + fprintf(stdout,"%c", matchP->errCodes[i]); + i++; + } + fprintf(stdout,"\n"); +#endif +} /* dumpMatch */ + + +Boolean testForNRepeat(SeqStructPtr seqP, + MatchStructPtr matchP) +{ + MatchStruct curMatch, recover, bestSoFar, bestOfABadLot; + + /* save matchP in case we fail altogether. */ + copyMSPtr(&curMatch, matchP); + /* keep track of the best score and return that if over thresh. */ + copyMSPtr(&bestSoFar, matchP); + + while ( (curMatch.testPos < seqP->seqLen) /* anything to test */ + && (curMatch.curScore > MATCH_FAIL_SCORE) ) /* above fail threshold */ + { + /* test a base */ + if (seqP->seqStr[curMatch.curPos+curMatch.testCtr] + == seqP->seqStr[curMatch.testPos]) + { + /* we matched. this is easy. */ + curMatch.curScore += EXACT_MATCH_POINTS; /* score your points */ + curMatch.testPos++; /* advance the downstream test position */ + bumpTestCtr(&curMatch); /* advance pos in the (presumed) repeating seq */ + } + else if ((seqP->seqStr[curMatch.testPos] == 'N') || (seqP->seqStr[curMatch.testPos] == '-')) + { + /* don't call it wrong, but no credit either */ + curMatch.testPos++; /* advance the downstream test position */ + bumpTestCtr(&curMatch); /* advance pos in the (presumed) repeating seq */ + } + else + { + /* no match. take the score penalty, but keep going (maybe). */ + curMatch.curScore += ERROR_MATCH_POINTS; + curMatch.testPos++; /* advance the downstream test position */ + bumpTestCtr(&curMatch); /* advance pos in seq */ + /* is the score too bad to continue, or are we + already too deep? */ + if ( (curMatch.curScore > MATCH_FAIL_SCORE) + && (curMatch.depth < MAX_RECURSION) ) + { + /* try simple missense */ + copyMSPtr(&recover,&curMatch); + if ((recover.testPos - recover.curPos) < MAX_ERRCODES) + recover.errCodes[recover.testPos - recover.curPos -1] = 'M'; + recover.missense++; + recover.depth++; + (void )testForNRepeat(seqP,&recover); + copyMSPtr(&bestOfABadLot,&recover); + + /* try deletion */ + copyMSPtr(&recover,&curMatch); + if ((recover.testPos - recover.curPos) < MAX_ERRCODES) + recover.errCodes[recover.testPos - recover.curPos -1] = 'D'; + recover.testPos--; /* DON'T advance downstream */ + recover.deletions++; + recover.depth++; + (void )testForNRepeat(seqP,&recover); + if (recover.curScore > bestOfABadLot.curScore) + copyMSPtr(&bestOfABadLot,&recover); + + /* try insertion */ + copyMSPtr(&recover,&curMatch); + if ((recover.testPos - recover.curPos) < MAX_ERRCODES) + recover.errCodes[recover.testPos - recover.curPos -1] = 'I'; + /* RETEST for this base in the repeating seq */ + if (recover.testCtr == 0) + recover.testCtr = recover.testLen - 1; + else + recover.testCtr--; + recover.insertions++; + recover.depth++; + (void )testForNRepeat(seqP,&recover); + if (recover.curScore > bestOfABadLot.curScore) + copyMSPtr(&bestOfABadLot,&recover); + + /* take the best of a bad lot */ + bestOfABadLot.depth--; /* dec recursion counter */ + copyMSPtr(&curMatch, &bestOfABadLot); + } /* it was worth carrying on */ + } /* no match, found best of bad lot */ + + /* whatever happened, the best we could do is now in matchP */ + if (curMatch.curScore > bestSoFar.curScore) + copyMSPtr(&bestSoFar, &curMatch); + + } /* while loop to test a single base */ + + /* for whatever reason, we've stopped searching for more of this + putative repeat. if there were any matches that passed + the global threshold, return the best of them. note that this + has the effect of NOT advancing the pointer(s) if nothing + rang the bell. remember that we will test the same position + for ntide repeats of several different lengths. */ + if (bestSoFar.curScore > MATCH_MIN_SCORE) + { + copyMSPtr(matchP, &bestSoFar); + return(True); + } + return(False); /* the whole thing was a waste of time */ +} /* testForNRepeat */ + + +/* + * returns True if the sequence we want to look for repeats of is + * + * a) all the same base (i.e. 'AAA' or 'GG'). This filters out + * single nucleotide repeats + * + * b) conains 'N'. we search against these, but don't use them + * as wildcards. + */ +Boolean ignoreSeq(SeqStructPtr seqP, + MatchStructPtr matchP) +{ + int i; + + /* firstly, never search for any pattern that contains N */ + for (i = 0; i < matchP->testLen; i++) + if ((seqP->seqStr[matchP->curPos+i] == 'N') || (seqP->seqStr[matchP->curPos+i] == '-')) + return(True); + + /* now test for mononucleotide repeat. other tests may get + added, in which case this one will beed to be changed. */ + for (i = 1; i < matchP->testLen; i++) + if (seqP->seqStr[matchP->curPos] != seqP->seqStr[matchP->curPos+i]) + return(False); /* they're not all the same */ + return (False); /* they ARE all same:changed by Guru to allow mononucleotide repeats */ +} + + +void findRepeats(SeqStructPtr seqP) +{ + int curPos; + Boolean anyMatchThisSeq, matchAtThisPos; + MatchStruct match; + + memset( (char *)&match, 0, sizeof(MatchStruct) ); /* clear match struct */ + + anyMatchThisSeq = False; /* avoid dumping description more than once. */ + /* loop on all positions in the sequence. note that a match + will advance curPos past all matching chars to the first + unmatched char. */ + while ( match.curPos <= seqP->seqLen) + { + /* now loop on all the different lengths of repeats we're + looking for (i.e. di, tri, tetra nucleotides. if we + find a match at a shorter repeat length, forego testing + for longer lengths. */ + match.testLen = MIN_UNIT_LENGTH; + matchAtThisPos = False; + while ((match.testLen <= MAX_UNIT_LENGTH) && (!matchAtThisPos)) + { + /* initialize the state of the match */ + match.curScore = 0; /* no points yet */ + match.testCtr = 0; /* no chars tested yet */ + match.testPos = match.curPos + match.testLen; + match.insertions = 0; + match.deletions = 0; + match.missense = 0; + /* there are some things we don't want to test for */ + if (! ignoreSeq(seqP,&match)) + matchAtThisPos = testForNRepeat(seqP, &match); + else + matchAtThisPos = False; + if (! matchAtThisPos) match.testLen++; + } + + if (matchAtThisPos) + { + dumpMatch(seqP,&match,anyMatchThisSeq); + anyMatchThisSeq |= matchAtThisPos; + match.curPos = match.testPos; + } + else + match.curPos++; /* no, so advance to next base. */ + } +} + + +main(int argc, char* argv[]) +{ + SeqStructPtr seqP; + int count; + + if (argc != 2) + { + fprintf(stderr,"Usage: %s <fasta format sequence file name>\n", argv[0]); + exit(1); + } + + openFile(argv[1]); + + initBuffer(); + + count = 0; + while (! endOfFile) + if (seqP = getSeq(argv[1])) + { +#ifdef DEBUG_SPUTNIK + fprintf(stdout,"processing sequence %d\n", count++); +#endif + /* dumpSeq(seqP); */ + findRepeats(seqP); + free((void *)seqP); + } +}

1 0

[hg] galaxy 1518: Add a wrapper for metadata inside of DatasetFi...
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/0f735b21dc12 changeset: 1518:0f735b21dc12 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Sep 18 16:48:29 2008 -0400 description: Add a wrapper for metadata inside of DatasetFilenameWrapper to allow proper string substitution in commandline and templates. 2 file(s) affected in this change: lib/galaxy/datatypes/metadata.py lib/galaxy/tools/__init__.py diffs (56 lines): diff -r 1d326855ba89 -r 0f735b21dc12 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py Thu Sep 18 15:41:23 2008 -0400 +++ b/lib/galaxy/datatypes/metadata.py Thu Sep 18 16:48:29 2008 -0400 @@ -211,6 +211,9 @@ elif not isinstance(value, list): MetadataParameter.__setattr__(self, name, [value]) + def __iter__( self ): + return iter( self.value ) + def __str__(self): if self.value in [None, []]: return str(self.spec.no_value) diff -r 1d326855ba89 -r 0f735b21dc12 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Thu Sep 18 15:41:23 2008 -0400 +++ b/lib/galaxy/tools/__init__.py Thu Sep 18 16:48:29 2008 -0400 @@ -1177,6 +1177,31 @@ Wraps a dataset so that __str__ returns the filename, but all other attributes are accessible. """ + + class MetadataWrapper: + """ + Wraps a Metadata Collection to return MetadataParameters wrapped according to the metadata spec. + Methods implemented to match behavior of a Metadata Collection. + """ + def __init__( self, metadata ): + self.metadata = metadata + def __getattr__( self, name ): + rval = self.metadata.get( name, None ) + if name in self.metadata.spec: + rval = self.metadata.spec[name].wrap( rval, self.metadata.parent ) + return rval + def __nonzero__( self ): + return self.metadata.__nonzero__() + def __iter__( self ): + return self.metadata.__iter__() + def get( self, key, default=None ): + try: + return getattr( self, key ) + except: + return default + def items( self ): + return iter( [ ( k, self.get( k ) ) for k, v in self.metadata.items() ] ) + def __init__( self, dataset, datatypes_registry = None, tool = None, name = None ): if not dataset: try: @@ -1187,6 +1212,7 @@ self.dataset = NoneDataset( datatypes_registry = datatypes_registry, ext = ext ) else: self.dataset = dataset + self.metadata = self.MetadataWrapper( dataset.metadata ) def __str__( self ): return self.dataset.file_name def __getattr__( self, key ):

1 0

[hg] galaxy 1519: Update GMAJ tool interface.
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/b2a9827178e2 changeset: 1519:b2a9827178e2 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Sep 19 12:27:20 2008 -0400 description: Update GMAJ tool interface. 1 file(s) affected in this change: tools/visualization/GMAJ.xml diffs (117 lines): diff -r 0f735b21dc12 -r b2a9827178e2 tools/visualization/GMAJ.xml --- a/tools/visualization/GMAJ.xml Thu Sep 18 16:48:29 2008 -0400 +++ b/tools/visualization/GMAJ.xml Fri Sep 19 12:27:20 2008 -0400 @@ -3,7 +3,10 @@ <command interpreter="python">GMAJ.py $out_file1 $maf_input $gmaj_file $filenames_file</command> <inputs> <param name="maf_input" type="data" format="maf" label="Alignment File" optional="False"/> - <param name="refseq" label="Reference Sequence" value="" type="text" help="Leave empty to allow interactive selection."/> + <param name="refseq" label="Reference Sequence" type="select"> + <option value="first" selected="true">First sequence in each block</option> + <option value="any">Any sequence</option> + </param> <repeat name="annotations" title="Annotations"> <conditional name="annotation_style"> <param name="style" type="select" label="Annotation Style" help="If your data is not in a style similar to what is available from Galaxy (and the UCSC table browser), choose 'Basic'."> @@ -11,7 +14,7 @@ <option value="basic">Basic</option> </param> <when value="galaxy"> - <param name="species" type="select" label="Species of Annotation" multiple="False"> + <param name="species" type="select" label="Species" multiple="False"> <options> <filter type="data_meta" ref="maf_input" key="species" /> </options> @@ -21,7 +24,6 @@ <param name="underlays_file" type="data" format="bed,gff" label="Underlays File" optional="True"/> <param name="repeats_file" type="data" format="bed,gff" label="Repeats File" optional="True"/> <param name="links_file" type="data" format="bed,gff" label="Links File" optional="True"/> - <param name="offset" label="Offset" value="0" type="integer"/> </when> <when value="basic"> <param name="seq_name" label="Full Sequence Name" value="" type="text"> @@ -44,6 +46,7 @@ <option name="Skipping unsupported paragraph (maf_paragraph)" value="maf_paragraph"/> <option name="Skipping all reconstruction scores: no species specified (recon_noseq)" value="recon_noseq"/> <option name="Skipping reconstruction scores in blocks with missing row (recon_missing)" value="recon_missing"/> + <option name="The first row in some blocks is not the specified reference sequence (refseq_not_first)" value="refseq_not_first"/> <option name="Skipping extra MAF File (unused_maf)" value="unused_maf"/> </option> <option name="Annotation Files" value="annotations"> @@ -71,12 +74,15 @@ </option> <option name="Red Flags" value="red"> <option name="Sequence name in annotation file does not match name in MAF (seqname_mismatch)" value="seqname_mismatch"/> - <option name="BED Start or end < 0 (bed_coord)" value="bed_coord"/> - <option name="GFF Start or end < 1 (gff_coord)" value="gff_coord"/> + <option name="BED start or end < 0 (bed_coord)" value="bed_coord"/> + <option name="GFF start or end < 1 (gff_coord)" value="gff_coord"/> <option name="Missing item name for URL substitution (url_subst)" value="url_subst"/> </option> </option> <option name="Miscellaneous" value="miscellaneous"> + <option name="No refseq specified; assuming 'first' (default_refseq)" value="default_refseq"/> + <option name="One or more bundle entries are not used in parameters file(unused_entry)" value="unused_entry"/> + <option name="Skipping blocks for export where reference sequence is hidden or all gaps (export_skip)" value="export_skip"/> <option name="Possible parse error: token ends with an escaped quote (escaped_quote)" value="escaped_quote"/> <option name="Draggable panel dividers will not be sticky (no_sticky)" value="no_sticky"/> </option> @@ -89,11 +95,7 @@ title = "Galaxy: $maf_input.name" alignfile = input.maf -#if $refseq.value: refseq = $refseq -#else: -refseq = any -#end if tabext = .bed .gff .gtf #if $nowarn.value: nowarn = $nowarn @@ -102,36 +104,35 @@ #set $seq_count = 0 #for $annotation_count, $annotation in $enumerate( $annotations ): #if $annotation.annotation_style.style == "galaxy": -#if $maf_input.metadata.species_chromosomes and $annotation.annotation_style['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]: -#set $seq_names = [ "%s.%s" % ( $annotation.annotation_style['species'].value, $chrom ) for $chrom in $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]] -#set $aliases = [ " %s" % $chrom for $chrom in $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]] +#if $maf_input.dataset.metadata.species_chromosomes and $annotation.annotation_style['species'].value in $maf_input.dataset.metadata.species_chromosomes and $maf_input.dataset.metadata.species_chromosomes[$annotation.annotation_style['species'].value]: +#set $seq_names = [ "%s.%s" % ( $annotation.annotation_style['species'].value, $chrom ) for $chrom in $maf_input.dataset.metadata.species_chromosomes[$annotation.annotation_style['species'].value]] #else: #set $seq_names = [$annotation.annotation_style['species']] -#set $aliases = [""] #end if #else: #set $seq_names = [$annotation.annotation_style['seq_name']] -#set $aliases = [""] #end if -#for $seq_name, $alias in $zip( $seq_names, $aliases ): +#for $seq_name in $seq_names: seq ${seq_count}: seqname = $seq_name #if $annotation.annotation_style['exons_file'].dataset: -exons = ${annotation_count}.exons.${annotation.annotation_style['exons_file'].extension}$alias +exons = ${annotation_count}.exons.${annotation.annotation_style['exons_file'].extension} #end if #if $annotation.annotation_style['repeats_file'].dataset: -repeats = ${annotation_count}.repeats.${annotation.annotation_style['repeats_file'].extension}$alias +repeats = ${annotation_count}.repeats.${annotation.annotation_style['repeats_file'].extension} #end if #if $annotation.annotation_style['links_file'].dataset: -links = ${annotation_count}.links.${annotation.annotation_style['links_file'].extension}$alias +links = ${annotation_count}.links.${annotation.annotation_style['links_file'].extension} #end if #if $annotation.annotation_style['underlays_file'].dataset: -underlays = ${annotation_count}.underlays.${annotation.annotation_style['underlays_file'].extension}$alias +underlays = ${annotation_count}.underlays.${annotation.annotation_style['underlays_file'].extension} #end if #if $annotation.annotation_style['highlights_file'].dataset: -highlights = ${annotation_count}.highlights.${annotation.annotation_style['highlights_file'].extension}$alias +highlights = ${annotation_count}.highlights.${annotation.annotation_style['highlights_file'].extension} #end if +#if $annotation.annotation_style.style == "basic": offset = $annotation.annotation_style['offset'] +#end if #set $seq_count = $seq_count + 1 #end for

1 0

[hg] galaxy 1520: Fix a bug in shrimp_wrapper and add a tool for...
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/9ef55e79068b changeset: 1520:9ef55e79068b user: wychung date: Fri Sep 19 12:02:13 2008 -0400 description: Fix a bug in shrimp_wrapper and add a tool for splitting paired-end reads. Update datatype/fastqsolexa so the number of sequences is correct. 7 file(s) affected in this change: lib/galaxy/datatypes/sequence.py test-data/split_paired_reads_test1.fastq test-data/split_paired_reads_test1.out1 tool_conf.xml.sample tools/metag_tools/shrimp_wrapper.py tools/metag_tools/split_paired_reads.py tools/metag_tools/split_paired_reads.xml diffs (216 lines): diff -r 0f735b21dc12 -r 9ef55e79068b lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Thu Sep 18 16:48:29 2008 -0400 +++ b/lib/galaxy/datatypes/sequence.py Fri Sep 19 12:02:13 2008 -0400 @@ -98,8 +98,8 @@ dataset.peek = data.get_file_peek( dataset.file_name ) count = size = 0 bases_regexp = re.compile("^[NGTAC]*$") - for line in file( dataset.file_name ): - if line and line[0] == "@": + for i, line in enumerate(file( dataset.file_name )): + if line and line[0] == "@" and i % 4 == 0: count += 1 elif bases_regexp.match(line): line = line.strip() diff -r 0f735b21dc12 -r 9ef55e79068b test-data/split_paired_reads_test1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/split_paired_reads_test1.fastq Fri Sep 19 12:02:13 2008 -0400 @@ -0,0 +1,21 @@ +@HWI-EAS91_1_30788AAXX:7:21:1542:1758 +GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA ++HWI-EAS91_1_30788AAXX:7:21:1542:1758 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR +@HWI-EAS91_1_30788AAXX:7:22:1621:462 +ATAATGGCTATTATTGTGGGGGGGATGATGCTGGAAACTAGCCCCAATATCAATCCTATATCAAATCTCACC ++HWI-EAS91_1_30788AAXX:7:22:1621:462 +hhhhhhhhhhhhQAhh@hhhhNhhhfhMbCIScC?hhJhhhhChhhJhhhRhhKhePhc\KhhV\KhXhJhh +@HWI-EAS91_1_30788AAXX:7:45:408:807 +TACCCGATTTTTTGCTTTCCACTTTATCCTACCCTTATGAGTGCTAGGATCAGGATGGAGAGGATTAGGGCT ++HWI-EAS91_1_30788AAXX:7:45:408:807 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hhhZh`hhhhhRXhhYh +@HWI-EAS91_1_30788AAXX:7:49:654:1439 +CTAACTCTATTTATTGTATTTCAACTAAAAATCTCATAGGTTTATTGATAGTTGTGTTGTTGGTGTAAATGG ++HWI-EAS91_1_30788AAXX:7:49:654:1439 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhdhh_hG\XhU@ +@HWI-EAS91_1_30788AAXX:7:64:947:234 +TATCAAAAAAGAATATAATCTGAATCAACACTACAACCTATTAGTGTGTAGAATAGGAAGTAGAGGCCTGCG ++HWI-EAS91_1_30788AAXX:7:64:947:234 +hhhhhhhhhhhhhhhhhhhhhhhRhhehhahhhhhJhhhhhhhh^hPhWfhhhhThWUhhfhh_hhNIVPUd + diff -r 0f735b21dc12 -r 9ef55e79068b test-data/split_paired_reads_test1.out1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/split_paired_reads_test1.out1 Fri Sep 19 12:02:13 2008 -0400 @@ -0,0 +1,20 @@ +@HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 +GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC ++HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_30788AAXX:7:22:1621:462/1 +ATAATGGCTATTATTGTGGGGGGGATGATGCTGGAA ++HWI-EAS91_1_30788AAXX:7:22:1621:462/1 +hhhhhhhhhhhhQAhh@hhhhNhhhfhMbCIScC?h +@HWI-EAS91_1_30788AAXX:7:45:408:807/1 +TACCCGATTTTTTGCTTTCCACTTTATCCTACCCTT ++HWI-EAS91_1_30788AAXX:7:45:408:807/1 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_30788AAXX:7:49:654:1439/1 +CTAACTCTATTTATTGTATTTCAACTAAAAATCTCA ++HWI-EAS91_1_30788AAXX:7:49:654:1439/1 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_30788AAXX:7:64:947:234/1 +TATCAAAAAAGAATATAATCTGAATCAACACTACAA ++HWI-EAS91_1_30788AAXX:7:64:947:234/1 +hhhhhhhhhhhhhhhhhhhhhhhRhhehhahhhhhJ diff -r 0f735b21dc12 -r 9ef55e79068b tool_conf.xml.sample --- a/tool_conf.xml.sample Thu Sep 18 16:48:29 2008 -0400 +++ b/tool_conf.xml.sample Fri Sep 19 12:02:13 2008 -0400 @@ -274,6 +274,7 @@ <tool file="metag_tools/short_reads_figure_high_quality_length.xml" /> <tool file="metag_tools/short_reads_trim_seq.xml" /> <tool file="metag_tools/blat_coverage_report.xml" /> + <tool file="metag_tools/split_paired_reads.xml" /> </section> <section name="Short Read Mapping" id="solexa_tools"> <tool file="metag_tools/shrimp_wrapper.xml" /> diff -r 0f735b21dc12 -r 9ef55e79068b tools/metag_tools/shrimp_wrapper.py --- a/tools/metag_tools/shrimp_wrapper.py Thu Sep 18 16:48:29 2008 -0400 +++ b/tools/metag_tools/shrimp_wrapper.py Fri Sep 19 12:02:13 2008 -0400 @@ -162,6 +162,7 @@ readname, endindex = line[1:].split('/') else: score = line + if score: # the last one if hits.has_key(readname): if len(hits[readname]) == hit_per_read: @@ -182,8 +183,9 @@ match_count = 0 if hit_per_read == 1: - matches = [ hits[readkey]['1'] ] - match_count = 1 + if len(hits[readkey]['1']) == 1: + matches = [ hits[readkey]['1'] ] + match_count = 1 else: end1_data = hits[readkey]['1'] end2_data = hits[readkey]['2'] @@ -591,6 +593,7 @@ if os.path.exists(query_qual_end2): os.remove(query_qual_end2) if os.path.exists(shrimp_log): os.remove(shrimp_log) + if __name__ == '__main__': __main__() diff -r 0f735b21dc12 -r 9ef55e79068b tools/metag_tools/split_paired_reads.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/metag_tools/split_paired_reads.py Fri Sep 19 12:02:13 2008 -0400 @@ -0,0 +1,46 @@ +#! /usr/bin/python + +""" +Split Solexa paired end reads +""" + +import os, sys + +if __name__ == '__main__': + + infile = sys.argv[1] + outfile_end1 = open(sys.argv[2], 'w') + outfile_end2 = open(sys.argv[3], 'w') + + for i, line in enumerate(file(infile)): + line = line.rstrip() + if not line or line.startswith('#'): continue + + end1 = '' + end2 = '' + + line_index = i % 4 + + if line_index == 0: + end1 = line + '/1' + end2 = line + '/2' + + elif line_index == 1: + seq_len = len(line)/2 + end1 = line[0:seq_len] + end2 = line[seq_len:] + + elif line_index == 2: + end1 = line + '/1' + end2 = line + '/2' + + else: + qual_len = len(line)/2 + end1 = line[0:qual_len] + end2 = line[qual_len:] + + outfile_end1.write('%s\n' %(end1)) + outfile_end2.write('%s\n' %(end2)) + + outfile_end1.close() + outfile_end2.close() \ No newline at end of file diff -r 0f735b21dc12 -r 9ef55e79068b tools/metag_tools/split_paired_reads.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/metag_tools/split_paired_reads.xml Fri Sep 19 12:02:13 2008 -0400 @@ -0,0 +1,56 @@ +<tool id="split_paired_reads" name="Split" version="1.0.0"> + <description>paired-end reads into two ends</description> + <command interpreter="python"> + split_paired_reads.py $input $output1 $output2 + </command> + <inputs> + <param name="input" type="data" format="fastqsolexa" label="Your paired-end file" /> + </inputs> + <outputs> + <data name="output1" format="fastqsolexa"/> + <data name="output2" format="fastqsolexa"/> + </outputs> + <tests> + <test> + <param name="input" value="split_paired_reads_test1.fastq" ftype="fastqsolexa" /> + <output name="output1" file="split_paired_reads_test1.out1" fype="fastqsolexa" /> + </test> + </tests> +<help> + +**What it does** + +This tool splits a single paired-end file in half and returns two files with each ends. + +----- + +**Input formats** + +A multiple-fastq file, for example:: + + @HWI-EAS91_1_30788AAXX:7:21:1542:1758 + GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA + +HWI-EAS91_1_30788AAXX:7:21:1542:1758 + hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR + + +----- + +**Outputs** + +One end:: + + @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 + GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC + +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 + hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh + +The other end:: + + @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 + GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA + +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 + hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR + +</help> +</tool>

1 0

[hg] galaxy 1521: Merge with b2a9827178e28d93e2a978f64033a556a72...
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/618210a97e62 changeset: 1521:618210a97e62 user: wychung date: Fri Sep 19 12:34:51 2008 -0400 description: Merge with b2a9827178e28d93e2a978f64033a556a72b4c51 0 file(s) affected in this change: diffs (117 lines): diff -r 9ef55e79068b -r 618210a97e62 tools/visualization/GMAJ.xml --- a/tools/visualization/GMAJ.xml Fri Sep 19 12:02:13 2008 -0400 +++ b/tools/visualization/GMAJ.xml Fri Sep 19 12:34:51 2008 -0400 @@ -3,7 +3,10 @@ <command interpreter="python">GMAJ.py $out_file1 $maf_input $gmaj_file $filenames_file</command> <inputs> <param name="maf_input" type="data" format="maf" label="Alignment File" optional="False"/> - <param name="refseq" label="Reference Sequence" value="" type="text" help="Leave empty to allow interactive selection."/> + <param name="refseq" label="Reference Sequence" type="select"> + <option value="first" selected="true">First sequence in each block</option> + <option value="any">Any sequence</option> + </param> <repeat name="annotations" title="Annotations"> <conditional name="annotation_style"> <param name="style" type="select" label="Annotation Style" help="If your data is not in a style similar to what is available from Galaxy (and the UCSC table browser), choose 'Basic'."> @@ -11,7 +14,7 @@ <option value="basic">Basic</option> </param> <when value="galaxy"> - <param name="species" type="select" label="Species of Annotation" multiple="False"> + <param name="species" type="select" label="Species" multiple="False"> <options> <filter type="data_meta" ref="maf_input" key="species" /> </options> @@ -21,7 +24,6 @@ <param name="underlays_file" type="data" format="bed,gff" label="Underlays File" optional="True"/> <param name="repeats_file" type="data" format="bed,gff" label="Repeats File" optional="True"/> <param name="links_file" type="data" format="bed,gff" label="Links File" optional="True"/> - <param name="offset" label="Offset" value="0" type="integer"/> </when> <when value="basic"> <param name="seq_name" label="Full Sequence Name" value="" type="text"> @@ -44,6 +46,7 @@ <option name="Skipping unsupported paragraph (maf_paragraph)" value="maf_paragraph"/> <option name="Skipping all reconstruction scores: no species specified (recon_noseq)" value="recon_noseq"/> <option name="Skipping reconstruction scores in blocks with missing row (recon_missing)" value="recon_missing"/> + <option name="The first row in some blocks is not the specified reference sequence (refseq_not_first)" value="refseq_not_first"/> <option name="Skipping extra MAF File (unused_maf)" value="unused_maf"/> </option> <option name="Annotation Files" value="annotations"> @@ -71,12 +74,15 @@ </option> <option name="Red Flags" value="red"> <option name="Sequence name in annotation file does not match name in MAF (seqname_mismatch)" value="seqname_mismatch"/> - <option name="BED Start or end < 0 (bed_coord)" value="bed_coord"/> - <option name="GFF Start or end < 1 (gff_coord)" value="gff_coord"/> + <option name="BED start or end < 0 (bed_coord)" value="bed_coord"/> + <option name="GFF start or end < 1 (gff_coord)" value="gff_coord"/> <option name="Missing item name for URL substitution (url_subst)" value="url_subst"/> </option> </option> <option name="Miscellaneous" value="miscellaneous"> + <option name="No refseq specified; assuming 'first' (default_refseq)" value="default_refseq"/> + <option name="One or more bundle entries are not used in parameters file(unused_entry)" value="unused_entry"/> + <option name="Skipping blocks for export where reference sequence is hidden or all gaps (export_skip)" value="export_skip"/> <option name="Possible parse error: token ends with an escaped quote (escaped_quote)" value="escaped_quote"/> <option name="Draggable panel dividers will not be sticky (no_sticky)" value="no_sticky"/> </option> @@ -89,11 +95,7 @@ title = "Galaxy: $maf_input.name" alignfile = input.maf -#if $refseq.value: refseq = $refseq -#else: -refseq = any -#end if tabext = .bed .gff .gtf #if $nowarn.value: nowarn = $nowarn @@ -102,36 +104,35 @@ #set $seq_count = 0 #for $annotation_count, $annotation in $enumerate( $annotations ): #if $annotation.annotation_style.style == "galaxy": -#if $maf_input.metadata.species_chromosomes and $annotation.annotation_style['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]: -#set $seq_names = [ "%s.%s" % ( $annotation.annotation_style['species'].value, $chrom ) for $chrom in $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]] -#set $aliases = [ " %s" % $chrom for $chrom in $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]] +#if $maf_input.dataset.metadata.species_chromosomes and $annotation.annotation_style['species'].value in $maf_input.dataset.metadata.species_chromosomes and $maf_input.dataset.metadata.species_chromosomes[$annotation.annotation_style['species'].value]: +#set $seq_names = [ "%s.%s" % ( $annotation.annotation_style['species'].value, $chrom ) for $chrom in $maf_input.dataset.metadata.species_chromosomes[$annotation.annotation_style['species'].value]] #else: #set $seq_names = [$annotation.annotation_style['species']] -#set $aliases = [""] #end if #else: #set $seq_names = [$annotation.annotation_style['seq_name']] -#set $aliases = [""] #end if -#for $seq_name, $alias in $zip( $seq_names, $aliases ): +#for $seq_name in $seq_names: seq ${seq_count}: seqname = $seq_name #if $annotation.annotation_style['exons_file'].dataset: -exons = ${annotation_count}.exons.${annotation.annotation_style['exons_file'].extension}$alias +exons = ${annotation_count}.exons.${annotation.annotation_style['exons_file'].extension} #end if #if $annotation.annotation_style['repeats_file'].dataset: -repeats = ${annotation_count}.repeats.${annotation.annotation_style['repeats_file'].extension}$alias +repeats = ${annotation_count}.repeats.${annotation.annotation_style['repeats_file'].extension} #end if #if $annotation.annotation_style['links_file'].dataset: -links = ${annotation_count}.links.${annotation.annotation_style['links_file'].extension}$alias +links = ${annotation_count}.links.${annotation.annotation_style['links_file'].extension} #end if #if $annotation.annotation_style['underlays_file'].dataset: -underlays = ${annotation_count}.underlays.${annotation.annotation_style['underlays_file'].extension}$alias +underlays = ${annotation_count}.underlays.${annotation.annotation_style['underlays_file'].extension} #end if #if $annotation.annotation_style['highlights_file'].dataset: -highlights = ${annotation_count}.highlights.${annotation.annotation_style['highlights_file'].extension}$alias +highlights = ${annotation_count}.highlights.${annotation.annotation_style['highlights_file'].extension} #end if +#if $annotation.annotation_style.style == "basic": offset = $annotation.annotation_style['offset'] +#end if #set $seq_count = $seq_count + 1 #end for

1 0

[hg] galaxy 1522: Adding a new set of toolss to perform multiple...
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/05974294cbf1 changeset: 1522:05974294cbf1 user: guru date: Sat Sep 20 18:14:24 2008 -0400 description: Adding a new set of toolss to perform multiple linear regression analysis. 9 file(s) affected in this change: test-data/rcve_out.dat test-data/reg_inp.tab tool_conf.xml.sample tools/regVariation/best_regression_subsets.py tools/regVariation/best_regression_subsets.xml tools/regVariation/linear_regression.py tools/regVariation/linear_regression.xml tools/regVariation/rcve.py tools/regVariation/rcve.xml diffs (700 lines): diff -r 618210a97e62 -r 05974294cbf1 test-data/rcve_out.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rcve_out.dat Sat Sep 20 18:14:24 2008 -0400 @@ -0,0 +1,8 @@ +#Model R-sq RCVE_Terms RCVE_Value +2 3 4 0.3997 - - +3 4 0.3319 2 0.1697 +2 4 0.2974 3 0.2561 +2 3 0.3985 4 0.0031 +4 0.1226 2 3 0.6934 +3 0.2733 2 4 0.3164 +2 0.2972 3 4 0.2564 diff -r 618210a97e62 -r 05974294cbf1 test-data/reg_inp.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reg_inp.tab Sat Sep 20 18:14:24 2008 -0400 @@ -0,0 +1,100 @@ +2.04 2.01 1070 5 +2.56 3.40 1254 6 +3.75 3.68 1466 6 +1.10 1.54 706 4 +3.00 3.32 1160 5 +0.05 0.33 756 3 +1.38 0.36 1058 2 +1.50 1.97 1008 7 +1.38 2.03 1104 4 +4.01 2.05 1200 7 +1.50 2.13 896 7 +1.29 1.34 848 3 +1.90 1.51 958 5 +3.11 3.12 1246 6 +1.92 2.14 1106 4 +0.81 2.60 790 5 +1.01 1.90 954 4 +3.66 3.06 1500 6 +2.00 1.60 1046 5 +2.05 1.96 1054 4 +2.60 1.96 1198 6 +2.55 1.56 940 3 +0.38 1.60 456 6 +2.48 1.92 1150 7 +2.74 3.09 636 6 +1.77 0.78 744 5 +1.61 2.12 644 5 +0.99 1.85 842 3 +1.62 1.78 852 5 +2.03 1.03 1170 3 +3.50 3.44 1034 10 +3.18 2.42 1202 5 +2.39 1.74 1018 5 +1.48 1.89 1180 5 +1.54 1.43 952 3 +1.57 1.64 1038 4 +2.46 2.69 1090 6 +2.42 1.79 694 5 +2.11 2.72 1096 6 +2.04 2.15 1114 5 +1.68 2.22 1256 6 +1.64 1.55 1208 5 +2.41 2.34 820 6 +2.10 2.92 1222 4 +1.40 2.10 1120 5 +2.03 1.64 886 4 +1.99 2.83 1126 7 +2.24 1.76 1158 4 +0.45 1.81 676 6 +2.31 2.68 1214 7 +2.41 2.55 1136 6 +2.56 2.70 1264 6 +2.50 1.66 1116 3 +2.92 2.23 1292 4 +2.35 2.01 604 5 +2.82 1.24 854 6 +1.80 1.95 814 6 +1.29 1.73 778 3 +1.68 1.08 800 2 +3.44 3.46 1424 7 +1.90 3.01 950 6 +2.06 0.54 1056 3 +3.30 3.20 956 8 +1.80 1.50 1352 5 +2.00 1.71 852 5 +1.68 1.99 1168 5 +1.94 2.76 970 6 +0.97 1.56 776 4 +1.12 1.78 854 6 +1.31 1.32 1232 5 +1.68 0.87 1140 6 +3.09 1.75 1084 4 +1.87 1.41 954 2 +2.00 2.77 1000 4 +2.39 1.78 1084 4 +1.50 1.34 1058 4 +1.82 1.52 816 5 +1.80 2.97 1146 7 +2.01 1.75 1000 6 +1.88 1.64 856 4 +1.64 1.80 798 4 +2.42 3.37 1324 6 +0.22 1.15 704 6 +2.31 1.72 1222 5 +0.95 2.27 948 6 +1.99 2.85 1182 8 +1.86 2.21 1000 6 +1.79 1.94 910 6 +3.02 4.25 1374 9 +1.85 1.83 1014 6 +1.98 2.75 1420 7 +2.15 1.71 400 6 +1.46 2.20 998 7 +2.29 2.13 776 6 +2.39 2.38 1134 7 +1.80 1.64 772 4 +2.64 1.87 1304 6 +2.08 2.53 1212 4 +0.70 1.78 818 6 +0.89 1.20 864 2 \ No newline at end of file diff -r 618210a97e62 -r 05974294cbf1 tool_conf.xml.sample --- a/tool_conf.xml.sample Fri Sep 19 12:34:51 2008 -0400 +++ b/tool_conf.xml.sample Sat Sep 20 18:14:24 2008 -0400 @@ -128,6 +128,11 @@ <tool file="regVariation/getIndels_2way.xml" /> <tool file="regVariation/getIndels_3way.xml" /> <tool file="regVariation/getIndelRates_3way.xml" /> + </section> + <section name="Multiple regression" id="multReg"> + <tool file="regVariation/linear_regression.xml" /> + <tool file="regVariation/best_regression_subsets.xml" /> + <tool file="regVariation/rcve.xml" /> </section> <section name="Evolution: HyPhy" id="hyphy"> <tool file="hyphy/hyphy_branch_lengths_wrapper.xml" /> diff -r 618210a97e62 -r 05974294cbf1 tools/regVariation/best_regression_subsets.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/regVariation/best_regression_subsets.py Sat Sep 20 18:14:24 2008 -0400 @@ -0,0 +1,90 @@ +#!/usr/bin/env python + +from galaxy import eggs + +import sys, string +from rpy import * +import numpy + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit() + +infile = sys.argv[1] +y_col = int(sys.argv[2])-1 +x_cols = sys.argv[3].split(',') +outfile = sys.argv[4] +outfile2 = sys.argv[5] +print "Predictor columns: %s; Response column: %d" %(x_cols,y_col+1) +fout = open(outfile,'w') + +for i, line in enumerate( file ( infile )): + line = line.rstrip('\r\n') + if len( line )>0 and not line.startswith( '#' ): + elems = line.split( '\t' ) + break + if i == 30: + break # Hopefully we'll never get here... + +if len( elems )<1: + stop_err( "The data in your input dataset is either missing or not formatted properly." ) + +y_vals = [] +x_vals = [] + +for k,col in enumerate(x_cols): + x_cols[k] = int(col)-1 + x_vals.append([]) + +NA = 'NA' +for ind,line in enumerate( file( infile )): + if line and not line.startswith( '#' ): + try: + fields = line.split("\t") + try: + yval = float(fields[y_col]) + except Exception, ey: + yval = r('NA') + y_vals.append(yval) + for k,col in enumerate(x_cols): + try: + xval = float(fields[col]) + except Exception, ex: + xval = r('NA') + x_vals[k].append(xval) + except: + pass + +response_term = "" + +x_vals1 = numpy.asarray(x_vals).transpose() + +dat= r.list(x=array(x_vals1), y=y_vals) + +r.library("leaps") + +set_default_mode(NO_CONVERSION) +try: + leaps = r.regsubsets(r("y ~ x"), data= r.na_exclude(dat)) +except RException, rex: + stop_err("Error performing linear regression on the input data.\nEither the response column or one of the predictor columns contain no numeric values.") +set_default_mode(BASIC_CONVERSION) + +summary = r.summary(leaps) +tot = len(x_vals) +pattern = "[" +for i in range(tot): + pattern = pattern + 'c' + str(int(x_cols[int(i)]) + 1) + ' ' +pattern = pattern.strip() + ']' +print >>fout, "#Vars\t%s\tR-sq\tAdj. R-sq\tC-p\tbic" %(pattern) +for ind,item in enumerate(summary['outmat']): + print >>fout, "%s\t%s\t%s\t%s\t%s\t%s" %(str(item).count('*'), item, summary['rsq'][ind], summary['adjr2'][ind], summary['cp'][ind], summary['bic'][ind]) + + +r.pdf( outfile2, 8, 8 ) +r.plot(leaps, scale="Cp", main="Best subsets using Cp Criterion") +r.plot(leaps, scale="r2", main="Best subsets using R-sq Criterion") +r.plot(leaps, scale="adjr2", main="Best subsets using Adjusted R-sq Criterion") +r.plot(leaps, scale="bic", main="Best subsets using bic Criterion") + +r.dev_off() diff -r 618210a97e62 -r 05974294cbf1 tools/regVariation/best_regression_subsets.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/regVariation/best_regression_subsets.xml Sat Sep 20 18:14:24 2008 -0400 @@ -0,0 +1,64 @@ +<tool id="BestSubsetsRegression1" name="Perform Best-subsets Regression"> + <description> </description> + <command interpreter="python"> + best_regression_subsets.py + $input1 + $response_col + $predictor_cols + $out_file1 + $out_file2 + 1>/dev/null + 2>/dev/null + </command> + <inputs> + <param format="tabular" name="input1" type="data" label="Select data" help="Query missing? See TIP below."/> + <param name="response_col" label="Response column (Y)" type="data_column" data_ref="input1" /> + <param name="predictor_cols" label="Predictor columns (X)" type="data_column" data_ref="input1" multiple="true" /> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="input1" /> + <data format="pdf" name="out_file2" /> + </outputs> + <requirements> + <requirement type="python-module">rpy</requirement> + </requirements> + <tests> +  + </tests> + <help> + +.. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Edit Queries->Convert characters* + +----- + +.. class:: infomark + +**What it does** + +This tool uses the 'regsubsets' function from R statistical package for regression subset selection. It outputs two files, one containing a table with the best subsets and the corresponding summary statistics, and the other containing the graphical representation of the results. + +----- + +.. class:: warningmark + +**Note** + +- This tool currently treats all predictor and response variables as continuous variables. + +- Rows containing non-numeric (or missing) data in any of the chosen columns will be skipped from the analysis. + +- The 6 columns in the output are described below: + + - Column 1 (Vars): denotes the number of variables in the model + - Column 2 ([c2 c3 c4...]): represents a list of the user-selected predictor variables (full model). An asterix denotes the presence of the corresponding predictor variable in the selected model. + - Column 3 (R-sq): the fraction of variance explained by the model + - Column 4 (Adj. R-sq): the above R-squared statistic adjusted, penalizing for higher number of predictors (p) + - Column 5 (Cp): Mallow's Cp statistics + - Column 6 (bic): Bayesian Information Criterion. + + + </help> +</tool> diff -r 618210a97e62 -r 05974294cbf1 tools/regVariation/linear_regression.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/regVariation/linear_regression.py Sat Sep 20 18:14:24 2008 -0400 @@ -0,0 +1,117 @@ +#!/usr/bin/env python + +from galaxy import eggs +import sys, string +from rpy import * +import numpy + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit() + +infile = sys.argv[1] +y_col = int(sys.argv[2])-1 +x_cols = sys.argv[3].split(',') +outfile = sys.argv[4] +outfile2 = sys.argv[5] + +print "Predictor columns: %s; Response column: %d" %(x_cols,y_col+1) +fout = open(outfile,'w') + +for i, line in enumerate( file ( infile )): + line = line.rstrip('\r\n') + if len( line )>0 and not line.startswith( '#' ): + elems = line.split( '\t' ) + break + if i == 30: + break # Hopefully we'll never get here... + +if len( elems )<1: + stop_err( "The data in your input dataset is either missing or not formatted properly." ) + +y_vals = [] +x_vals = [] + +for k,col in enumerate(x_cols): + x_cols[k] = int(col)-1 + x_vals.append([]) + +NA = 'NA' +for ind,line in enumerate( file( infile )): + if line and not line.startswith( '#' ): + try: + fields = line.split("\t") + try: + yval = float(fields[y_col]) + except: + yval = r('NA') + y_vals.append(yval) + for k,col in enumerate(x_cols): + try: + xval = float(fields[col]) + except: + xval = r('NA') + x_vals[k].append(xval) + except: + pass + +x_vals1 = numpy.asarray(x_vals).transpose() + +dat= r.list(x=array(x_vals1), y=y_vals) + +set_default_mode(NO_CONVERSION) +try: + linear_model = r.lm(r("y ~ x"), data = r.na_exclude(dat)) +except RException, rex: + stop_err("Error performing linear regression on the input data.\nEither the response column or one of the predictor columns contain only non-numeric or invalid values.") +set_default_mode(BASIC_CONVERSION) + +coeffs=linear_model.as_py()['coefficients'] +yintercept= coeffs['(Intercept)'] +print >>fout, "Y-intercept\t%s" %(yintercept) +summary = r.summary(linear_model) + +co = summary.get('coefficients', 'NA') +""" +if len(co) != len(x_vals)+1: + stop_err("Stopped performing linear regression on the input data, since one of the predictor columns contains only non-numeric or invalid values.") +""" +print >>fout, "p-value (Y-intercept)\t%s" %(co[0][3]) + +if len(x_vals) == 1: #Simple linear regression case with 1 predictor variable + try: + slope = coeffs['x'] + except: + slope = 'NA' + try: + pval = co[1][3] + except: + pval = 'NA' + print >>fout, "Slope (c%d)\t%s" %(x_cols[0]+1,slope) + print >>fout, "p-value (c%d)\t%s" %(x_cols[0]+1,pval) +else: #Multiple regression case with >1 predictors + ind=1 + while ind < len(coeffs.keys()): + print >>fout, "Slope (c%d)\t%s" %(x_cols[ind-1]+1,coeffs['x'+str(ind)]) + try: + pval = co[ind][3] + except: + pval = 'NA' + print >>fout, "p-value (c%d)\t%s" %(x_cols[ind-1]+1,pval) + ind+=1 + +print >>fout, "R-squared\t%s" %(summary.get('r.squared','NA')) +print >>fout, "Adjusted R-squared\t%s" %(summary.get('adj.r.squared','NA')) +print >>fout, "F-statistic\t%s" %(summary.get('fstatistic','NA')) +print >>fout, "Sigma\t%s" %(summary.get('sigma','NA')) + +r.pdf( outfile2, 8, 8 ) +if len(x_vals) == 1: #Simple linear regression case with 1 predictor variable + sub_title = "Slope = %s; Y-int = %s" %(slope,yintercept) + r.plot(x=x_vals[0], y=y_vals, xlab="X", ylab="Y", sub=sub_title, main="Scatterplot with regression") + r.abline(a=yintercept, b=slope, col="red") +else: + r.pairs(dat, main="Scatterplot Matrix", col="blue") + +r.plot(linear_model) +r.dev_off() diff -r 618210a97e62 -r 05974294cbf1 tools/regVariation/linear_regression.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/regVariation/linear_regression.xml Sat Sep 20 18:14:24 2008 -0400 @@ -0,0 +1,62 @@ +<tool id="LinearRegression1" name="Perform Linear Regression"> + <description> </description> + <command interpreter="python"> + linear_regression.py + $input1 + $response_col + $predictor_cols + $out_file1 + $out_file2 + 1>/dev/null + </command> + <inputs> + <param format="tabular" name="input1" type="data" label="Select data" help="Query missing? See TIP below."/> + <param name="response_col" label="Response column (Y)" type="data_column" data_ref="input1" /> + <param name="predictor_cols" label="Predictor columns (X)" type="data_column" data_ref="input1" multiple="true" /> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="input1" /> + <data format="pdf" name="out_file2" /> + </outputs> + <requirements> + <requirement type="python-module">rpy</requirement> + </requirements> + <tests> +  + </tests> + <help> + + +.. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Edit Queries->Convert characters* + +----- + +.. class:: infomark + +**What it does** + +This tool uses the 'lm' function from R statistical package to perform linear regression on the input data. It outputs two files, one containing the summary statistics of the performed regression, and the other containing diagnostic plots to check whether model assumptions are satisfied. + +----- + +.. class:: warningmark + +**Note** + +- This tool currently treats all predictor and response variables as continuous variables. + +- Rows containing non-numeric (or missing) data in any of the chosen columns will be skipped from the analysis. + +- The summary statistics in the output are described below: + + - sigma: the square root of the estimated variance of the random error (standard error of the residiuals) + - R-squared: the fraction of variance explained by the model + - Adjusted R-squared: the above R-squared statistic adjusted, penalizing for the number of the predictors (p) + - p-value: p-value for the t-test of the null hypothesis that the corresponding slope is equal to zero against the two-sided alternative. + + + </help> +</tool> diff -r 618210a97e62 -r 05974294cbf1 tools/regVariation/rcve.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/regVariation/rcve.py Sat Sep 20 18:14:24 2008 -0400 @@ -0,0 +1,143 @@ +#!/usr/bin/env python + +from galaxy import eggs + +import sys, string +from rpy import * +import numpy + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit() + +def sscombs(s): + if len(s) == 1: + return [s] + else: + ssc = sscombs(s[1:]) + return [s[0]] + [s[0]+comb for comb in ssc] + ssc + + +infile = sys.argv[1] +y_col = int(sys.argv[2])-1 +x_cols = sys.argv[3].split(',') +outfile = sys.argv[4] + +print "Predictor columns: %s; Response column: %d" %(x_cols,y_col+1) +fout = open(outfile,'w') + +for i, line in enumerate( file ( infile )): + line = line.rstrip('\r\n') + if len( line )>0 and not line.startswith( '#' ): + elems = line.split( '\t' ) + break + if i == 30: + break # Hopefully we'll never get here... + +if len( elems )<1: + stop_err( "The data in your input dataset is either missing or not formatted properly." ) + +y_vals = [] +x_vals = [] + +for k,col in enumerate(x_cols): + x_cols[k] = int(col)-1 + x_vals.append([]) + """ + try: + float( elems[x_cols[k]] ) + except: + try: + msg = "This operation cannot be performed on non-numeric column %d containing value '%s'." %( col, elems[x_cols[k]] ) + except: + msg = "This operation cannot be performed on non-numeric data." + stop_err( msg ) + """ +NA = 'NA' +for ind,line in enumerate( file( infile )): + if line and not line.startswith( '#' ): + try: + fields = line.split("\t") + try: + yval = float(fields[y_col]) + except Exception, ey: + yval = r('NA') + #print >>sys.stderr, "ey = %s" %ey + y_vals.append(yval) + for k,col in enumerate(x_cols): + try: + xval = float(fields[col]) + except Exception, ex: + xval = r('NA') + #print >>sys.stderr, "ex = %s" %ex + x_vals[k].append(xval) + except: + pass + +x_vals1 = numpy.asarray(x_vals).transpose() +dat= r.list(x=array(x_vals1), y=y_vals) + +set_default_mode(NO_CONVERSION) +try: + full = r.lm(r("y ~ x"), data= r.na_exclude(dat)) #full model includes all the predictor variables specified by the user +except RException, rex: + stop_err("Error performing linear regression on the input data.\nEither the response column or one of the predictor columns contain no numeric values.") +set_default_mode(BASIC_CONVERSION) + +summary = r.summary(full) +fullr2 = summary.get('r.squared','NA') + +if fullr2 == 'NA': + stop_error("Error in linear regression") + +if len(x_vals) < 10: + s = "" + for ch in range(len(x_vals)): + s += str(ch) +else: + stop_err("This tool only works with less than 10 predictors.") + +print >>fout, "#Model\tR-sq\tRCVE_Terms\tRCVE_Value" +all_combos = sorted(sscombs(s), key=len) +all_combos.reverse() +for j,cols in enumerate(all_combos): + #if len(cols) == len(s): #Same as the full model above + # continue + if len(cols) == 1: + x_vals1 = x_vals[int(cols)] + else: + x_v = [] + for col in cols: + x_v.append(x_vals[int(col)]) + x_vals1 = numpy.asarray(x_v).transpose() + dat= r.list(x=array(x_vals1), y=y_vals) + set_default_mode(NO_CONVERSION) + red = r.lm(r("y ~ x"), data= dat) #Reduced model + set_default_mode(BASIC_CONVERSION) + summary = r.summary(red) + redr2 = summary.get('r.squared','NA') + try: + rcve = (float(fullr2)-float(redr2))/float(fullr2) + except: + rcve = 'NA' + col_str = "" + for col in cols: + col_str = col_str + str(int(x_cols[int(col)]) + 1) + " " + col_str.strip() + rcve_col_str = "" + for col in s: + if col not in cols: + rcve_col_str = rcve_col_str + str(int(x_cols[int(col)]) + 1) + " " + rcve_col_str.strip() + if len(cols) == len(s): #full model + rcve_col_str = "-" + rcve = "-" + try: + redr2 = "%.4f" %(float(redr2)) + except: + pass + try: + rcve = "%.4f" %(float(rcve)) + except: + pass + print >>fout, "%s\t%s\t%s\t%s" %(col_str,redr2,rcve_col_str,rcve) diff -r 618210a97e62 -r 05974294cbf1 tools/regVariation/rcve.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/regVariation/rcve.xml Sat Sep 20 18:14:24 2008 -0400 @@ -0,0 +1,68 @@ +<tool id="rcve1" name="Compute RCVE" version="1.0.0"> + <description> </description> + <command interpreter="python"> + rcve.py + $input1 + $response_col + $predictor_cols + $out_file1 + 1>/dev/null + </command> + <inputs> + <param format="tabular" name="input1" type="data" label="Select data" help="Query missing? See TIP below."/> + <param name="response_col" label="Response column (Y)" type="data_column" data_ref="input1" /> + <param name="predictor_cols" label="Predictor columns (X)" type="data_column" data_ref="input1" multiple="true" /> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="input1" /> + </outputs> + <requirements> + <requirement type="python-module">rpy</requirement> + </requirements> + <tests> +  + <test> + <param name="input1" value="reg_inp.tab"/> + <param name="response_col" value="1"/> + <param name="predictor_cols" value="2,3,4"/> + <output name="out_file1" file="rcve_out.dat"/> + </test> + + </tests> + <help> + +.. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Edit Queries->Convert characters* + +----- + +.. class:: infomark + +**What it does** + +This tool computes the RCVE (Relative Contribution to Variance) for all possible variable subsets using the following formula: + +**RCVE(i) = [R-sq (full: 1,2,..,i..,p-1) - R-sq(without i: 1,2,...,p-1)] / R-sq (full: 1,2,..,i..,p-1)**, +which denotes the case where the 'i'th predictor is dropped. + + +In general, +**RCVE(X+) = [R-sq (full: {X,X+}) - R-sq(reduced: {X})] / R-sq (full: {X,X+})**, +where, + +- {X,X+} denotes the set of all predictors, +- X+ is the set of predictors for which we compute RCVE (and therefore drop from the full model to obtain a reduced one), +- {X} is the set of the predictors that are left in the reduced model after excluding {X+} + + +The 4 columns in the output are described below: + +- Column 1 (Model): denotes the variables present in the model ({X}) +- Column 2 (R-sq): denotes the R-squared value corresponding to the model in Column 1 +- Column 3 (RCVE_Terms): denotes the variable/s for which RCVE is computed ({X+}). These are the variables that are absent in the reduced model in Column 1. A '-' in this column indicates that the model in Column 1 is the Full model. +- Column 4 (RCVE): denotes the RCVE value corresponding to the variable/s in Column 3. A '-' in this column indicates that the model in Column 1 is the Full model. + + + </help> +</tool>

1 0

[hg] galaxy 1523: Adding tools to compute Substitution rates.
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/dabed25dfbaf changeset: 1523:dabed25dfbaf user: guru date: Sun Sep 21 17:36:28 2008 -0400 description: Adding tools to compute Substitution rates. 7 file(s) affected in this change: test-data/subRates1.out test-data/subs.out tool_conf.xml.sample tools/regVariation/substitution_rates.py tools/regVariation/substitution_rates.xml tools/regVariation/substitutions.py tools/regVariation/substitutions.xml diffs (1734 lines): diff -r 05974294cbf1 -r dabed25dfbaf test-data/subRates1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subRates1.out Sun Sep 21 17:36:28 2008 -0400 @@ -0,0 +1,13 @@ +#Seq1 Start1 End1 Seq2 Start2 End2 L N p +hg17.chrX 3816458 3816983 fr1.chrUn 343715247 343715776 525 188 0.3581 +hg17.chrX 3795168 3795525 fr1.chrUn 343710815 343711179 357 92 0.2577 +hg17.chrX 3787425 3787599 fr1.chrUn 343708230 343708404 174 37 0.2126 +hg17.chrX 3787284 3787384 fr1.chrUn 62078707 62078816 100 33 0.3300 +hg17.chrX 3776942 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333536475 +hg17.chrX 3639563 3639564 +fr1.chrUn 333536480 333536481 +hg17.chrX 3639572 3639572 +fr1.chrUn 333536489 333536489 +hg17.chrX 3639576 3639577 +fr1.chrUn 333536493 333536494 +hg17.chrX 3639579 3639579 +fr1.chrUn 333536496 333536496 +hg17.chrX 3639588 3639588 +fr1.chrUn 333536505 333536505 +hg17.chrX 3639592 3639592 +fr1.chrUn 333536509 333536509 +hg17.chrX 3639598 3639598 +fr1.chrUn 333536515 333536515 +hg17.chrX 3639600 3639600 +fr1.chrUn 333536517 333536517 +hg17.chrX 3639603 3639603 +fr1.chrUn 333536520 333536520 +hg17.chrX 3639606 3639606 +fr1.chrUn 333536523 333536523 +hg17.chrX 3639612 3639612 +fr1.chrUn 333536529 333536529 +hg17.chrX 3639615 3639615 +fr1.chrUn 333536532 333536532 +hg17.chrX 3639622 3639622 +fr1.chrUn 333536539 333536539 +hg17.chrX 3639642 3639642 +fr1.chrUn 333536559 333536559 diff -r 05974294cbf1 -r dabed25dfbaf tool_conf.xml.sample --- a/tool_conf.xml.sample Sat Sep 20 18:14:24 2008 -0400 +++ b/tool_conf.xml.sample Sun Sep 21 17:36:28 2008 -0400 @@ -128,6 +128,8 @@ <tool file="regVariation/getIndels_2way.xml" /> <tool file="regVariation/getIndels_3way.xml" /> <tool file="regVariation/getIndelRates_3way.xml" /> + <tool file="regVariation/substitutions.xml" /> + <tool file="regVariation/substitution_rates.xml" /> </section> <section name="Multiple regression" id="multReg"> <tool file="regVariation/linear_regression.xml" /> diff -r 05974294cbf1 -r dabed25dfbaf tools/regVariation/substitution_rates.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/regVariation/substitution_rates.py Sun Sep 21 17:36:28 2008 -0400 @@ -0,0 +1,118 @@ +#! /usr/bin/python +#guruprasad Ananda +""" +Estimates substitution rates from pairwise alignments using JC69 model. +""" + +from galaxy import eggs +from galaxy.tools.util.galaxyops import * +from galaxy.tools.util import maf_utilities +import bx.align.maf +import sys, fileinput + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit() + +if len(sys.argv) < 3: + stop_err("Incorrect number of arguments.") + +inp_file = sys.argv[1] +out_file = sys.argv[2] +fout = open(out_file, 'w') +int_file = sys.argv[3] +if int_file != "None": #The user has specified an interval file + dbkey_i = sys.argv[4] + chr_col_i, start_col_i, end_col_i, strand_col_i = parse_cols_arg( sys.argv[5] ) + + +def rateEstimator(block): + global alignlen, mismatches + + src1 = block.components[0].src + sequence1 = block.components[0].text + start1 = block.components[0].start + end1 = block.components[0].end + len1 = int(end1)-int(start1) + len1_withgap = len(sequence1) + mismatch = 0.0 + + for seq in range (1,len(block.components)): + src2 = block.components[seq].src + sequence2 = block.components[seq].text + start2 = block.components[seq].start + end2 = block.components[seq].end + len2 = int(end2)-int(start2) + for nt in range(len1_withgap): + if sequence1[nt] not in '-#$^*?' and sequence2[nt] not in '-#$^*?': #Not a gap or masked character + if sequence1[nt].upper() != sequence2[nt].upper(): + mismatch += 1 + + if int_file == "None": + p = mismatch/min(len1,len2) + print >>fout, "%s\t%s\t%s\t%s\t%s\t%s\t%d\t%d\t%.4f" %(src1,start1,end1,src2,start2,end2,min(len1,len2),mismatch,p) + else: + mismatches += mismatch + alignlen += min(len1,len2) + +def main(): + skipped = 0 + not_pairwise = 0 + + if int_file == "None": + try: + maf_reader = bx.align.maf.Reader( open(inp_file, 'r') ) + except: + stop_err("Your MAF file appears to be malformed.") + print >>fout, "#Seq1\tStart1\tEnd1\tSeq2\tStart2\tEnd2\tL\tN\tp" + for block in maf_reader: + if len(block.components) != 2: + not_pairwise += 1 + continue + try: + rateEstimator(block) + except: + skipped += 1 + else: + index, index_filename = maf_utilities.build_maf_index( inp_file, species = [dbkey_i] ) + if index is None: + print >> sys.stderr, "Your MAF file appears to be malformed." + sys.exit() + win = NiceReaderWrapper( fileinput.FileInput( int_file ), + chrom_col=chr_col_i, + start_col=start_col_i, + end_col=end_col_i, + strand_col=strand_col_i, + fix_strand=True) + species=None + mincols = 0 + global alignlen, mismatches + + for interval in win: + alignlen = 0 + mismatches = 0.0 + src = "%s.%s" % ( dbkey_i, interval.chrom ) + for block in maf_utilities.get_chopped_blocks_for_region( index, src, interval, species, mincols ): + if len(block.components) != 2: + not_pairwise += 1 + continue + try: + rateEstimator(block) + except: + skipped += 1 + if alignlen: + p = mismatches/alignlen + else: + p = 'NA' + interval.fields.append(str(alignlen)) + interval.fields.append(str(mismatches)) + interval.fields.append(str(p)) + print >>fout, "\t".join(interval.fields) + #num_blocks += 1 + + if not_pairwise: + print "Skipped %d non-pairwise blocks" %(not_pairwise) + if skipped: + print "Skipped %d blocks as invalid" %(skipped) +if __name__ == "__main__": + main() diff -r 05974294cbf1 -r dabed25dfbaf tools/regVariation/substitution_rates.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/regVariation/substitution_rates.xml Sun Sep 21 17:36:28 2008 -0400 @@ -0,0 +1,61 @@ +<tool id="subRate1" name="Estimate substitution rates " version="1.0.0"> + <description> for non-coding regions</description> + <command interpreter="python"> + substitution_rates.py + $input + $out_file1 + #if $region.type == "win": + ${region.input2} ${region.input2.dbkey} ${region.input2.metadata.chromCol},$region.input2.metadata.startCol,$region.input2.metadata.endCol,$region.input2.metadata.strandCol + #else: + "None" + #end if + </command> + <inputs> + <param format="maf" name="input" type="data" label="Select pair-wise alignment data"/> + <conditional name="region"> + <param name="type" type="select" label="Estimate rates corresponding to" multiple="false"> + <option value="align">Alignment block</option> + <option value="win">Intervals in your history</option> + </param> + <when value="win"> + <param format="interval" name="input2" type="data" label="Choose intervals"> + <validator type="unspecified_build" /> + </param> + </when> + <when value="align" /> + </conditional> + </inputs> + <outputs> + <data format="tabular" name="out_file1" metadata_source="input"/> + </outputs> + + <tests> + <test> + <param name="input" value="Interval2Maf_pairwise_out.maf"/> + <param name="type" value="align"/> + <output name="out_file1" file="subRates1.out"/> + </test> + </tests> + + <help> + +.. class:: infomark + +**What it does** + +This tool takes a pairwise MAF file as input and estimates substitution rate according to Jukes-Cantor JC69 model. The 3 new columns appended to the output are explanied below: + +- L: number of nucleotides compared +- N: number of different nucleotides +- p = N/L + +----- + +.. class:: warningmark + +**Note** + +Any block/s not containing exactly two sequences, will be omitted. + + </help> +</tool> \ No newline at end of file diff -r 05974294cbf1 -r dabed25dfbaf tools/regVariation/substitutions.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/regVariation/substitutions.py Sun Sep 21 17:36:28 2008 -0400 @@ -0,0 +1,87 @@ +#! /usr/bin/python +#Guruprasad ANanda +""" +Fetches substitutions from pairwise alignments. +""" + +from galaxy import eggs + +from galaxy.tools.util import maf_utilities + +import bx.align.maf +import sys +import os, fileinput +def stop_err(msg): + sys.stderr.write(msg) + sys.exit() + +if len(sys.argv) < 3: + stop_err("Incorrect number of arguments.") + +inp_file = sys.argv[1] +out_file = sys.argv[2] +fout = open(out_file, 'w') + +def fetchSubs(block): + + src1 = block.components[0].src + sequence1 = block.components[0].text + start1 = block.components[0].start + end1 = block.components[0].end + len1 = int(end1)-int(start1) + len1_withgap = len(sequence1) + + for seq in range (1,len(block.components)): + src2 = block.components[seq].src + sequence2 = block.components[seq].text + start2 = block.components[seq].start + end2 = block.components[seq].end + len2 = int(end2)-int(start2) + sub_begin = None + sub_end = None + begin = False + + for nt in range(len1_withgap): + if sequence1[nt] not in '-#$^*?' and sequence2[nt] not in '-#$^*?': #Not a gap or masked character + if sequence1[nt].upper() != sequence2[nt].upper(): + if not(begin): + sub_begin = nt + begin = True + sub_end = nt + else: + if begin: + print >>fout, "%s\t%s\t%s" %(src1,start1+sub_begin-sequence1[0:sub_begin].count('-'),start1+sub_end-sequence1[0:sub_end].count('-')) + print >>fout, "%s\t%s\t%s" %(src2,start2+sub_begin-sequence2[0:sub_begin].count('-'),start2+sub_end-sequence2[0:sub_end].count('-')) + begin = False + + else: + if begin: + print >>fout, "%s\t%s\t%s" %(src1,start1+sub_begin-sequence1[0:sub_begin].count('-'),end1+sub_end-sequence1[0:sub_end].count('-')) + print >>fout, "%s\t%s\t%s" %(src2,start2+sub_begin-sequence2[0:sub_begin].count('-'),end2+sub_end-sequence2[0:sub_end].count('-')) + begin = False + ended = False + + +def main(): + skipped = 0 + not_pairwise = 0 + try: + maf_reader = bx.align.maf.Reader( open(inp_file, 'r') ) + except: + stop_err("Your MAF file appears to be malformed.") + print >>fout, "#Chr\tStart\tEnd" + for block in maf_reader: + if len(block.components) != 2: + not_pairwise += 1 + continue + try: + fetchSubs(block) + except: + skipped += 1 + + if not_pairwise: + print "Skipped %d non-pairwise blocks" %(not_pairwise) + if skipped: + print "Skipped %d blocks" %(skipped) +if __name__ == "__main__": + main() diff -r 05974294cbf1 -r dabed25dfbaf tools/regVariation/substitutions.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/regVariation/substitutions.xml Sun Sep 21 17:36:28 2008 -0400 @@ -0,0 +1,38 @@ +<tool id="substitutions1" name="Fetch substitutions " version="1.0.0"> + <description> from pairwise alignments</description> + <command interpreter="python"> + substitutions.py + $input + $out_file1 + </command> + <inputs> + <param format="maf" name="input" type="data" label="Select pair-wise alignment data"/> + </inputs> + <outputs> + <data format="tabular" name="out_file1" metadata_source="input"/> + </outputs> + + <tests> + <test> + <param name="input" value="Interval2Maf_pairwise_out.maf"/> + <output name="out_file1" file="subs.out"/> + </test> + </tests> + <help> + +.. class:: infomark + +**What it does** + +This tool takes a pairwise MAF file as input and fetches substitutions per alignment block. + +----- + +.. class:: warningmark + +**Note** + +Any block/s not containing exactly two sequences, will be omitted. + + </help> +</tool> \ No newline at end of file

1 0

[hg] galaxy 1507: add SHRiMP mapper for short reads analysis.
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/842f1883cf53 changeset: 1507:842f1883cf53 user: wychung date: Mon Sep 15 15:04:41 2008 -0400 description: add SHRiMP mapper for short reads analysis. 6 file(s) affected in this change: test-data/shrimp_phix_anc.fa test-data/shrimp_wrapper_test1.fastq test-data/shrimp_wrapper_test1.out1 tool_conf.xml.sample tools/metag_tools/shrimp_wrapper.py tools/metag_tools/shrimp_wrapper.xml diffs (853 lines): diff -r 26825f08d362 -r 842f1883cf53 test-data/shrimp_phix_anc.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/shrimp_phix_anc.fa Mon Sep 15 15:04:41 2008 -0400 @@ -0,0 +1,2 @@ +>PHIX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTT GAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCG CGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTC TTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATG CCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTT GTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA diff -r 26825f08d362 -r 842f1883cf53 test-data/shrimp_wrapper_test1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/shrimp_wrapper_test1.fastq Mon Sep 15 15:04:41 2008 -0400 @@ -0,0 +1,40 @@ +@HWI-EAS91_1_306UPAAXX:6:1:959:874 +GCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCG ++HWI-EAS91_1_306UPAAXX:6:1:959:874 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_306UPAAXX:6:1:1630:1975 +GAAAGAAAATCAGCAACAGTGGCATCGATTTTACGG ++HWI-EAS91_1_306UPAAXX:6:1:1630:1975 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_306UPAAXX:6:1:770:994 +GCAGGCAGCGTGCTGCGAGTCTTTTCGAATGATAAG ++HWI-EAS91_1_306UPAAXX:6:1:770:994 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_306UPAAXX:6:1:1274:306 +GTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGC ++HWI-EAS91_1_306UPAAXX:6:1:1274:306 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh\h +@HWI-EAS91_1_306UPAAXX:6:1:1339:209 +GTTTGGTCAGTTCCATCAACATCATAGCCAGATGCC ++HWI-EAS91_1_306UPAAXX:6:1:1339:209 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_306UPAAXX:6:1:203:1240 +GATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTA ++HWI-EAS91_1_306UPAAXX:6:1:203:1240 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_306UPAAXX:6:1:869:448 +GCTGGCCATCAGTTCGCGGATACCGGCGGCAAACAT ++HWI-EAS91_1_306UPAAXX:6:1:869:448 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhKhhhhhhh +@HWI-EAS91_1_306UPAAXX:6:1:939:928 +GGAGGCCTCCAGCAATCTTGAACACTCATCCTTAAT ++HWI-EAS91_1_306UPAAXX:6:1:939:928 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_306UPAAXX:6:1:1756:1476 +GCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGC ++HWI-EAS91_1_306UPAAXX:6:1:1756:1476 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_306UPAAXX:6:1:1528:181 +GGCTGGTCAGTATTTTACCAATGACCAAATCAAAGA ++HWI-EAS91_1_306UPAAXX:6:1:1528:181 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh diff -r 26825f08d362 -r 842f1883cf53 test-data/shrimp_wrapper_test1.out1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/shrimp_wrapper_test1.out1 Mon Sep 15 15:04:41 2008 -0400 @@ -0,0 +1,7 @@ +#FORMAT: readname contigname strand contigstart contigend readstart readend readlength score editstring +>HWI-EAS91_1_306UPAAXX:6:1:1528:181 PHIX174 + 3644 3679 1 36 36 3600 36 +>HWI-EAS91_1_306UPAAXX:6:1:1756:1476 PHIX174 + 4505 4540 1 36 36 3600 36 +>HWI-EAS91_1_306UPAAXX:6:1:203:1240 PHIX174 + 310 345 1 36 36 3600 36 +>HWI-EAS91_1_306UPAAXX:6:1:1274:306 PHIX174 + 933 968 1 36 36 3600 36 +>HWI-EAS91_1_306UPAAXX:6:1:939:928 PHIX174 - 4458 4493 1 36 36 3600 36 +>HWI-EAS91_1_306UPAAXX:6:1:1339:209 PHIX174 - 1732 1767 1 36 36 3600 36 diff -r 26825f08d362 -r 842f1883cf53 tool_conf.xml.sample --- a/tool_conf.xml.sample Sun Sep 14 14:58:50 2008 -0400 +++ b/tool_conf.xml.sample Mon Sep 15 15:04:41 2008 -0400 @@ -276,6 +276,7 @@ <tool file="metag_tools/blat_coverage_report.xml" /> </section> <section name="Short Read Mapping" id="solexa_tools"> + <tool file="metag_tools/shrimp_wrapper.xml" /> <tool file="sr_mapping/lastz_wrapper.xml" /> <tool file="metag_tools/megablast_wrapper.xml" /> <tool file="metag_tools/megablast_xml_parser.xml" /> diff -r 26825f08d362 -r 842f1883cf53 tools/metag_tools/shrimp_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/metag_tools/shrimp_wrapper.py Mon Sep 15 15:04:41 2008 -0400 @@ -0,0 +1,577 @@ +#! /usr/bin/python + +""" +SHRiMP wrapper + +Inputs: + reference seq and reads + +Outputs: + table of 8 columns: + chrom ref_loc read_id read_loc ref_nuc read_nuc quality coverage + SHRiMP output + +Parameters: + -s Spaced Seed (default: 111111011111) + -n Seed Matches per Window (default: 2) + -t Seed Hit Taboo Length (default: 4) + -9 Seed Generation Taboo Length (default: 0) + -w Seed Window Length (default: 115.00%) + -o Maximum Hits per Read (default: 100) + -r Maximum Read Length (default: 1000) + -d Kmer Std. Deviation Limit (default: -1 [None]) + + -m S-W Match Value (default: 100) + -i S-W Mismatch Value (default: -150) + -g S-W Gap Open Penalty (Reference) (default: -400) + -q S-W Gap Open Penalty (Query) (default: -400) + -e S-W Gap Extend Penalty (Reference) (default: -70) + -f S-W Gap Extend Penalty (Query) (default: -70) + -h S-W Hit Threshold (default: 68.00%) + +Command: +%rmapper -s spaced_seed -n seed_matches_per_window -t seed_hit_taboo_length -9 seed_generation_taboo_length -w seed_window_length -o max_hits_per_read -r max_read_length -d kmer -m sw_match_value -i sw_mismatch_value -g sw_gap_open_ref -q sw_gap_open_query -e sw_gap_ext_ref -f sw_gap_ext_query -h sw_hit_threshold <query> <target> > <output> 2> <log> + +SHRiMP output: +>7:2:1147:982/1 chr3 + 36586562 36586595 2 35 36 2900 3G16G13 +>7:2:1147:982/1 chr3 + 95338194 95338225 4 35 36 2700 9T7C14 +>7:2:587:93/1 chr3 + 14913541 14913577 1 35 36 2960 19--16 + +Testing: +%python shrimp_wrapper.py single ~/Desktop/shrimp_wrapper/phix_anc.fa tmp tmp1 ~/Desktop/shrimp_wrapper/phix.10.solexa.fastq +%python shrimp_wrapper.py paired ~/Desktop/shrimp_wrapper/eca_ref_chrMT.fa tmp tmp1 ~/Desktop/shrimp_wrapper/eca.5.solexa_1.fastq ~/Desktop/shrimp_wrapper/eca.5.solexa_2.fastq + +""" + +import os, sys, tempfile, os.path + +assert sys.version_info[:2] >= (2.4) + +def stop_err( msg ): + + sys.stderr.write( "%s\n" % msg ) + sys.exit() + +def reverse_complement(s): + + complement_dna = {"A":"T", "T":"A", "C":"G", "G":"C", "a":"t", "t":"a", "c":"g", "g":"c", "N":"N", "n":"n" , ".":".", "-":"-"} + reversed_s = [] + for i in s: + reversed_s.append(complement_dna[i]) + reversed_s.reverse() + return "".join(reversed_s) + +def generate_sub_table(result_file, ref_file, score_files, table_outfile, hit_per_read): + + """ + TODO: the cross-over error has not been addressed yet. + """ + + insertion_size = 600 + + all_score_file = score_files.split('&') + + if len(all_score_file) != hit_per_read: stop_err('Un-equal number of files!') + + temp_table_name = tempfile.NamedTemporaryFile().name + temp_table = open(temp_table_name, 'w') + + outfile = open(table_outfile,'w') + + # reference seq: not a single fasta seq + refseq = {} + chrom_cov = {} + seq = '' + + for i, line in enumerate(file(ref_file)): + line = line.rstrip() + if not line or line.startswith('#'): continue + + if line.startswith('>'): + if seq: + if refseq.has_key(title): + pass + else: + refseq[title] = seq + chrom_cov[title] = {} + seq = '' + title = line[1:] + else: + seq += line + if seq: + if not refseq.has_key(title): + refseq[title] = seq + chrom_cov[title] = {} + + # find hits : one end and/or the other + hits = {} + for i, line in enumerate(file(result_file)): + line = line.rstrip() + if not line or line.startswith('#'): continue + + #FORMAT: readname contigname strand contigstart contigend readstart readend readlength score editstring + fields = line.split('\t') + readname = fields[0][1:] + chrom = fields[1] + strand = fields[2] + chrom_start = int(fields[3]) - 1 + chrom_end = int(fields[4]) + read_start = fields[5] + read_end = fields[6] + read_len = fields[7] + score = fields[8] + editstring = fields[9] + + if hit_per_read == 1: + endindex = '1' + else: + readname, endindex = readname.split('/') + + if hits.has_key(readname): + if hits[readname].has_key(endindex): + hits[readname][endindex].append([strand, editstring, chrom_start, chrom_end, read_start, chrom]) + else: + hits[readname][endindex] = [[strand, editstring, chrom_start, chrom_end, read_start, chrom]] + else: + hits[readname] = {} + hits[readname][endindex] = [[strand, editstring, chrom_start, chrom_end, read_start, chrom]] + + # find score : one end and the other end + hits_score = {} + readname = '' + score = '' + for num_score_file in range(len(all_score_file)): + score_file = all_score_file[num_score_file] + for i, line in enumerate(file(score_file)): + line = line.rstrip() + if not line or line.startswith('#'): continue + + if line.startswith('>'): + if score: + if hits.has_key(readname): + if len(hits[readname]) == hit_per_read: + if hits_score.has_key(readname): + if hits_score[readname].has_key(endindex): + pass + else: + hits_score[readname][endindex] = score + else: + hits_score[readname] = {} + hits_score[readname][endindex] = score + score = '' + if hit_per_read == 1: + readname = line[1:] + endindex = '1' + else: + readname, endindex = line[1:].split('/') + else: + score = line + if score: # the last one + if hits.has_key(readname): + if len(hits[readname]) == hit_per_read: + if hits_score.has_key(readname): + if hits_score[readname].has_key(endindex): + pass + else: + hits_score[readname][endindex] = score + else: + hits_score[readname] = {} + hits_score[readname][endindex] = score + + # mutation call to all mappings + for readkey in hits.keys(): + if len(hits[readkey]) != hit_per_read: continue + + matches = [] + match_count = 0 + + if hit_per_read == 1: + matches = [ hits[readkey]['1'] ] + match_count = 1 + else: + end1_data = hits[readkey]['1'] + end2_data = hits[readkey]['2'] + + for i, end1_hit in enumerate(end1_data): + crin_strand = {'+': False, '-': False} + crin_insertSize = {'+': False, '-': False} + + crin_strand[end1_hit[0]] = True + crin_insertSize[end1_hit[0]] = int(end1_hit[2]) + + for j, end2_hit in enumerate(end2_data): + crin_strand[end2_hit[0]] = True + crin_insertSize[end2_hit[0]] = int(end2_hit[2]) + + if end1_hit[-1] != end2_hit[-1] : continue + + if crin_strand['+'] and crin_strand['-']: + if (crin_insertSize['-'] - crin_insertSize['+']) <= insertion_size: + matches.append([end1_hit, end2_hit]) + match_count += 1 + + if match_count == 1: + for x, end_data in enumerate(matches[0]): + + end_strand, end_editstring, end_chr_start, end_chr_end, end_read_start, end_chrom = end_data + end_read_start = int(end_read_start) - 1 + + if end_strand == '-': + refsegment = reverse_complement(refseq[end_chrom][end_chr_start:end_chr_end]) + else: + refsegment = refseq[end_chrom][end_chr_start:end_chr_end] + + match_len = 0 + editindex = 0 + gap_read = 0 + + while editindex < len(end_editstring): + editchr = end_editstring[editindex] + chrA = '' + chrB = '' + locIndex = [] + if editchr.isdigit(): + editcode = '' + while editchr.isdigit() and editindex < len(end_editstring): + editcode += editchr + editindex += 1 + if editindex < len(end_editstring): editchr = end_editstring[editindex] + for baseIndex in range(int(editcode)): + chrA += refsegment[match_len+baseIndex] + chrB = chrA + match_len += int(editcode) + elif editchr == 'x': + # crossover: inserted between the appropriate two bases + # Two sequencing errors: 4x15x6 (25 matches with 2 crossovers) + # Treated as errors in the reads; Do nothing. + editindex += 1 + + elif editchr.isalpha(): + editcode = editchr + editindex += 1 + chrA = refsegment[match_len] + chrB = editcode + match_len += len(editcode) + + elif editchr == '-': + editcode = editchr + editindex += 1 + chrA = refsegment[match_len] + chrB = editcode + match_len += len(editcode) + gap_read += 1 + + elif editchr == '(': + editcode = '' + while editchr != ')' and editindex < len(end_editstring): + if editindex < len(end_editstring): editchr = end_editstring[editindex] + editcode += editchr + editindex += 1 + editcode = editcode[1:-1] + chrA = '-'*len(editcode) + chrB = editcode + + else: + print 'Warning! Unknown symbols', editchr + + if end_strand == '-': + chrA = reverse_complement(chrA) + chrB = reverse_complement(chrB) + + pos_line = '' + rev_line = '' + + for mappingIndex in range(len(chrA)): + # reference + chrAx = chrA[mappingIndex] + # read + chrBx = chrB[mappingIndex] + + if chrAx and chrBx and chrBx.upper() != 'N': + if end_strand == '+': + chrom_loc = end_chr_start+match_len-len(chrA)+mappingIndex + read_loc = end_read_start+match_len-len(chrA)+mappingIndex-gap_read + if chrAx == '-': chrom_loc -= 1 + + if chrBx == '-': + scoreBx = '-1' + else: + scoreBx = hits_score[readkey][str(x+1)].split()[read_loc] + + # 1-based on chrom_loc and read_loc + pos_line = pos_line + '\t'.join([end_chrom, str(chrom_loc+1), readkey+'/'+str(x+1), str(read_loc+1), chrAx, chrBx, scoreBx]) + '\n' + else: + chrom_loc = end_chr_end-match_len+mappingIndex + read_loc = end_read_start+match_len-1-mappingIndex-gap_read + if chrAx == '-': chrom_loc -= 1 + + if chrBx == '-': + scoreBx = '-1' + else: + scoreBx = hits_score[readkey][str(x+1)].split()[read_loc] + + # 1-based on chrom_loc and read_loc + rev_line = '\t'.join([end_chrom, str(chrom_loc+1), readkey+'/'+str(x+1), str(read_loc+1), chrAx, chrBx, scoreBx]) +'\n' + rev_line + + if chrom_cov.has_key(end_chrom): + if chrom_cov[end_chrom].has_key(chrom_loc): + chrom_cov[end_chrom][chrom_loc] += 1 + else: + chrom_cov[end_chrom][chrom_loc] = 1 + else: + chrom_cov[end_chrom] = {} + chrom_cov[end_chrom][chrom_loc] = 1 + + if pos_line: temp_table.write('%s\n' %(pos_line.rstrip('\r\n'))) + if rev_line: temp_table.write('%s\n' %(rev_line.rstrip('\r\n'))) + + temp_table.close() + + # chrom-wide coverage + for i, line in enumerate(open(temp_table_name)): + line = line.rstrip() + if not line or line.startswith('#'): continue + + fields = line.split() + chrom = fields[0] + eachBp = int(fields[1]) + readname = fields[2] + + if hit_per_read == 1: + fields[2] = readname.split('/')[0] + + if chrom_cov[chrom].has_key(eachBp): + outfile.write('%s\t%d\n' %('\t'.join(fields), chrom_cov[chrom][eachBp])) + else: + outfile.write('%s\t%d\n' %('\t'.join(fields), 0)) + + outfile.close() + + if os.path.exists(temp_table_name): os.remove(temp_table_name) + + return True + +def convert_fastqsolexa_to_fasta_qual(infile_name, query_fasta, query_qual): + + outfile_seq = open( query_fasta, 'w' ) + outfile_score = open( query_qual, 'w' ) + + seq_title_startswith = '' + qual_title_startswith = '' + + default_coding_value = 64 + fastq_block_lines = 0 + + for i, line in enumerate( file( infile_name ) ): + line = line.rstrip() + if not line or line.startswith( '#' ): continue + + fastq_block_lines = ( fastq_block_lines + 1 ) % 4 + line_startswith = line[0:1] + + if fastq_block_lines == 1: + # first line is @title_of_seq + if not seq_title_startswith: + seq_title_startswith = line_startswith + + if line_startswith != seq_title_startswith: + outfile_seq.close() + outfile_score.close() + stop_err( 'Invalid fastqsolexa format at line %d: %s.' % ( i + 1, line ) ) + + read_title = line[1:] + outfile_seq.write( '>%s\n' % line[1:] ) + + elif fastq_block_lines == 2: + # second line is nucleotides + read_length = len( line ) + outfile_seq.write( '%s\n' % line ) + + elif fastq_block_lines == 3: + # third line is +title_of_qualityscore ( might be skipped ) + if not qual_title_startswith: + qual_title_startswith = line_startswith + + if line_startswith != qual_title_startswith: + outfile_seq.close() + outfile_score.close() + stop_err( 'Invalid fastqsolexa format at line %d: %s.' % ( i + 1, line ) ) + + quality_title = line[1:] + if quality_title and read_title != quality_title: + outfile_seq.close() + outfile_score.close() + stop_err( 'Invalid fastqsolexa format at line %d: sequence title "%s" differes from score title "%s".' % ( i + 1, read_title, quality_title ) ) + + if not quality_title: + outfile_score.write( '>%s\n' % read_title ) + else: + outfile_score.write( '>%s\n' % line[1:] ) + + else: + # fourth line is quality scores + qual = '' + fastq_integer = True + # peek: ascii or digits? + val = line.split()[0] + try: + check = int( val ) + fastq_integer = True + except: + fastq_integer = False + + if fastq_integer: + # digits + qual = line + else: + # ascii + quality_score_length = len( line ) + if quality_score_length == read_length + 1: + # first char is qual_score_startswith + qual_score_startswith = ord( line[0:1] ) + line = line[1:] + elif quality_score_length == read_length: + qual_score_startswith = default_coding_value + else: + stop_err( 'Invalid fastqsolexa format at line %d: the number of quality scores ( %d ) is not the same as bases ( %d ).' % ( i + 1, quality_score_length, read_length ) ) + + for j, char in enumerate( line ): + score = ord( char ) - qual_score_startswith # 64 + qual = "%s%s " % ( qual, str( score ) ) + + outfile_score.write( '%s\n' % qual ) + + outfile_seq.close() + outfile_score.close() + + return True + +def __main__(): + + # I/O + type_of_reads = sys.argv[1] # single or paired + input_target = sys.argv[2] # fasta + shrimp_outfile = sys.argv[3] # shrimp output + table_outfile = sys.argv[4] # table output + + # SHRiMP parameters: total = 15 + # TODO: put threshold on each of these parameters + if len(sys.argv) == 21 or len(sys.argv) == 22: + spaced_seed = sys.argv[5] + seed_matches_per_window = sys.argv[6] + seed_hit_taboo_length = sys.argv[7] + seed_generation_taboo_length = sys.argv[8] + seed_window_length = sys.argv[9] + max_hits_per_read = sys.argv[10] + max_read_length = sys.argv[11] + kmer = sys.argv[12] + sw_match_value = sys.argv[13] + sw_mismatch_value = sys.argv[14] + sw_gap_open_ref = sys.argv[15] + sw_gap_open_query = sys.argv[16] + sw_gap_ext_ref = sys.argv[17] + sw_gap_ext_query = sys.argv[18] + sw_hit_threshold = sys.argv[19] + + # Single-end parameters + if type_of_reads == 'single': + input_query = sys.argv[20] # single-end + hit_per_read = 1 + query_fasta = tempfile.NamedTemporaryFile().name + query_qual = tempfile.NamedTemporaryFile().name + else: # Paired-end parameters + input_query_end1 = sys.argv[20] # paired-end + input_query_end2 = sys.argv[21] + hit_per_read = 2 + query_fasta_end1 = tempfile.NamedTemporaryFile().name + query_fasta_end2 = tempfile.NamedTemporaryFile().name + query_qual_end1 = tempfile.NamedTemporaryFile().name + query_qual_end2 = tempfile.NamedTemporaryFile().name + else: + spaced_seed = '111111011111' + seed_matches_per_window = '2' + seed_hit_taboo_length = '4' + seed_generation_taboo_length = '0' + seed_window_length = '115.0' + max_hits_per_read = '100' + max_read_length = '1000' + kmer = '-1' + sw_match_value = '100' + sw_mismatch_value = '-150' + sw_gap_open_ref = '-400' + sw_gap_open_query = '-400' + sw_gap_ext_ref = '-70' + sw_gap_ext_query = '-70' + sw_hit_threshold = '68.0' + + # Single-end parameters + if type_of_reads == 'single': + input_query = sys.argv[5] # single-end + hit_per_read = 1 + query_fasta = tempfile.NamedTemporaryFile().name + query_qual = tempfile.NamedTemporaryFile().name + else: # Paired-end parameters + input_query_end1 = sys.argv[5] # paired-end + input_query_end2 = sys.argv[6] + hit_per_read = 2 + query_fasta_end1 = tempfile.NamedTemporaryFile().name + query_fasta_end2 = tempfile.NamedTemporaryFile().name + query_qual_end1 = tempfile.NamedTemporaryFile().name + query_qual_end2 = tempfile.NamedTemporaryFile().name + + + # temp file for shrimp log file + shrimp_log = tempfile.NamedTemporaryFile().name + + # convert fastq to fasta and quality score files + if type_of_reads == 'single': + return_value = convert_fastqsolexa_to_fasta_qual(input_query, query_fasta, query_qual) + else: + return_value = convert_fastqsolexa_to_fasta_qual(input_query_end1, query_fasta_end1, query_qual_end1) + return_value = convert_fastqsolexa_to_fasta_qual(input_query_end2, query_fasta_end2, query_qual_end2) + + # SHRiMP command + if type_of_reads == 'single': + command = ' '.join(['rmapper-ls', '-s', spaced_seed, '-n', seed_matches_per_window, '-t', seed_hit_taboo_length, '-9', seed_generation_taboo_length, '-w', seed_window_length, '-o', max_hits_per_read, '-r', max_read_length, '-d', kmer, '-m', sw_match_value, '-i', sw_mismatch_value, '-g', sw_gap_open_ref, '-q', sw_gap_open_query, '-e', sw_gap_ext_ref, '-f', sw_gap_ext_query, '-h', sw_hit_threshold, query_fasta, input_target, '>', shrimp_outfile, '2>', shrimp_log]) + + try: + os.system(command) + except Exception, e: + if os.path.exists(query_fasta): os.remove(query_fasta) + if os.path.exists(query_qual): os.remove(query_qual) + stop_err(str(e)) + + else: + command_end1 = ' '.join(['rmapper-ls', '-s', spaced_seed, '-n', seed_matches_per_window, '-t', seed_hit_taboo_length, '-9', seed_generation_taboo_length, '-w', seed_window_length, '-o', max_hits_per_read, '-r', max_read_length, '-d', kmer, '-m', sw_match_value, '-i', sw_mismatch_value, '-g', sw_gap_open_ref, '-q', sw_gap_open_query, '-e', sw_gap_ext_ref, '-f', sw_gap_ext_query, '-h', sw_hit_threshold, query_fasta_end1, input_target, '>', shrimp_outfile, '2>', shrimp_log]) + command_end2 = ' '.join(['rmapper-ls', '-s', spaced_seed, '-n', seed_matches_per_window, '-t', seed_hit_taboo_length, '-9', seed_generation_taboo_length, '-w', seed_window_length, '-o', max_hits_per_read, '-r', max_read_length, '-d', kmer, '-m', sw_match_value, '-i', sw_mismatch_value, '-g', sw_gap_open_ref, '-q', sw_gap_open_query, '-e', sw_gap_ext_ref, '-f', sw_gap_ext_query, '-h', sw_hit_threshold, query_fasta_end2, input_target, '>>', shrimp_outfile, '2>>', shrimp_log]) + + try: + os.system(command_end1) + os.system(command_end2) + except Exception, e: + if os.path.exists(query_fasta_end1): os.remove(query_fasta_end1) + if os.path.exists(query_fasta_end2): os.remove(query_fasta_end2) + if os.path.exists(query_qual_end1): os.remove(query_qual_end1) + if os.path.exists(query_qual_end2): os.remove(query_qual_end2) + stop_err(str(e)) + + # convert to table + if type_of_reads == 'single': + return_value = generate_sub_table(shrimp_outfile, input_target, query_qual, table_outfile, hit_per_read) + else: + return_value = generate_sub_table(shrimp_outfile, input_target, query_qual_end1+'&'+query_qual_end2, table_outfile, hit_per_read) + + # remove temp. files + if type_of_reads == 'single': + if os.path.exists(query_fasta): os.remove(query_fasta) + if os.path.exists(query_qual): os.remove(query_qual) + else: + if os.path.exists(query_fasta_end1): os.remove(query_fasta_end1) + if os.path.exists(query_fasta_end2): os.remove(query_fasta_end2) + if os.path.exists(query_qual_end1): os.remove(query_qual_end1) + if os.path.exists(query_qual_end2): os.remove(query_qual_end2) + + if os.path.exists(shrimp_log): os.remove(shrimp_log) + +if __name__ == '__main__': __main__() + diff -r 26825f08d362 -r 842f1883cf53 tools/metag_tools/shrimp_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/metag_tools/shrimp_wrapper.xml Mon Sep 15 15:04:41 2008 -0400 @@ -0,0 +1,196 @@ +<tool id="shrimp_wrapper" name="SHRiMP" version="1.0.0"> + <description>SHort Read Mapping Package</description> + <command interpreter="python"> + #if ($type_of_reads.single_or_paired=="single" and $param.skip_or_full=="skip"):#shrimp_wrapper.py $type_of_reads.single_or_paired $input_target $output1 $output2 $input_query + #elif ($type_of_reads.single_or_paired=="paired" and $param.skip_or_full=="skip"):#shrimp_wrapper.py $type_of_reads.single_or_paired $input_target $output1 $output2 ${type_of_reads.input1} ${type_of_reads.input2} + #elif ($type_of_reads.single_or_paired=="single" and $param.skip_or_full=="full"):#shrimp_wrapper.py $type_of_reads.single_or_paired $input_target $output1 $output2 $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_hit_threshold $input_query + #elif ($type_of_reads.single_or_paired=="paired" and $param.skip_or_full=="full"):#shrimp_wrapper.py $type_of_reads.single_or_paired $input_target $output1 $output2 $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_hit_threshold ${type_of_reads.input1} ${type_of_reads.input2} + #end if + </command> + <inputs> + <page> + <param name="input_target" type="data" format="fasta" label="Reference sequence" /> + <conditional name="type_of_reads"> + <param name="single_or_paired" type="select" label="Single- or Paired-ends"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + </param> + <when value="single"> + <param name="input_query" type="data" format="fastqsolexa" label="Sequence file" /> + </when> + <when value="paired"> + <param name="input1" type="data" format="fastqsolexa" label="One end" /> + <param name="input2" type="data" format="fastqsolexa" label="The other end" /> + </when> + </conditional> + <conditional name="param"> + <param name="skip_or_full" type="select" label="SHRiMP parameter selection"> + <option value="skip">Default setting</option> + <option value="full">Full list</option> + </param> + <when value="skip" /> + <when value="full"> + <param name="spaced_seed" type="text" size="30" value="111111011111" label="Spaced Seed" /> + <param name="seed_matches_per_window" type="integer" size="5" value="2" label="Seed Matches per Window" /> + <param name="seed_hit_taboo_length" type="integer" size="5" value="4" label="Seed Hit Taboo Length" /> + <param name="seed_generation_taboo_length" type="integer" size="5" value="0" label="Seed Generation Taboo Length" /> + <param name="seed_window_length" type="float" size="10" value="115.0" label="Seed Window Length" help="in percentage"/> + <param name="max_hits_per_read" type="integer" size="10" value="100" label="Maximum Hits per Read" /> + <param name="max_read_length" type="integer" size="10" value="1000" label="Maximum Read Length" /> + <param name="kmer" type="integer" size="10" value="-1" label="Kmer Std. Deviation Limit" help="-1 as None"/> + <param name="sw_match_value" type="integer" size="10" value="100" label="S-W Match Value" /> + <param name="sw_mismatch_value" type="integer" size="10" value="-150" label="S-W Mismatch Value" /> + <param name="sw_gap_open_ref" type="integer" size="10" value="-400" label="S-W Gap Open Penalty (Reference)" /> + <param name="sw_gap_open_query" type="integer" size="10" value="-400" label="S-W Gap Open Penalty (Query)" /> + <param name="sw_gap_ext_ref" type="integer" size="10" value="-70" label="S-W Gap Extend Penalty (Reference)" /> + <param name="sw_gap_ext_query" type="integer" size="10" value="-70" label="S-W Gap Extend Penalty (Query)" /> + <param name="sw_hit_threshold" type="float" size="10" value="68.0" label="S-W Hit Threshold" help="in percentage"/> + </when> + </conditional> + </page> + </inputs> + <outputs> + <data name="output1" format="tabular"/> + <data name="output2" format="tabular"/> + </outputs> + <requirements> + <requirement type="binary">SHRiMP_rmapper</requirement> + </requirements> + <tests> + <test> + <param name="single_or_paired" value="single" /> + <param name="skip_or_full" value="skip" /> + <param name="input_target" value="shrimp_phix_anc.fa" ftype="fasta" /> + <param name="input_query" value="shrimp_wrapper_test1.fastq" ftype="fastqsolexa"/> + <output name="output1" file="shrimp_wrapper_test1.out1" /> + </test> +  + </tests> +<help> + +.. class:: warningmark + +Only nucleotide sequences as query. + +----- + +**What it does** + +Run SHRiMP on letter-space reads. + +----- + +**Example** + +- Input a multiple-fastq file like the following:: + + @seq1 + TACCCGATTTTTTGCTTTCCACTTTATCCTACCCTT + +seq2 + hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh + +- Use default settings (for detail explanations, please see **Parameters** section) + +- Search against your own uploaded file, result will be in the following format:: + + +-------+-------+--------+----------+----------+---------+--------+--------+-------+------------+ + | id | chrom | strand | t.start | t.end | q.start | q.end | length | score | editstring | + +-------+-------+--------+----------+----------+---------+--------+--------+-------+------------+ + | >seq1 | chrMT | + | 14712 | 14747 | 1 | 36 | 36 | 3350 | 24T11 | + +-------+-------+--------+----------+----------+---------+--------+--------+-------+------------+ + +- The result will be formatted Table:: + + +-------+---------+---------+----------+---------+----------+---------+----------+ + | chrom | ref_loc | read_id | read_loc | ref_nuc | read_nuc | quality | coverage | + +-------+---------+---------+----------+---------+----------+---------+----------+ + | chrMT | 14711 | seq1 | 0 | T | T | 40 | 1 | + | chrMT | 14712 | seq1 | 1 | A | A | 40 | 1 | + | chrMT | 14713 | seq1 | 2 | C | C | 40 | 1 | + +-------+---------+---------+----------+---------+----------+---------+----------+ + +----- + +**Parameters** + +Parameter list with default value settings:: + + -s Spaced Seed (default: 111111011111) + -n Seed Matches per Window (default: 2) + -t Seed Hit Taboo Length (default: 4) + -9 Seed Generation Taboo Length (default: 0) + -w Seed Window Length (default: 115.00%) + -o Maximum Hits per Read (default: 100) + -r Maximum Read Length (default: 1000) + -d Kmer Std. Deviation Limit (default: -1 [None]) + + -m S-W Match Value (default: 100) + -i S-W Mismatch Value (default: -150) + -g S-W Gap Open Penalty (Reference) (default: -400) + -q S-W Gap Open Penalty (Query) (default: -400) + -e S-W Gap Extend Penalty (Reference) (default: -70) + -f S-W Gap Extend Penalty (Query) (default: -70) + -h S-W Hit Threshold (default: 68.00%) + +----- + +**Reference** + + **SHRiMP**: Stephen M. Rumble, Michael Brudno, Phil Lacroute, Vladimir Yanovsky, Marc Fiume, Adrian Dalca. shrimp at cs dot toronto dot edu. + +</help> +</tool>

1 0

[hg] galaxy 1509: Rewrote "Compare two queries" tool in Python.
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/eb941905fd70 changeset: 1509:eb941905fd70 user: guru date: Tue Sep 16 14:09:16 2008 -0400 description: Rewrote "Compare two queries" tool in Python. 2 file(s) affected in this change: tools/filters/compare.xml tools/filters/joinWrapper.py diffs (68 lines): diff -r ec547440ec97 -r eb941905fd70 tools/filters/compare.xml --- a/tools/filters/compare.xml Tue Sep 16 13:25:42 2008 -0400 +++ b/tools/filters/compare.xml Tue Sep 16 14:09:16 2008 -0400 @@ -1,6 +1,6 @@ <tool id="comp1" name="Compare two Queries"> <description>to find common or distinct rows</description> - <command interpreter="perl">joinWrapper.pl $input1 $input2 $field1 $field2 $mode "Y" $out_file1</command> + <command interpreter="python">joinWrapper.py $input1 $input2 $field1 $field2 $mode $out_file1</command> <inputs> <param format="tabular" name="input1" type="data" label="Compare"/> <param name="field1" label="Using column" type="data_column" data_ref="input1" /> diff -r ec547440ec97 -r eb941905fd70 tools/filters/joinWrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/filters/joinWrapper.py Tue Sep 16 14:09:16 2008 -0400 @@ -0,0 +1,53 @@ +#!/usr/bin/env python +#Guruprasad Ananda +""" +This tool provides the UNIX "join" functionality. +""" +import sys, os, tempfile + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit() + +def main(): + infile1 = sys.argv[1] + infile2 = sys.argv[2] + field1 = int(sys.argv[3]) + field2 = int(sys.argv[4]) + mode =sys.argv[5] + outfile = sys.argv[6] + + tmpfile1 = tempfile.NamedTemporaryFile() + tmpfile2 = tempfile.NamedTemporaryFile() + + try: + #Sort the two files based on specified fields + os.system("sort -k %d -o %s %s" %(field1, tmpfile1.name, infile1)) + os.system("sort -k %d -o %s %s" %(field2, tmpfile2.name, infile2)) + except Exception, exc: + stop_err( 'Initialization error -> %s' %str(exc) ) + + option = "" + for line in file(tmpfile1.name): + line = line.strip() + if line: + elems = line.split('\t') + for j in range(1,len(elems)+1): + if j == 1: + option = "1.1" + else: + option = option + ",1." + str(j) + break + + if mode == "V": + cmdline = 'join -v 1 -o %s -1 %d -2 %d %s %s | tr " " "\t" > %s' %(option, field1, field2, tmpfile1.name, tmpfile2.name, outfile) + else: + cmdline = 'join -o %s -1 %d -2 %d %s %s | tr " " "\t" > %s' %(option, field1, field2, tmpfile1.name, tmpfile2.name, outfile) + + try: + os.system(cmdline) + except Exception, exj: + stop_err('Error joining the two datasets -> %s' %str(exj)) + +if __name__ == "__main__": + main()

1 0

[hg] galaxy 1508: Small update for maf stats tool.
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/ec547440ec97 changeset: 1508:ec547440ec97 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Tue Sep 16 13:25:42 2008 -0400 description: Small update for maf stats tool. 2 file(s) affected in this change: lib/galaxy/tools/util/maf_utilities.py tools/maf/maf_stats.py diffs (99 lines): diff -r 842f1883cf53 -r ec547440ec97 lib/galaxy/tools/util/maf_utilities.py --- a/lib/galaxy/tools/util/maf_utilities.py Mon Sep 15 15:04:41 2008 -0400 +++ b/lib/galaxy/tools/util/maf_utilities.py Tue Sep 16 13:25:42 2008 -0400 @@ -199,7 +199,7 @@ yield block def get_chopped_blocks_with_index_offset_for_region( index, src, region, species = None, mincols = 0, force_strand = None ): for block, idx, offset in index.get_as_iterator_with_index_and_offset( src, region.start, region.end ): - block = chop_block_by_region( block, src, region, species, mincols ) + block = chop_block_by_region( block, src, region, species, mincols, force_strand ) if block is not None: yield block, idx, offset @@ -209,6 +209,25 @@ else: alignment = RegionAlignment( end - start, primary_species ) return fill_region_alignment( alignment, index, primary_species, chrom, start, end, strand, species, mincols ) +#reduces a block to only positions exisiting in the src provided +def reduce_block_by_primary_genome( block, species, chromosome, region_start ): + #returns ( startIndex, {species:texts} + #where texts' contents are reduced to only positions existing in the primary genome + src = "%s.%s" % ( species, chromosome ) + ref = block.get_component_by_src( src ) + start_offset = ref.start - region_start + species_texts = {} + for c in block.components: + species_texts[ c.src.split( '.' )[0] ] = list( c.text ) + #remove locations which are gaps in the primary species, starting from the downstream end + for i in range( len( species_texts[ species ] ) - 1, -1, -1 ): + if species_texts[ species ][i] == '-': + for text in species_texts.values(): + text.pop( i ) + for spec, text in species_texts.items(): + species_texts[spec] = ''.join( text ) + return ( start_offset, species_texts ) + #fills a region alignment def fill_region_alignment( alignment, index, primary_species, chrom, start, end, strand = '+', species = None, mincols = 0 ): region = bx.intervals.Interval( start, end ) @@ -216,22 +235,7 @@ region.strand = strand primary_src = "%s.%s" % ( primary_species, chrom ) - def reduce_block_by_primary_genome( block ): - #returns ( startIndex, {species:texts} - #where texts' contents are reduced to only positions existing in the primary genome - ref = block.get_component_by_src( primary_src ) - start_offset = ref.start - start - species_texts = {} - for c in block.components: - species_texts[ c.src.split( '.' )[0] ] = list( c.text ) - #remove locations which are gaps in the primary species, starting from the downstream end - for i in range( len( species_texts[ primary_species ] ) - 1, -1, -1 ): - if species_texts[ primary_species ][i] == '-': - for text in species_texts.values(): - text.pop( i ) - for spec, text in species_texts.items(): - species_texts[spec] = ''.join( text ) - return ( start_offset, species_texts ) + #Order blocks overlaping this position by score, lowest first blocks = [] @@ -248,7 +252,7 @@ for block_dict in blocks: block = chop_block_by_region( block_dict[1].get_at_offset( block_dict[2] ), primary_src, region, species, mincols, strand ) if block is None: continue - start_offset, species_texts = reduce_block_by_primary_genome( block ) + start_offset, species_texts = reduce_block_by_primary_genome( block, primary_species, chrom, start ) for spec, text in species_texts.items(): try: alignment.set_range( start_offset, spec, text ) diff -r 842f1883cf53 -r ec547440ec97 tools/maf/maf_stats.py --- a/tools/maf/maf_stats.py Mon Sep 15 15:04:41 2008 -0400 +++ b/tools/maf/maf_stats.py Tue Sep 16 13:25:42 2008 -0400 @@ -64,19 +64,11 @@ for c in block.components: spec = c.src.split( '.' )[0] if spec not in coverage: coverage[spec] = zeros( region.end - region.start, dtype = bool ) - ref = block.get_component_by_src( src ) - #skip gap locations due to insertions in secondary species relative to primary species - start_offset = ref.start - region.start - num_gaps = 0 - for i in range( len( ref.text.rstrip().rstrip( "-" ) ) ): - if ref.text[i] in ["-"]: - num_gaps += 1 - continue - #Toggle base if covered - for comp in block.components: - spec = comp.src.split( '.' )[0] - if comp.text and comp.text[i] not in ['-']: - coverage[spec][start_offset + i - num_gaps] = True + start_offset, alignment = maf_utilities.reduce_block_by_primary_genome( block, dbkey, region.chrom, region.start ) + for i in range( len( alignment[dbkey] ) ): + for spec, text in alignment.items(): + if text[i] != '-': + coverage[spec][start_offset + i] = True if summary: #record summary for key in coverage.keys():

1 0

[hg] galaxy 1510: Strip whitespace from columns in file for data...
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/f8e3770c23f6 changeset: 1510:f8e3770c23f6 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Tue Sep 16 14:10:53 2008 -0400 description: Strip whitespace from columns in file for dataset_metadata_in_file validator. 1 file(s) affected in this change: lib/galaxy/tools/parameters/validation.py diffs (12 lines): diff -r ec547440ec97 -r f8e3770c23f6 lib/galaxy/tools/parameters/validation.py --- a/lib/galaxy/tools/parameters/validation.py Tue Sep 16 13:25:42 2008 -0400 +++ b/lib/galaxy/tools/parameters/validation.py Tue Sep 16 14:10:53 2008 -0400 @@ -247,7 +247,7 @@ if line_startswith is None or line.startswith( line_startswith ): fields = line.split( '\t' ) if metadata_column < len( fields ): - self.valid_values.append( fields[metadata_column] ) + self.valid_values.append( fields[metadata_column].strip() ) def validate( self, value, history = None ): if not value: return if hasattr( value, "metadata" ):

1 0

[hg] galaxy 1511: Merge local heads
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/c3ce08879473 changeset: 1511:c3ce08879473 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Tue Sep 16 14:26:14 2008 -0400 description: Merge local heads 0 file(s) affected in this change: diffs (12 lines): diff -r eb941905fd70 -r c3ce08879473 lib/galaxy/tools/parameters/validation.py --- a/lib/galaxy/tools/parameters/validation.py Tue Sep 16 14:09:16 2008 -0400 +++ b/lib/galaxy/tools/parameters/validation.py Tue Sep 16 14:26:14 2008 -0400 @@ -247,7 +247,7 @@ if line_startswith is None or line.startswith( line_startswith ): fields = line.split( '\t' ) if metadata_column < len( fields ): - self.valid_values.append( fields[metadata_column] ) + self.valid_values.append( fields[metadata_column].strip() ) def validate( self, value, history = None ): if not value: return if hasattr( value, "metadata" ):

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[hg] galaxy 1512: The MetadataCollection object is now created o...
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/1e408bab8941 changeset: 1512:1e408bab8941 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Tue Sep 16 15:23:23 2008 -0400 description: The MetadataCollection object is now created only once per dataset object instance (and when datatype is changed), instead of each time dataset.metadata is called. The 'no_value' attribute for a metadata element's spec is returned when the metadata element's value is None. 2 file(s) affected in this change: lib/galaxy/datatypes/metadata.py lib/galaxy/model/__init__.py diffs (89 lines): diff -r c3ce08879473 -r 1e408bab8941 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py Tue Sep 16 14:26:14 2008 -0400 +++ b/lib/galaxy/datatypes/metadata.py Tue Sep 16 15:23:23 2008 -0400 @@ -151,9 +151,16 @@ """ def __init__(self, parent, spec): self.parent = parent - self.bunch = parent._metadata or dict() if spec is None: self.spec = MetadataSpecCollection() else: self.spec = spec + + #set default metadata values + if not self.parent._metadata: + self.parent._metadata = {} + for name, value in self.spec.items(): + if name not in self.bunch: + self.bunch[name] = value.default + def __iter__(self): return self.bunch.__iter__() def get( self, key, default=None ): @@ -168,19 +175,21 @@ def __nonzero__(self): return self.bunch.__nonzero__() def __getattr__(self, name): - if self.bunch.get( name ): - return self.bunch.get( name ) + if name == "bunch": + return self.parent._metadata + rval = self.bunch.get( name ) + if rval is None: + rval = self.spec.get( name, None ) + if rval: + rval = rval.no_value + return rval + def __setattr__(self, name, value): + if name in ["parent","spec"]: + self.__dict__[name] = value + elif name == "bunch": + self.parent._metadata = value else: - if self.spec.get(name, None): - return self.spec[name].default - else: - return None - def __setattr__(self, name, value): - if name in ["parent","bunch","spec"]: - self.__dict__[name] = value - else: - self.__dict__["bunch"][name] = value - self.bunch = self.parent._metadata = dict( self.bunch ) + self.bunch[name] = value MetadataElement = Statement(MetadataElementSpec) diff -r c3ce08879473 -r 1e408bab8941 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Tue Sep 16 14:26:14 2008 -0400 +++ b/lib/galaxy/model/__init__.py Tue Sep 16 15:23:23 2008 -0400 @@ -113,7 +113,7 @@ self.peek = peek self.extension = extension self.designation = designation - self._metadata = metadata or dict() + self.metadata = metadata or dict() self.dbkey = dbkey self.deleted = deleted self.visible = visible @@ -159,9 +159,9 @@ return datatypes_registry.get_datatype_by_extension( self.extension ) def get_metadata( self ): - if not self._metadata: - self._metadata = dict() - return MetadataCollection( self, self.datatype.metadata_spec ) + if not hasattr( self, '_metadata_collection' ): + self._metadata_collection = MetadataCollection( self, self.datatype.metadata_spec ) + return self._metadata_collection def set_metadata( self, bunch ): # Needs to accept a MetadataCollection, a bunch, or a dict self._metadata = dict( bunch.items() ) @@ -191,6 +191,8 @@ def change_datatype( self, new_ext ): self.clear_associated_files() + if hasattr( self, '_metadata_collection' ): + del self._metadata_collection datatypes_registry.change_datatype( self, new_ext ) def get_size( self ): """Returns the size of the data on disk"""

1 0

[hg] galaxy 1513: Quick 'n easy solution to the EMBOSS stage in/...
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/cf17b5a16eff changeset: 1513:cf17b5a16eff user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Sep 17 10:45:20 2008 -0400 description: Quick 'n easy solution to the EMBOSS stage in/out problem: read the outputs from the "real" galaxy path instead of the temp stage path. 1 file(s) affected in this change: lib/galaxy/jobs/runners/pbs.py diffs (31 lines): diff -r 1e408bab8941 -r cf17b5a16eff lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py Tue Sep 16 15:23:23 2008 -0400 +++ b/lib/galaxy/jobs/runners/pbs.py Wed Sep 17 10:45:20 2008 -0400 @@ -146,7 +146,7 @@ if self.app.config.pbs_application_server: pbs_ofile = self.app.config.pbs_application_server + ':' + ofile pbs_efile = self.app.config.pbs_application_server + ':' + efile - stagein = self.get_stage_in_out( job_wrapper.get_input_fnames() + job_wrapper.get_output_fnames() ) + stagein = self.get_stage_in_out( job_wrapper.get_input_fnames() + job_wrapper.get_output_fnames(), symlink=True ) stageout = self.get_stage_in_out( job_wrapper.get_output_fnames() ) job_attrs = pbs.new_attropl(5) job_attrs[0].name = pbs.ATTR_o @@ -372,15 +372,15 @@ self.queue.put( self.STOP_SIGNAL ) log.info( "pbs job runner stopped" ) - def get_stage_in_out( self, fnames ): + def get_stage_in_out( self, fnames, symlink=False ): """Convenience function to create a stagein/stageout list""" stage = '' for fname in fnames: if os.access(fname, os.R_OK): - if stage != '': + if stage: stage += ',' # pathnames are now absolute - if self.app.config.pbs_stage_path != '': + if symlink and self.app.config.pbs_stage_path: stage_name = os.path.join(self.app.config.pbs_stage_path, os.path.split(fname)[1]) else: stage_name = fname

1 0

[hg] galaxy 1515: Forgot to update tool_conf.sample with the new...
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/280e8b68f845 changeset: 1515:280e8b68f845 user: guru date: Wed Sep 17 17:14:59 2008 -0400 description: Forgot to update tool_conf.sample with the new tool details. 1 file(s) affected in this change: tool_conf.xml.sample diffs (10 lines): diff -r 33e06a98b6d8 -r 280e8b68f845 tool_conf.xml.sample --- a/tool_conf.xml.sample Wed Sep 17 16:42:08 2008 -0400 +++ b/tool_conf.xml.sample Wed Sep 17 17:14:59 2008 -0400 @@ -281,5 +281,6 @@ <tool file="metag_tools/megablast_wrapper.xml" /> <tool file="metag_tools/megablast_xml_parser.xml" /> <tool file="metag_tools/blat_wrapper.xml" /> + <tool file="metag_tools/mapping_to_ucsc.xml" /> </section> </toolbox>

1 0

[hg] galaxy 1514: New tool to format short read mapping data as ...
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/33e06a98b6d8 changeset: 1514:33e06a98b6d8 user: guru date: Wed Sep 17 16:42:08 2008 -0400 description: New tool to format short read mapping data as a UCSC custom track,. 2 file(s) affected in this change: tools/metag_tools/mapping_to_ucsc.py tools/metag_tools/mapping_to_ucsc.xml diffs (415 lines): diff -r cf17b5a16eff -r 33e06a98b6d8 tools/metag_tools/mapping_to_ucsc.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/metag_tools/mapping_to_ucsc.py Wed Sep 17 16:42:08 2008 -0400 @@ -0,0 +1,204 @@ +#! /usr/bin/python + +from galaxy import eggs +import sys, tempfile, os + +assert sys.version_info[:2] >= (2.4) + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit() + +def main(): + + out_fname = sys.argv[1] + in_fname = sys.argv[2] + chr_col = int(sys.argv[3])-1 + coord_col = int(sys.argv[4])-1 + track_type = sys.argv[5] + if track_type == 'coverage' or track_type == 'both': + coverage_col = int(sys.argv[6])-1 + cname = sys.argv[7] + cdescription = sys.argv[8] + ccolor = sys.argv[9].replace('-',',') + cvisibility = sys.argv[10] + if track_type == 'snp' or track_type == 'both': + if track_type == 'both': + j = 5 + else: + j = 0 + #sname = sys.argv[7+j] + sdescription = sys.argv[6+j] + svisibility = sys.argv[7+j] + #ref_col = int(sys.argv[10+j])-1 + read_col = int(sys.argv[8+j])-1 + + + # Sort the input file based on chromosome (alphabetically) and start co-ordinates (numerically) + sorted_infile = tempfile.NamedTemporaryFile() + try: + os.system("sort -k %d,%d -k %dn -o %s %s" %(chr_col+1,chr_col+1,coord_col+1,sorted_infile.name,in_fname)) + except Exception, exc: + stop_err( 'Initialization error -> %s' %str(exc) ) + + #generate chr list + sorted_infile.seek(0) + chr_vals = [] + for line in file( sorted_infile.name ): + line = line.strip() + if not(line): + continue + try: + fields = line.split('\t') + chr = fields[chr_col] + if chr not in chr_vals: + chr_vals.append(chr) + except: + pass + if not(chr_vals): + stop_err("Skipped all lines as invalid.") + + if track_type == 'coverage' or track_type == 'both': + if track_type == 'coverage': + fout = open( out_fname, "w" ) + else: + fout = tempfile.NamedTemporaryFile() + fout.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \ + % ( cname, cdescription, ccolor, cvisibility )) + if track_type == 'snp' or track_type == 'both': + fout_a = tempfile.NamedTemporaryFile() + fout_t = tempfile.NamedTemporaryFile() + fout_g = tempfile.NamedTemporaryFile() + fout_c = tempfile.NamedTemporaryFile() + fout_ref = tempfile.NamedTemporaryFile() + + fout_a.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \ + % ( "Track A", sdescription, '255,0,0', svisibility )) + fout_t.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \ + % ( "Track T", sdescription, '0,255,0', svisibility )) + fout_g.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \ + % ( "Track G", sdescription, '0,0,255', svisibility )) + fout_c.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \ + % ( "Track C", sdescription, '255,0,255', svisibility )) + + + sorted_infile.seek(0) + for line in file( sorted_infile.name ): + line = line.strip() + if not(line): + continue + try: + fields = line.split('\t') + chr = fields[chr_col] + start = int(fields[coord_col]) + assert start > 0 + except: + continue + try: + ind = chr_vals.index(chr) #encountered chr for the 1st time + del chr_vals[ind] + prev_start = '' + header = "variableStep chrom=%s\n" %(chr) + if track_type == 'coverage' or track_type == 'both': + coverage = int(fields[coverage_col]) + line1 = "%s\t%s\n" %(start,coverage) + fout.write("%s%s" %(header,line1)) + if track_type == 'snp' or track_type == 'both': + a = t = g = c = 0 + fout_a.write("%s" %(header)) + fout_t.write("%s" %(header)) + fout_g.write("%s" %(header)) + fout_c.write("%s" %(header)) + try: + #ref_nt = fields[ref_col].capitalize() + read_nt = fields[read_col].capitalize() + try: + nt_ind = ['A','T','G','C'].index(read_nt) + if nt_ind == 0: + a+=1 + elif nt_ind == 1: + t+=1 + elif nt_ind == 2: + g+=1 + else: + c+=1 + except ValueError: + pass + except: + pass + prev_start = start + except ValueError: + if start != prev_start: + if track_type == 'coverage' or track_type == 'both': + coverage = int(fields[coverage_col]) + fout.write("%s\t%s\n" %(start,coverage)) + if track_type == 'snp' or track_type == 'both': + if a: + fout_a.write("%s\t%s\n" %(prev_start,a)) + if t: + fout_t.write("%s\t%s\n" %(prev_start,t)) + if g: + fout_g.write("%s\t%s\n" %(prev_start,g)) + if c: + fout_c.write("%s\t%s\n" %(prev_start,c)) + a = t = g = c = 0 + try: + #ref_nt = fields[ref_col].capitalize() + read_nt = fields[read_col].capitalize() + try: + nt_ind = ['A','T','G','C'].index(read_nt) + if nt_ind == 0: + a+=1 + elif nt_ind == 1: + t+=1 + elif nt_ind == 2: + g+=1 + else: + c+=1 + except ValueError: + pass + except: + pass + prev_start = start + else: + if track_type == 'snp' or track_type == 'both': + try: + #ref_nt = fields[ref_col].capitalize() + read_nt = fields[read_col].capitalize() + try: + nt_ind = ['A','T','G','C'].index(read_nt) + if nt_ind == 0: + a+=1 + elif nt_ind == 1: + t+=1 + elif nt_ind == 2: + g+=1 + else: + c+=1 + except ValueError: + pass + except: + pass + + if track_type == 'snp' or track_type == 'both': + if a: + fout_a.write("%s\t%s\n" %(prev_start,a)) + if t: + fout_t.write("%s\t%s\n" %(prev_start,t)) + if g: + fout_g.write("%s\t%s\n" %(prev_start,g)) + if c: + fout_c.write("%s\t%s\n" %(prev_start,c)) + + fout_a.seek(0) + fout_g.seek(0) + fout_t.seek(0) + fout_c.seek(0) + + if track_type == 'snp': + os.system("cat %s %s %s %s >> %s" %(fout_a.name,fout_t.name,fout_g.name,fout_c.name,out_fname)) + elif track_type == 'both': + fout.seek(0) + os.system("cat %s %s %s %s %s | cat > %s" %(fout.name,fout_a.name,fout_t.name,fout_g.name,fout_c.name,out_fname)) +if __name__ == "__main__": + main() \ No newline at end of file diff -r cf17b5a16eff -r 33e06a98b6d8 tools/metag_tools/mapping_to_ucsc.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/metag_tools/mapping_to_ucsc.xml Wed Sep 17 16:42:08 2008 -0400 @@ -0,0 +1,202 @@ +<tool id="mapToUCSC" name="Format mapping data" version="1.0.0"> + <description> as UCSC custom track</description> + <command interpreter="python"> + mapping_to_ucsc.py + $out_file1 + $input + $chr_col + $coord_col + $track.track_type + #if $track.track_type == "coverage" or $track.track_type == "both" + $track.coverage_col + "${track.cname}" + "${track.cdescription}" + "${track.ccolor}" + "${track.cvisibility}" + #end if + #if $track.track_type == "snp" or $track.track_type == "both" + "${track.sdescription}" + "${track.svisibility}" + $track.col2 + #end if + </command> + <inputs> + <param format="tabular" name="input" type="data" label="Select mapping data"/> + <param name="chr_col" type="data_column" data_ref="input" label="Column for reference chromosome" /> + <param name="coord_col" type="data_column" data_ref="input" numerical="True" label="Numerical column for reference co-ordinate" /> + <conditional name="track"> + <param name="track_type" type="select" label="Display"> + <option value="snp" selected="true">SNPs</option> + <option value="coverage">Read coverage</option> + <option value="both">Both</option> + </param> + <when value = "coverage"> + <param name="coverage_col" type="data_column" data_ref="input" numerical="True" label="Numerical column for read coverage" /> + <param name="cname" type="text" size="15" value="User Track" label="Coverage track name"> + <validator type="length" max="15"/> + </param> + <param name="cdescription" type="text" value="User Supplied Coverage Track (from Galaxy)" label="Coverage track description"> + <validator type="length" max="60" size="15"/> + </param> + <param label="Coverage track Color" name="ccolor" type="select"> + <option selected="yes" value="0-0-0">Black</option> + <option value="255-0-0">Red</option> + <option value="0-255-0">Green</option> + <option value="0-0-255">Blue</option> + <option value="255-0-255">Magenta</option> + <option value="0-255-255">Cyan</option> + <option value="255-215-0">Gold</option> + <option value="160-32-240">Purple</option> + <option value="255-140-0">Orange</option> + <option value="255-20-147">Pink</option> + <option value="92-51-23">Dark Chocolate</option> + <option value="85-107-47">Olive green</option> + </param> + <param label="Coverage track Visibility" name="cvisibility" type="select"> + <option selected="yes" value="1">Dense</option> + <option value="2">Full</option> + <option value="3">Pack</option> + <option value="4">Squish</option> + <option value="0">Hide</option> + </param> + </when> + + <when value = "snp"> +  + <param name="col2" type="data_column" data_ref="input" label="Column containing the read nucleotide" /> +  + <param name="sdescription" type="text" value="User Supplied Track (from Galaxy)" label="SNP track description"> + <validator type="length" max="60" size="15"/> + </param> + <param label="SNP track Visibility" name="svisibility" type="select"> + <option selected="yes" value="1">Dense</option> + <option value="2">Full</option> + <option value="3">Pack</option> + <option value="4">Squish</option> + <option value="0">Hide</option> + </param> + </when> + + <when value = "both"> + <param name="coverage_col" type="data_column" data_ref="input" numerical="True" label="Numerical column for read coverage" /> + <param name="cname" type="text" size="15" value="User Track" label="Coverage track name"> + <validator type="length" max="15"/> + </param> + <param name="cdescription" type="text" size="15" value="User Supplied Track (from Galaxy)" label="Coverage track description"> + <validator type="length" max="60"/> + </param> + <param label="Coverage track Color" name="ccolor" type="select"> + <option selected="yes" value="0-0-0">Black</option> + <option value="255-0-0">Red</option> + <option value="0-255-0">Green</option> + <option value="0-0-255">Blue</option> + <option value="255-0-255">Magenta</option> + <option value="0-255-255">Cyan</option> + <option value="255-215-0">Gold</option> + <option value="160-32-240">Purple</option> + <option value="255-140-0">Orange</option> + <option value="255-20-147">Pink</option> + <option value="92-51-23">Dark Chocolate</option> + <option value="85-107-47">Olive green</option> + </param> + <param label="Coverage track Visibility" name="cvisibility" type="select"> + <option selected="yes" value="1">Dense</option> + <option value="2">Full</option> + <option value="3">Pack</option> + <option value="4">Squish</option> + <option value="0">Hide</option> + </param> +  + <param name="col2" type="data_column" data_ref="input" label="Column containing the read nucleotide" /> +  + <param name="sdescription" type="text" size="15" value="User Supplied Track (from Galaxy)" label="SNP track description"> + <validator type="length" max="60"/> + </param> + <param label="SNP track Visibility" name="svisibility" type="select"> + <option selected="yes" value="1">Dense</option> + <option value="2">Full</option> + <option value="3">Pack</option> + <option value="4">Squish</option> + <option value="0">Hide</option> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data format="customtrack" name="out_file1"/> + </outputs> + + + <help> + +.. class:: infomark + +**What it does** + +This tool formats mapping data generated by short read mappers, as a custom track that can be displayed at UCSC genome browser. + +----- + +.. class:: warningmark + +**Note** + +This tool requires the mapping data to contain at least the following information: + +chromosome, genome coordinate, read nucleotide (if option to display is SNPs), read coverage (if option to display is Read coverage). + +----- + +**Example** + +For the following Mapping data:: + + #chr g_start read_id read_coord g_nt read_nt qual read_coverage + chrM 1 1:29:1672:1127/1 11 G G 40 134 + chrM 1 1:32:93:933/1 4 G A 40 134 + chrM 1 1:34:116:2032/1 11 G A 40 134 + chrM 1 1:39:207:964/1 1 G G 40 134 + chrM 2 1:3:359:848/1 1 G C 40 234 + chrM 2 1:40:1435:1013/1 1 G G 40 234 + chrM 3 1:40:730:972/1 9 G G 40 334 + chrM 4 1:42:1712:921/2 31 G T 35 434 + chrM 4 1:44:1649:493/1 4 G G 40 434 + +running this tool to display both SNPs and Read coverage will return the following tracks, containing aggregated data per genome co-ordinate:: + + track type=wiggle_0 name="Coverage Track" description="User Supplied Track (from Galaxy)" color=0,0,0 visibility=1 + variableStep chrom=chrM + 1 134 + 2 234 + 3 334 + 4 434 + track type=wiggle_0 name="Track A" description="User Supplied SNP Track (from Galaxy)" color=255,0,0 visibility=1 + variableStep chrom=chrM + 1 2 + track type=wiggle_0 name="Track T" description="User Supplied SNP Track (from Galaxy)" color=0,255,0 visibility=1 + variableStep chrom=chrM + 4 1 + track type=wiggle_0 name="Track G" description="User Supplied SNP Track (from Galaxy)" color=0,0,255 visibility=1 + variableStep chrom=chrM + 1 2 + 2 1 + 3 1 + 4 1 + track type=wiggle_0 name="Track C" description="User Supplied SNP Track (from Galaxy)" color=255,0,255 visibility=1 + variableStep chrom=chrM + 2 1 + + </help> +</tool>

1 0

[hg] galaxy 1516: Update to latest gmaj.
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/f1da9b95549b changeset: 1516:f1da9b95549b user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Sep 18 15:24:51 2008 -0400 description: Update to latest gmaj. 1 file(s) affected in this change: static/gmaj/gmaj.jar diffs (2 lines): diff -r 280e8b68f845 -r f1da9b95549b static/gmaj/gmaj.jar Binary file static/gmaj/gmaj.jar has changed

1 0

[hg] galaxy 1517: update shrimp_wrapper.
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/1d326855ba89 changeset: 1517:1d326855ba89 user: wychung date: Thu Sep 18 15:41:23 2008 -0400 description: update shrimp_wrapper. 2 file(s) affected in this change: tools/metag_tools/shrimp_wrapper.py tools/metag_tools/shrimp_wrapper.xml diffs (621 lines): diff -r f1da9b95549b -r 1d326855ba89 tools/metag_tools/shrimp_wrapper.py --- a/tools/metag_tools/shrimp_wrapper.py Thu Sep 18 15:24:51 2008 -0400 +++ b/tools/metag_tools/shrimp_wrapper.py Thu Sep 18 15:41:23 2008 -0400 @@ -61,17 +61,13 @@ reversed_s.reverse() return "".join(reversed_s) -def generate_sub_table(result_file, ref_file, score_files, table_outfile, hit_per_read): +def generate_sub_table(result_file, ref_file, score_files, table_outfile, hit_per_read, insertion_size): - """ - TODO: the cross-over error has not been addressed yet. - """ + invalid_editstring_char = 0 - insertion_size = 600 + all_score_file = score_files.split(',') - all_score_file = score_files.split('&') - - if len(all_score_file) != hit_per_read: stop_err('Un-equal number of files!') + if len(all_score_file) != hit_per_read: stop_err('One or more query files is missing. Please check your dataset.') temp_table_name = tempfile.NamedTemporaryFile().name temp_table = open(temp_table_name, 'w') @@ -178,7 +174,7 @@ hits_score[readname] = {} hits_score[readname][endindex] = score - # mutation call to all mappings + # call to all mappings for readkey in hits.keys(): if len(hits[readkey]) != hit_per_read: continue @@ -211,6 +207,7 @@ match_count += 1 if match_count == 1: + for x, end_data in enumerate(matches[0]): end_strand, end_editstring, end_chr_start, end_chr_end, end_read_start, end_chrom = end_data @@ -226,20 +223,26 @@ gap_read = 0 while editindex < len(end_editstring): + editchr = end_editstring[editindex] chrA = '' chrB = '' locIndex = [] + if editchr.isdigit(): editcode = '' + while editchr.isdigit() and editindex < len(end_editstring): editcode += editchr editindex += 1 if editindex < len(end_editstring): editchr = end_editstring[editindex] + for baseIndex in range(int(editcode)): chrA += refsegment[match_len+baseIndex] chrB = chrA + match_len += int(editcode) + elif editchr == 'x': # crossover: inserted between the appropriate two bases # Two sequencing errors: 4x15x6 (25 matches with 2 crossovers) @@ -263,18 +266,21 @@ elif editchr == '(': editcode = '' + while editchr != ')' and editindex < len(end_editstring): if editindex < len(end_editstring): editchr = end_editstring[editindex] editcode += editchr editindex += 1 + editcode = editcode[1:-1] chrA = '-'*len(editcode) chrB = editcode else: - print 'Warning! Unknown symbols', editchr - + invalid_editstring_char += 1 + if end_strand == '-': + chrA = reverse_complement(chrA) chrB = reverse_complement(chrB) @@ -288,9 +294,12 @@ chrBx = chrB[mappingIndex] if chrAx and chrBx and chrBx.upper() != 'N': + if end_strand == '+': + chrom_loc = end_chr_start+match_len-len(chrA)+mappingIndex read_loc = end_read_start+match_len-len(chrA)+mappingIndex-gap_read + if chrAx == '-': chrom_loc -= 1 if chrBx == '-': @@ -300,9 +309,12 @@ # 1-based on chrom_loc and read_loc pos_line = pos_line + '\t'.join([end_chrom, str(chrom_loc+1), readkey+'/'+str(x+1), str(read_loc+1), chrAx, chrBx, scoreBx]) + '\n' + else: + chrom_loc = end_chr_end-match_len+mappingIndex read_loc = end_read_start+match_len-1-mappingIndex-gap_read + if chrAx == '-': chrom_loc -= 1 if chrBx == '-': @@ -314,11 +326,14 @@ rev_line = '\t'.join([end_chrom, str(chrom_loc+1), readkey+'/'+str(x+1), str(read_loc+1), chrAx, chrBx, scoreBx]) +'\n' + rev_line if chrom_cov.has_key(end_chrom): + if chrom_cov[end_chrom].has_key(chrom_loc): chrom_cov[end_chrom][chrom_loc] += 1 else: chrom_cov[end_chrom][chrom_loc] = 1 + else: + chrom_cov[end_chrom] = {} chrom_cov[end_chrom][chrom_loc] = 1 @@ -329,6 +344,7 @@ # chrom-wide coverage for i, line in enumerate(open(temp_table_name)): + line = line.rstrip() if not line or line.startswith('#'): continue @@ -348,6 +364,9 @@ outfile.close() if os.path.exists(temp_table_name): os.remove(temp_table_name) + + if invalid_editstring_char: + print 'Skip ', invalid_editstring_char, ' invalid characters in editstrings' return True @@ -359,7 +378,7 @@ seq_title_startswith = '' qual_title_startswith = '' - default_coding_value = 64 + default_coding_value = 64 # Solexa ascii-code fastq_block_lines = 0 for i, line in enumerate( file( infile_name ) ): @@ -448,16 +467,63 @@ def __main__(): + # SHRiMP path + shrimp = 'rmapper-ls' + # I/O - type_of_reads = sys.argv[1] # single or paired - input_target = sys.argv[2] # fasta - shrimp_outfile = sys.argv[3] # shrimp output - table_outfile = sys.argv[4] # table output - - # SHRiMP parameters: total = 15 - # TODO: put threshold on each of these parameters - if len(sys.argv) == 21 or len(sys.argv) == 22: - spaced_seed = sys.argv[5] + input_target_file = sys.argv[1] # fasta + shrimp_outfile = sys.argv[2] # shrimp output + table_outfile = sys.argv[3] # table output + single_or_paired = sys.argv[4].split(',') + + insertion_size = 600 + + if len(single_or_paired) == 1: # single or paired + type_of_reads = 'single' + hit_per_read = 1 + input_query = single_or_paired[0] + query_fasta = tempfile.NamedTemporaryFile().name + query_qual = tempfile.NamedTemporaryFile().name + + else: # paired-end + type_of_reads = 'paired' + hit_per_read = 2 + input_query_end1 = single_or_paired[0] + input_query_end2 = single_or_paired[1] + insertion_size = int(single_or_paired[2]) + query_fasta_end1 = tempfile.NamedTemporaryFile().name + query_fasta_end2 = tempfile.NamedTemporaryFile().name + query_qual_end1 = tempfile.NamedTemporaryFile().name + query_qual_end2 = tempfile.NamedTemporaryFile().name + + # SHRiMP parameters: total = 15, default values + spaced_seed = '111111011111' + seed_matches_per_window = '2' + seed_hit_taboo_length = '4' + seed_generation_taboo_length = '0' + seed_window_length = '115.0' + max_hits_per_read = '100' + max_read_length = '1000' + kmer = '-1' + sw_match_value = '100' + sw_mismatch_value = '-150' + sw_gap_open_ref = '-400' + sw_gap_open_query = '-400' + sw_gap_ext_ref = '-70' + sw_gap_ext_query = '-70' + sw_hit_threshold = '68.0' + + # TODO: put the threshold on each of these parameters + if len(sys.argv) > 5: + + try: + if sys.argv[5].isdigit(): + spaced_seed = sys.argv[5] + else: + stop_err('Error in assigning parameter: Spaced seed.') + except: + stop_err('Spaced seed must be a combination of 1s and 0s.') + seed_matches_per_window = sys.argv[6] seed_hit_taboo_length = sys.argv[7] seed_generation_taboo_length = sys.argv[8] @@ -473,53 +539,6 @@ sw_gap_ext_query = sys.argv[18] sw_hit_threshold = sys.argv[19] - # Single-end parameters - if type_of_reads == 'single': - input_query = sys.argv[20] # single-end - hit_per_read = 1 - query_fasta = tempfile.NamedTemporaryFile().name - query_qual = tempfile.NamedTemporaryFile().name - else: # Paired-end parameters - input_query_end1 = sys.argv[20] # paired-end - input_query_end2 = sys.argv[21] - hit_per_read = 2 - query_fasta_end1 = tempfile.NamedTemporaryFile().name - query_fasta_end2 = tempfile.NamedTemporaryFile().name - query_qual_end1 = tempfile.NamedTemporaryFile().name - query_qual_end2 = tempfile.NamedTemporaryFile().name - else: - spaced_seed = '111111011111' - seed_matches_per_window = '2' - seed_hit_taboo_length = '4' - seed_generation_taboo_length = '0' - seed_window_length = '115.0' - max_hits_per_read = '100' - max_read_length = '1000' - kmer = '-1' - sw_match_value = '100' - sw_mismatch_value = '-150' - sw_gap_open_ref = '-400' - sw_gap_open_query = '-400' - sw_gap_ext_ref = '-70' - sw_gap_ext_query = '-70' - sw_hit_threshold = '68.0' - - # Single-end parameters - if type_of_reads == 'single': - input_query = sys.argv[5] # single-end - hit_per_read = 1 - query_fasta = tempfile.NamedTemporaryFile().name - query_qual = tempfile.NamedTemporaryFile().name - else: # Paired-end parameters - input_query_end1 = sys.argv[5] # paired-end - input_query_end2 = sys.argv[6] - hit_per_read = 2 - query_fasta_end1 = tempfile.NamedTemporaryFile().name - query_fasta_end2 = tempfile.NamedTemporaryFile().name - query_qual_end1 = tempfile.NamedTemporaryFile().name - query_qual_end2 = tempfile.NamedTemporaryFile().name - - # temp file for shrimp log file shrimp_log = tempfile.NamedTemporaryFile().name @@ -532,7 +551,7 @@ # SHRiMP command if type_of_reads == 'single': - command = ' '.join(['rmapper-ls', '-s', spaced_seed, '-n', seed_matches_per_window, '-t', seed_hit_taboo_length, '-9', seed_generation_taboo_length, '-w', seed_window_length, '-o', max_hits_per_read, '-r', max_read_length, '-d', kmer, '-m', sw_match_value, '-i', sw_mismatch_value, '-g', sw_gap_open_ref, '-q', sw_gap_open_query, '-e', sw_gap_ext_ref, '-f', sw_gap_ext_query, '-h', sw_hit_threshold, query_fasta, input_target, '>', shrimp_outfile, '2>', shrimp_log]) + command = ' '.join([shrimp, '-s', spaced_seed, '-n', seed_matches_per_window, '-t', seed_hit_taboo_length, '-9', seed_generation_taboo_length, '-w', seed_window_length, '-o', max_hits_per_read, '-r', max_read_length, '-d', kmer, '-m', sw_match_value, '-i', sw_mismatch_value, '-g', sw_gap_open_ref, '-q', sw_gap_open_query, '-e', sw_gap_ext_ref, '-f', sw_gap_ext_query, '-h', sw_hit_threshold, query_fasta, input_target_file, '>', shrimp_outfile, '2>', shrimp_log]) try: os.system(command) @@ -541,9 +560,9 @@ if os.path.exists(query_qual): os.remove(query_qual) stop_err(str(e)) - else: - command_end1 = ' '.join(['rmapper-ls', '-s', spaced_seed, '-n', seed_matches_per_window, '-t', seed_hit_taboo_length, '-9', seed_generation_taboo_length, '-w', seed_window_length, '-o', max_hits_per_read, '-r', max_read_length, '-d', kmer, '-m', sw_match_value, '-i', sw_mismatch_value, '-g', sw_gap_open_ref, '-q', sw_gap_open_query, '-e', sw_gap_ext_ref, '-f', sw_gap_ext_query, '-h', sw_hit_threshold, query_fasta_end1, input_target, '>', shrimp_outfile, '2>', shrimp_log]) - command_end2 = ' '.join(['rmapper-ls', '-s', spaced_seed, '-n', seed_matches_per_window, '-t', seed_hit_taboo_length, '-9', seed_generation_taboo_length, '-w', seed_window_length, '-o', max_hits_per_read, '-r', max_read_length, '-d', kmer, '-m', sw_match_value, '-i', sw_mismatch_value, '-g', sw_gap_open_ref, '-q', sw_gap_open_query, '-e', sw_gap_ext_ref, '-f', sw_gap_ext_query, '-h', sw_hit_threshold, query_fasta_end2, input_target, '>>', shrimp_outfile, '2>>', shrimp_log]) + else: # paired + command_end1 = ' '.join([shrimp, '-s', spaced_seed, '-n', seed_matches_per_window, '-t', seed_hit_taboo_length, '-9', seed_generation_taboo_length, '-w', seed_window_length, '-o', max_hits_per_read, '-r', max_read_length, '-d', kmer, '-m', sw_match_value, '-i', sw_mismatch_value, '-g', sw_gap_open_ref, '-q', sw_gap_open_query, '-e', sw_gap_ext_ref, '-f', sw_gap_ext_query, '-h', sw_hit_threshold, query_fasta_end1, input_target_file, '>', shrimp_outfile, '2>', shrimp_log]) + command_end2 = ' '.join([shrimp, '-s', spaced_seed, '-n', seed_matches_per_window, '-t', seed_hit_taboo_length, '-9', seed_generation_taboo_length, '-w', seed_window_length, '-o', max_hits_per_read, '-r', max_read_length, '-d', kmer, '-m', sw_match_value, '-i', sw_mismatch_value, '-g', sw_gap_open_ref, '-q', sw_gap_open_query, '-e', sw_gap_ext_ref, '-f', sw_gap_ext_query, '-h', sw_hit_threshold, query_fasta_end2, input_target_file, '>>', shrimp_outfile, '2>>', shrimp_log]) try: os.system(command_end1) @@ -557,9 +576,9 @@ # convert to table if type_of_reads == 'single': - return_value = generate_sub_table(shrimp_outfile, input_target, query_qual, table_outfile, hit_per_read) + return_value = generate_sub_table(shrimp_outfile, input_target_file, query_qual, table_outfile, hit_per_read, insertion_size) else: - return_value = generate_sub_table(shrimp_outfile, input_target, query_qual_end1+'&'+query_qual_end2, table_outfile, hit_per_read) + return_value = generate_sub_table(shrimp_outfile, input_target_file, query_qual_end1+','+query_qual_end2, table_outfile, hit_per_read, insertion_size) # remove temp. files if type_of_reads == 'single': diff -r f1da9b95549b -r 1d326855ba89 tools/metag_tools/shrimp_wrapper.xml --- a/tools/metag_tools/shrimp_wrapper.xml Thu Sep 18 15:24:51 2008 -0400 +++ b/tools/metag_tools/shrimp_wrapper.xml Thu Sep 18 15:41:23 2008 -0400 @@ -1,50 +1,51 @@ <tool id="shrimp_wrapper" name="SHRiMP" version="1.0.0"> <description>SHort Read Mapping Package</description> <command interpreter="python"> - #if ($type_of_reads.single_or_paired=="single" and $param.skip_or_full=="skip"):#shrimp_wrapper.py $type_of_reads.single_or_paired $input_target $output1 $output2 $input_query - #elif ($type_of_reads.single_or_paired=="paired" and $param.skip_or_full=="skip"):#shrimp_wrapper.py $type_of_reads.single_or_paired $input_target $output1 $output2 ${type_of_reads.input1} ${type_of_reads.input2} - #elif ($type_of_reads.single_or_paired=="single" and $param.skip_or_full=="full"):#shrimp_wrapper.py $type_of_reads.single_or_paired $input_target $output1 $output2 $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_hit_threshold $input_query - #elif ($type_of_reads.single_or_paired=="paired" and $param.skip_or_full=="full"):#shrimp_wrapper.py $type_of_reads.single_or_paired $input_target $output1 $output2 $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_hit_threshold ${type_of_reads.input1} ${type_of_reads.input2} + #if ($type_of_reads.single_or_paired=="single" and $param.skip_or_full=="skip"):#shrimp_wrapper.py $input_target $output1 $output2 $input_query + #elif ($type_of_reads.single_or_paired=="paired" and $param.skip_or_full=="skip"):#shrimp_wrapper.py $input_target $output1 $output2 $type_of_reads.input1,$type_of_reads.input2,$type_of_reads.insertion_size + #elif ($type_of_reads.single_or_paired=="single" and $param.skip_or_full=="full"):#shrimp_wrapper.py $input_target $output1 $output2 $input_query $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_hit_threshold + #elif ($type_of_reads.single_or_paired=="paired" and $param.skip_or_full=="full"):#shrimp_wrapper.py $input_target $output1 $output2 $type_of_reads.input1,$type_of_reads.input2,$type_of_reads.insertion_size $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_hit_threshold #end if </command> <inputs> <page> - <param name="input_target" type="data" format="fasta" label="Reference sequence" /> <conditional name="type_of_reads"> <param name="single_or_paired" type="select" label="Single- or Paired-ends"> <option value="single">Single-end</option> <option value="paired">Paired-end</option> </param> <when value="single"> - <param name="input_query" type="data" format="fastqsolexa" label="Sequence file" /> + <param name="input_query" type="data" format="fastqsolexa" label="Align sequencing reads" /> </when> <when value="paired"> - <param name="input1" type="data" format="fastqsolexa" label="One end" /> - <param name="input2" type="data" format="fastqsolexa" label="The other end" /> + <param name="insertion_size" type="integer" size="5" value="600" label="Insertion length between two ends" help="bp" /> + <param name="input1" type="data" format="fastqsolexa" label="Align sequencing reads, one end" /> + <param name="input2" type="data" format="fastqsolexa" label="and the other end" /> </when> </conditional> + <param name="input_target" type="data" format="fasta" label="against reference" /> <conditional name="param"> - <param name="skip_or_full" type="select" label="SHRiMP parameter selection"> - <option value="skip">Default setting</option> - <option value="full">Full list</option> + <param name="skip_or_full" type="select" label="SHRiMP settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full List"> + <option value="skip">Commonly used</option> + <option value="full">Full Parameter List</option> </param> <when value="skip" /> <when value="full"> - <param name="spaced_seed" type="text" size="30" value="111111011111" label="Spaced Seed" /> - <param name="seed_matches_per_window" type="integer" size="5" value="2" label="Seed Matches per Window" /> - <param name="seed_hit_taboo_length" type="integer" size="5" value="4" label="Seed Hit Taboo Length" /> - <param name="seed_generation_taboo_length" type="integer" size="5" value="0" label="Seed Generation Taboo Length" /> - <param name="seed_window_length" type="float" size="10" value="115.0" label="Seed Window Length" help="in percentage"/> - <param name="max_hits_per_read" type="integer" size="10" value="100" label="Maximum Hits per Read" /> - <param name="max_read_length" type="integer" size="10" value="1000" label="Maximum Read Length" /> - <param name="kmer" type="integer" size="10" value="-1" label="Kmer Std. Deviation Limit" help="-1 as None"/> - <param name="sw_match_value" type="integer" size="10" value="100" label="S-W Match Value" /> - <param name="sw_mismatch_value" type="integer" size="10" value="-150" label="S-W Mismatch Value" /> - <param name="sw_gap_open_ref" type="integer" size="10" value="-400" label="S-W Gap Open Penalty (Reference)" /> - <param name="sw_gap_open_query" type="integer" size="10" value="-400" label="S-W Gap Open Penalty (Query)" /> - <param name="sw_gap_ext_ref" type="integer" size="10" value="-70" label="S-W Gap Extend Penalty (Reference)" /> - <param name="sw_gap_ext_query" type="integer" size="10" value="-70" label="S-W Gap Extend Penalty (Query)" /> - <param name="sw_hit_threshold" type="float" size="10" value="68.0" label="S-W Hit Threshold" help="in percentage"/> + <param name="spaced_seed" type="text" size="30" value="111111011111" label="Spaced Seed" /> + <param name="seed_matches_per_window" type="integer" size="5" value="2" label="Seed Matches per Window" /> + <param name="seed_hit_taboo_length" type="integer" size="5" value="4" label="Seed Hit Taboo Length" /> + <param name="seed_generation_taboo_length" type="integer" size="5" value="0" label="Seed Generation Taboo Length" /> + <param name="seed_window_length" type="float" size="10" value="115.0" label="Seed Window Length" help="in percentage"/> + <param name="max_hits_per_read" type="integer" size="10" value="100" label="Maximum Hits per Read" /> + <param name="max_read_length" type="integer" size="10" value="1000" label="Maximum Read Length" /> + <param name="kmer" type="integer" size="10" value="-1" label="Kmer Std. Deviation Limit" help="-1 as None"/> + <param name="sw_match_value" type="integer" size="10" value="100" label="S-W Match Value" /> + <param name="sw_mismatch_value" type="integer" size="10" value="-150" label="S-W Mismatch Value" /> + <param name="sw_gap_open_ref" type="integer" size="10" value="-400" label="S-W Gap Open Penalty (Reference)" /> + <param name="sw_gap_open_query" type="integer" size="10" value="-400" label="S-W Gap Open Penalty (Query)" /> + <param name="sw_gap_ext_ref" type="integer" size="10" value="-70" label="S-W Gap Extend Penalty (Reference)" /> + <param name="sw_gap_ext_query" type="integer" size="10" value="-70" label="S-W Gap Extend Penalty (Query)" /> + <param name="sw_hit_threshold" type="float" size="10" value="68.0" label="S-W Hit Threshold" help="in percentage"/> </when> </conditional> </page> @@ -54,7 +55,7 @@ <data name="output2" format="tabular"/> </outputs> <requirements> - <requirement type="binary">SHRiMP_rmapper</requirement> + <requirement type="binary">rmapper-ls</requirement> </requirements> <tests> <test> @@ -64,13 +65,14 @@ <param name="input_query" value="shrimp_wrapper_test1.fastq" ftype="fastqsolexa"/> <output name="output1" file="shrimp_wrapper_test1.out1" /> </test> -  @@ -124,67 +127,146 @@ .. class:: warningmark -Only nucleotide sequences as query. +Please note that only **nucleotide** sequences (letter-space) can be used as query. ----- **What it does** -Run SHRiMP on letter-space reads. - +SHRiMP (SHort Read Mapping Package) is a software package for aligning genomic reads against a target genome. + +This wrapper post-processes the default SHRiMP/rmapper-ls output and generates a table with all information from reads and reference for the mapping. The tool takes single- or paired-end reads. For single-end reads, only uniquely mapped alignment is considered. In paired-end reads, only pairs that meet the following criteria will be used to generate the table: 1). the ends fall within the insertion size; 2). the ends are mapped at the opposite directions. If there are still multiple mappings after applying the criteria, this paired-end read will be discarded. + + ----- - -**Example** - -- Input a multiple-fastq file like the following:: + +**Input formats** + +A multiple-fastq file, for example:: @seq1 TACCCGATTTTTTGCTTTCCACTTTATCCTACCCTT - +seq2 + +seq1 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh -- Use default settings (for detail explanations, please see **Parameters** section) - -- Search against your own uploaded file, result will be in the following format:: - - +-------+-------+--------+----------+----------+---------+--------+--------+-------+------------+ - | id | chrom | strand | t.start | t.end | q.start | q.end | length | score | editstring | - +-------+-------+--------+----------+----------+---------+--------+--------+-------+------------+ - | >seq1 | chrMT | + | 14712 | 14747 | 1 | 36 | 36 | 3350 | 24T11 | - +-------+-------+--------+----------+----------+---------+--------+--------+-------+------------+ - -- The result will be formatted Table:: - - +-------+---------+---------+----------+---------+----------+---------+----------+ - | chrom | ref_loc | read_id | read_loc | ref_nuc | read_nuc | quality | coverage | - +-------+---------+---------+----------+---------+----------+---------+----------+ - | chrMT | 14711 | seq1 | 0 | T | T | 40 | 1 | - | chrMT | 14712 | seq1 | 1 | A | A | 40 | 1 | - | chrMT | 14713 | seq1 | 2 | C | C | 40 | 1 | - +-------+---------+---------+----------+---------+----------+---------+----------+ ----- -**Parameters** +**Outputs** -Parameter list with default value settings:: +The tool gives two outputs. + +**Table output** + +Table output contains 8 columns:: + + 1 2 3 4 5 6 7 8 + ---------------------------------------------------- + chrM 14711 seq1 0 T A 40 1 + chrM 14712 seq1 1 T T 40 1 + +where:: + + 1. (chrM) - Reference sequence id + 2. (14711) - Position of the mapping in the reference + 3. (seq1) - Read id + 4. (0) - Position of the mapping in the read + 5. (T) - Nucleotide in the reference + 6. (A) - Nucleotide in the read + 7. (40) - Quality score for the nucleotide in the position of the read + 8. (1) - The number of times this position is covered by reads + + +**SHRiMP output** + +This is the default output from SHRiMP/rmapper-ls:: + + 1 2 3 4 5 6 7 8 9 10 + ------------------------------------------------------------------- + seq1 chrM + 3644 3679 1 36 36 3600 36 + +where:: + + 1. (seq1) - Read id + 2. (chrM) - Reference sequence id + 3. (+) - Strand of the read + 4. (3466) - Start position of the alignment in the reference + 5. (3679) - End position of the alignment in the reference + 6. (1) - Start position of the alignment in the read + 7. (36) - End position of the alignment in the read + 8. (36) - Length of the read + 9. (3600) - Score + 10. (36) - Edit string + + +----- + +**SHRiMP parameter list** + +The commonly used parameters with default value setting:: -s Spaced Seed (default: 111111011111) + The spaced seed is a single contiguous string of 0's and 1's. + 0's represent wildcards, or positions which will always be + considered as matching, whereas 1's dictate positions that + must match. A string of all 1's will result in a simple kmer scan. -n Seed Matches per Window (default: 2) + The number of seed matches per window dictates how many seeds + must match within some window length of the genome before that + region is considered for Smith-Waterman alignment. A lower + value will increase sensitivity while drastically increasing + running time. Higher values will have the opposite effect. -t Seed Hit Taboo Length (default: 4) + The seed taboo length specifies how many target genome bases + or colours must exist prior to a previous seed match in order + to count another seed match as a hit. -9 Seed Generation Taboo Length (default: 0) + -w Seed Window Length (default: 115.00%) + This parameter specifies the genomic span in bases (or colours) + in which *seed_matches_per_window* must exist before the read + is given consideration by the Simth-Waterman alignment machinery. -o Maximum Hits per Read (default: 100) + This parameter specifies how many hits to remember for each read. + If more hits are encountered, ones with lower scores are dropped + to make room. -r Maximum Read Length (default: 1000) + This parameter specifies the maximum length of reads that will + be encountered in the dataset. If larger reads than the default + are used, an appropriate value must be passed to *rmapper*. -d Kmer Std. Deviation Limit (default: -1 [None]) + This option permits pruning read kmers, which occur with + frequencies greater than *kmer_std_dev_limit* standard + deviations above the average. This can shorten running + time at the cost of some sensitivity. + *Note*: A negative value disables this option. + -m S-W Match Value (default: 100) + The value applied to matches during the Smith-Waterman score calculation. + -i S-W Mismatch Value (default: -150) + The value applied to mismatches during the Smith-Waterman + score calculation. + -g S-W Gap Open Penalty (Reference) (default: -400) + The value applied to gap opens along the reference sequence + during the Smith-Waterman score calculation. + *Note*: Note that for backward compatibility, if -g is set + and -q is not set, the gap open penalty for the query will + be set to the same value as specified for the reference. + -q S-W Gap Open Penalty (Query) (default: -400) + The value applied to gap opens along the query sequence during + the Smith-Waterman score calculation. + -e S-W Gap Extend Penalty (Reference) (default: -70) + The value applied to gap extends during the Smith-Waterman score calculation. + *Note*: Note that for backward compatibility, if -e is set + and -f is not set, the gap exten penalty for the query will + be set to the same value as specified for the reference. + -f S-W Gap Extend Penalty (Query) (default: -70) + The value applied to gap extends during the Smith-Waterman score calculation. + -h S-W Hit Threshold (default: 68.00%) + In letter-space, this parameter determines the threshold + score for both vectored and full Smith-Waterman alignments. + Any values less than this quanitity will be thrown away. + *Note* This option differs slightly in meaning between letter-space and colour-space. - -m S-W Match Value (default: 100) - -i S-W Mismatch Value (default: -150) - -g S-W Gap Open Penalty (Reference) (default: -400) - -q S-W Gap Open Penalty (Query) (default: -400) - -e S-W Gap Extend Penalty (Reference) (default: -70) - -f S-W Gap Extend Penalty (Query) (default: -70) - -h S-W Hit Threshold (default: 68.00%) -----

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[hg] galaxy 1504: Typos
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/4e2ed1801931 changeset: 1504:4e2ed1801931 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Fri Sep 12 15:35:50 2008 -0400 description: Typos 1 file(s) affected in this change: tools/sr_mapping/lastz_wrapper.xml diffs (17 lines): diff -r 777e41dbdf1f -r 4e2ed1801931 tools/sr_mapping/lastz_wrapper.xml --- a/tools/sr_mapping/lastz_wrapper.xml Fri Sep 12 15:14:20 2008 -0400 +++ b/tools/sr_mapping/lastz_wrapper.xml Fri Sep 12 15:35:50 2008 -0400 @@ -216,11 +216,11 @@ **Full Parameter List** -The modes gives you a fuller control over lastz. The description of these and other parameters is found at the end of this page. Note, that not all parameters are included in this interface. If you would like to make additional options available through Galaxy, e-mail us at galaxy-bugs(a)bx.psu.edu. +This modes gives you a fuller control over lastz. The description of these and other parameters is found at the end of this page. Note, that not all parameters are included in this interface. If you would like to make additional options available through Galaxy, e-mail us at galaxy-bugs(a)bx.psu.edu. ------ -** Do you want to modify reference name?** +**Do you want to modify reference name?** This option allows you set the name of the reference sequence manually. This is helpful when, for example, you would like to make reference name compatible with the UCSC naming conventions to be able to display your lastz results as a custom track at UCSC Genome Browser.

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[hg] galaxy 1505: Update MAF stitcher to be more efficient. Requ...
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/b6ff467f4522 changeset: 1505:b6ff467f4522 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Sep 12 15:50:20 2008 -0400 description: Update MAF stitcher to be more efficient. Requires bx-pyhon rev>=449. 2 file(s) affected in this change: eggs.ini lib/galaxy/tools/util/maf_utilities.py diffs (188 lines): diff -r 4e2ed1801931 -r b6ff467f4522 eggs.ini --- a/eggs.ini Fri Sep 12 15:35:50 2008 -0400 +++ b/eggs.ini Fri Sep 12 15:50:20 2008 -0400 @@ -55,12 +55,12 @@ MySQL_python = _5.0.51a_static python_lzo = _static flup = .dev_r2311 -bx_python = _dev_r448 +bx_python = _dev_r449 nose = .dev_r101 ; source location, necessary for scrambling [source] -bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r448.tar.bz2 +bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r449.tar.bz2 Cheetah = http://umn.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar.gz DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://mysql.mirrors.pair.com/Downloads/MySQL-5.0/mysql-5.0.51a.tar.gz diff -r 4e2ed1801931 -r b6ff467f4522 lib/galaxy/tools/util/maf_utilities.py --- a/lib/galaxy/tools/util/maf_utilities.py Fri Sep 12 15:35:50 2008 -0400 +++ b/lib/galaxy/tools/util/maf_utilities.py Fri Sep 12 15:50:20 2008 -0400 @@ -54,11 +54,15 @@ #sets a position for a species def set_position( self, index, species, base ): + if len( base ) != 1: raise "A genomic position can only have a length of 1." + return self.set_range( index, species, base ) + #sets a range for a species + def set_range( self, index, species, bases ): if index >= self.size or index < 0: raise "Your index (%i) is out of range (0 - %i)." % ( index, self.size - 1 ) - if len(base) != 1: raise "A genomic position can only have a length of 1." + if len( bases ) == 0: raise "A set of genomic positions can only have a positive length." if species not in self.sequences.keys(): self.add_species( species ) self.sequences[species].seek( index ) - self.sequences[species].write( base ) + self.sequences[species].write( bases ) #Flush temp file of specified species, or all species def flush( self, species = None ): @@ -164,32 +168,40 @@ except: return ( None, None ) +def chop_block_by_region( block, src, region, species = None, mincols = 0, force_strand = None ): + ref = block.get_component_by_src( src ) + #We want our block coordinates to be from positive strand + if ref.strand == "-": + block = block.reverse_complement() + ref = block.get_component_by_src( src ) + + #save old score here for later use + old_score = block.score + slice_start = max( region.start, ref.start ) + slice_end = min( region.end, ref.end ) + + #slice block by reference species at determined limits + block = block.slice_by_component( ref, slice_start, slice_end ) + + if block.text_size > mincols: + if ( force_strand is None and region.strand != ref.strand ) or ( force_strand is not None and force_strand != ref.strand ): + block = block.reverse_complement() + # restore old score, may not be accurate, but it is better than 0 for everything + block.score = old_score + if species is not None: + block = block.limit_to_species( species ) + block.remove_all_gap_columns() + return block + return None #generator yielding only chopped and valid blocks for a specified region def get_chopped_blocks_for_region( index, src, region, species = None, mincols = 0, force_strand = None ): - for block in index.get_as_iterator( src, region.start, region.end ): - ref = block.get_component_by_src( src ) - #We want our block coordinates to be from positive strand - if ref.strand == "-": - block = block.reverse_complement() - ref = block.get_component_by_src( src ) - - #save old score here for later use - old_score = block.score - slice_start = max( region.start, ref.start ) - slice_end = min( region.end, ref.end ) - - #slice block by reference species at determined limits - block = block.slice_by_component( ref, slice_start, slice_end ) - - if block.text_size > mincols: - if ( force_strand is None and region.strand != ref.strand ) or ( force_strand is not None and force_strand != ref.strand ): - block = block.reverse_complement() - # restore old score, may not be accurate, but it is better than 0 for everything - block.score = old_score - if species is not None: - block = block.limit_to_species( species ) - block.remove_all_gap_columns() - yield block + for block, idx, offset in get_chopped_blocks_with_index_offset_for_region( index, src, region, species, mincols, force_strand ): + yield block +def get_chopped_blocks_with_index_offset_for_region( index, src, region, species = None, mincols = 0, force_strand = None ): + for block, idx, offset in index.get_as_iterator_with_index_and_offset( src, region.start, region.end ): + block = chop_block_by_region( block, src, region, species, mincols ) + if block is not None: + yield block, idx, offset #returns a filled region alignment for specified regions def get_region_alignment( index, primary_species, chrom, start, end, strand = '+', species = None, mincols = 0 ): @@ -199,46 +211,51 @@ #fills a region alignment def fill_region_alignment( alignment, index, primary_species, chrom, start, end, strand = '+', species = None, mincols = 0 ): - #first step through blocks, save index and score in array, then order by score (array will start as 0=index0,scoreX) - #step through ordered list, step through maf blocks, stopping at index, store, then break inner loop region = bx.intervals.Interval( start, end ) region.chrom = chrom region.strand = strand primary_src = "%s.%s" % ( primary_species, chrom ) - + + def reduce_block_by_primary_genome( block ): + #returns ( startIndex, {species:texts} + #where texts' contents are reduced to only positions existing in the primary genome + ref = block.get_component_by_src( primary_src ) + start_offset = ref.start - start + species_texts = {} + for c in block.components: + species_texts[ c.src.split( '.' )[0] ] = list( c.text ) + #remove locations which are gaps in the primary species, starting from the downstream end + for i in range( len( species_texts[ primary_species ] ) - 1, -1, -1 ): + if species_texts[ primary_species ][i] == '-': + for text in species_texts.values(): + text.pop( i ) + for spec, text in species_texts.items(): + species_texts[spec] = ''.join( text ) + return ( start_offset, species_texts ) + #Order blocks overlaping this position by score, lowest first - blocks_order = [] - for i, block in enumerate( get_chopped_blocks_for_region( index, primary_src, region, species, mincols ) ): - for j in range( 0, len( blocks_order ) ): - if float( block.score ) < float( blocks_order[j]['score'] ): - blocks_order.insert( j, {'index':i, 'score':block.score} ) + blocks = [] + for block, idx, offset in index.get_as_iterator_with_index_and_offset( primary_src, start, end ): + score = float( block.score ) + for i in range( 0, len( blocks ) ): + if score < blocks[i][0]: + blocks.insert( i, ( score, idx, offset ) ) break else: - blocks_order.append( {'index':i, 'score':block.score} ) + blocks.append( ( score, idx, offset ) ) - #Loop through ordered block indexes and layer blocks by score - for block_dict in blocks_order: - for block_index, block in enumerate( get_chopped_blocks_for_region( index, primary_src, region, species, mincols ) ): - if block_index == block_dict['index']: - ref = block.get_component_by_src( primary_src ) - #skip gap locations due to insertions in secondary species relative to primary species - start_offset = ref.start - start - num_gaps = 0 - for i in range( len( ref.text.rstrip().rstrip("-") ) ): - if ref.text[i] in ["-"]: - num_gaps += 1 - continue - #Set base for all species - for spec in [ c.src.split( '.' )[0] for c in block.components ]: - try: - #NB: If a gap appears in higher scoring secondary species block, - #it will overwrite any bases that have been set by lower scoring blocks - #this seems more proper than allowing, e.g. a single base from lower scoring alignment to exist outside of its genomic context - alignment.set_position( start_offset + i - num_gaps, spec, block.get_component_by_src_start( spec ).text[i] ) - except: - #species/sequence for species does not exist - pass - break + #Loop through ordered blocks and layer by increasing score + for block_dict in blocks: + block = chop_block_by_region( block_dict[1].get_at_offset( block_dict[2] ), primary_src, region, species, mincols, strand ) + if block is None: continue + start_offset, species_texts = reduce_block_by_primary_genome( block ) + for spec, text in species_texts.items(): + try: + alignment.set_range( start_offset, spec, text ) + except: + #species/sequence for species does not exist + pass + return alignment #returns a filled spliced region alignment for specified region with start and end lists

1 0

[hg] galaxy 1506: Forgot two test datasets
by greg＠scofield.bx.psu.edu 22 Sep '08

22 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/26825f08d362 changeset: 1506:26825f08d362 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Sun Sep 14 14:58:50 2008 -0400 description: Forgot two test datasets 2 file(s) affected in this change: test-data/B1.fa test-data/phiX.fa diffs (1087 lines): diff -r b6ff467f4522 -r 26825f08d362 test-data/B1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/B1.fa Sun Sep 14 14:58:50 2008 -0400 @@ -0,0 +1,1000 @@ +>HWI-EAS91_1_306UPAAXX:6:1:1503:1160 +GGTGGTCTATAGTGTTATTAATATCAAGTTGGGGGG +>HWI-EAS91_1_306UPAAXX:6:1:1564:1179 +GCGAGCAGTAGACTCCTTCTGTTGATAAGCAAGCAT +>HWI-EAS91_1_306UPAAXX:6:1:1704:1082 +GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC +>HWI-EAS91_1_306UPAAXX:6:1:1588:1797 +GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT +>HWI-EAS91_1_306UPAAXX:6:1:1304:1526 +GTAGTTGAAATGGTAATAAGACGACCAATCTGACCT +>HWI-EAS91_1_306UPAAXX:6:1:1490:1582 +GTCGTGTTCAACAGACCTATAAACATTCTGTGCCGC +>HWI-EAS91_1_306UPAAXX:6:1:1356:1339 +GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC +>HWI-EAS91_1_306UPAAXX:6:1:1311:853 +GGTTGGTTTATCGTTTTTGACACTCTCACGTTGTCT +>HWI-EAS91_1_306UPAAXX:6:1:1257:1552 +GTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTC +>HWI-EAS91_1_306UPAAXX:6:1:1486:1402 +GTTACTGAGAAGTTAATGGATGAATTGGCACAATGC +>HWI-EAS91_1_306UPAAXX:6:1:1028:1081 +GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT +>HWI-EAS91_1_306UPAAXX:6:1:1167:752 +GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC +>HWI-EAS91_1_306UPAAXX:6:1:1507:1113 +GTCAACGTTATATTTTGATAGTTTGACGGTTAATTC +>HWI-EAS91_1_306UPAAXX:6:1:1654:1311 +GGATGAAAATGCTCACAATGACAAATCTGTCCACGG +>HWI-EAS91_1_306UPAAXX:6:1:1386:1060 +GTTCTTGGTCAGTATGCAAATTAGCATAAGCAGCTT +>HWI-EAS91_1_306UPAAXX:6:1:1070:1356 +GGTTACAGTATGCCCATCGCAGTTCGCTACACGCAG +>HWI-EAS91_1_306UPAAXX:6:1:787:1032 +GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCA +>HWI-EAS91_1_306UPAAXX:6:1:834:1017 +GCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGT +>HWI-EAS91_1_306UPAAXX:6:1:1703:1155 +GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT +>HWI-EAS91_1_306UPAAXX:6:1:1406:593 +GTTGAGTTCGATAATGGTGATATGTATGTTTACGGC +>HWI-EAS91_1_306UPAAXX:6:1:1411:886 +GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCAT +>HWI-EAS91_1_306UPAAXX:6:1:923:972 +GCATGACAAGTAAAGGACGGTTGTCAGCGTCATAAG +>HWI-EAS91_1_306UPAAXX:6:1:1279:1004 +GCCATAGCACCAGAAACAAAACTAGGGGCGGCCTCT +>HWI-EAS91_1_306UPAAXX:6:1:1070:840 +GGTTGTCAGCGTCATAAGAGGTTTTACCTCCAAATG +>HWI-EAS91_1_306UPAAXX:6:1:1595:1040 +GTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT +>HWI-EAS91_1_306UPAAXX:6:1:1002:559 +GAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG +>HWI-EAS91_1_306UPAAXX:6:1:999:974 +GTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGC +>HWI-EAS91_1_306UPAAXX:6:1:896:982 +GTGGCTGGAGACAAATAATCTCTTTAATAACCTTAT +>HWI-EAS91_1_306UPAAXX:6:1:1366:741 +GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGC +>HWI-EAS91_1_306UPAAXX:6:1:749:1469 +GTTTATGGTGAACAGTGGATTAAGTTCATGAAGGAT +>HWI-EAS91_1_306UPAAXX:6:1:1010:592 +GAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT +>HWI-EAS91_1_306UPAAXX:6:1:1393:650 +GTGACTCATATCTAAACCAGTCCTTGACGAACGTGC +>HWI-EAS91_1_306UPAAXX:6:1:1238:1731 +GAGAAATAAAAGTCTGAAACATGATTAAACTCCTAA +>HWI-EAS91_1_306UPAAXX:6:1:1629:908 +GATGCGGTTATCCATCTGCTTATGGAAGCCAAGCAT +>HWI-EAS91_1_306UPAAXX:6:1:1560:849 +GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAG +>HWI-EAS91_1_306UPAAXX:6:1:1029:783 +GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT +>HWI-EAS91_1_306UPAAXX:6:1:1152:1324 +GACAATCAGAAAGAGATTGCCGAGATGCAAAATGAG +>HWI-EAS91_1_306UPAAXX:6:1:1614:2042 +GAAATGCCACAAGCCTCAATAGCAGGTTTAAGAGCC +>HWI-EAS91_1_306UPAAXX:6:1:1398:439 +GATGGTTGGTTTATCGTTTTTGACACTCTCACGTTG +>HWI-EAS91_1_306UPAAXX:6:1:955:616 +GACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC +>HWI-EAS91_1_306UPAAXX:6:1:1672:753 +GAATGCCAGCAATCTCTTTTTGAGTCTCATTTTGCT +>HWI-EAS91_1_306UPAAXX:6:1:1195:1293 +GCAATGCGACAGGCTCATGCTGATGGTTGGTTTATC +>HWI-EAS91_1_306UPAAXX:6:1:1074:755 +GCAAGAGTAAACATAGTGCCATGCTCAGGAACAAAG +>HWI-EAS91_1_306UPAAXX:6:1:984:499 +GACTTAGTTCATCAGCAAACGCAGAATCAGCGGTAT +>HWI-EAS91_1_306UPAAXX:6:1:1452:1833 +GCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGT +>HWI-EAS91_1_306UPAAXX:6:1:863:710 +GAGTTCGATAATGGTGATATGTATGTTGACGGCCAT +>HWI-EAS91_1_306UPAAXX:6:1:885:649 +GCAGAAGTTAACACTTTCGGATATTTCTGATGAGTC +>HWI-EAS91_1_306UPAAXX:6:1:917:1214 +GACAGATGTATCCATCTGAATGCAATGAAGAAAACC +>HWI-EAS91_1_306UPAAXX:6:1:892:1254 +GCTCAGGAAATGCAGCAGCAAGATAATCACGAGTAT +>HWI-EAS91_1_306UPAAXX:6:1:1555:1005 +GCATTTGGCGCATAATCTCGGAAACCTGCTGTTGCT +>HWI-EAS91_1_306UPAAXX:6:1:1637:1413 +GATGCTGTTCAACCACTAATAGGTAAGAAATCATGT +>HWI-EAS91_1_306UPAAXX:6:1:1102:1567 +GGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAA +>HWI-EAS91_1_306UPAAXX:6:1:799:1337 +GTATATGCACAAAATGAGATGCTTGCTTATCAACAG +>HWI-EAS91_1_306UPAAXX:6:1:1353:1843 +GCAGACCCATAATGTCAATAGATGTGGTAGAAGTCG +>HWI-EAS91_1_306UPAAXX:6:1:1196:789 +GCGGCATACGCTCGGCGCCAGTTTGAATATTAGACA +>HWI-EAS91_1_306UPAAXX:6:1:1056:1676 +GTAAAATACTGACCAGCCGTTTGAGCTTGAGTAAGC +>HWI-EAS91_1_306UPAAXX:6:1:1349:1836 +GGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTC +>HWI-EAS91_1_306UPAAXX:6:1:1027:788 +GGTGTTAATGCCACTCCTCTCCCGACTGTTAACACT +>HWI-EAS91_1_306UPAAXX:6:1:990:1283 +GCTTAGGGATTTTATTGGTATCAGGGTTAATCGTGC +>HWI-EAS91_1_306UPAAXX:6:1:904:939 +GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT +>HWI-EAS91_1_306UPAAXX:6:1:1732:793 +GTCAACATACATATCACCATTATCGAACTCAACGCC +>HWI-EAS91_1_306UPAAXX:6:1:1355:2003 +GTTAGACCAAACCATGAAACCAACATAAACATTATT +>HWI-EAS91_1_306UPAAXX:6:1:1337:977 +GCACCAGAAACAAAACTAGGGGCGGCCTCATCAGGG +>HWI-EAS91_1_306UPAAXX:6:1:1605:1175 +GGAGGTAAAACCTCTTATGACGCTGACAACCGTCCT +>HWI-EAS91_1_306UPAAXX:6:1:1763:1192 +GACAGGCCGTTTGAATGTTGACGGGATGAACATAAT +>HWI-EAS91_1_306UPAAXX:6:1:722:483 +GTTATTATACCGTCAAGGACTGTGTGACTATTGACT +>HWI-EAS91_1_306UPAAXX:6:1:1760:1136 +GCAAAGCATTGGGATTATCATAAAACGCCTCTAATC +>HWI-EAS91_1_306UPAAXX:6:1:1088:798 +GGAAACCTGCTGTTGCTTGGAAAGATTGGTGTTTTC +>HWI-EAS91_1_306UPAAXX:6:1:633:1076 +GCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAG +>HWI-EAS91_1_306UPAAXX:6:1:673:754 +GTCATGGAAGCGATAAAACTCTGCAGGTTGGATATT +>HWI-EAS91_1_306UPAAXX:6:1:1759:2019 +GTAAAGGACGGTTGTCAGCGTCATAAGAGGTTTTAC +>HWI-EAS91_1_306UPAAXX:6:1:1064:1797 +GCGGTTATCCATCTGCTTATGGAAGCCAAGCATTGG +>HWI-EAS91_1_306UPAAXX:6:1:1112:1669 +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACT +>HWI-EAS91_1_306UPAAXX:6:1:510:1447 +GCATTAAGCTCAGGAAATGCAGCAGCAAGATAATCA +>HWI-EAS91_1_306UPAAXX:6:1:877:1573 +GTGCTATTGCTGGCGGTATTTCTTCTTCTTTTTTTT +>HWI-EAS91_1_306UPAAXX:6:1:870:542 +GAATGTCACGCTGATTATTTTGACTTTGAGCGTATC +>HWI-EAS91_1_306UPAAXX:6:1:966:384 +GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA +>HWI-EAS91_1_306UPAAXX:6:1:1186:1903 +GCCAGCGATAACCGGAGTAGTTGAAATGGTAATAAG +>HWI-EAS91_1_306UPAAXX:6:1:1632:1742 +GCATCACCCATGCCTACAGTATTGTTATCGGTAGCC +>HWI-EAS91_1_306UPAAXX:6:1:1521:559 +GAGAGCGCCAACGGCGTCCATCTCGAAGGAGTCGCC +>HWI-EAS91_1_306UPAAXX:6:1:683:454 +GCTTATTATGTTCATCCCGTCAACATTCAAACGTCC +>HWI-EAS91_1_306UPAAXX:6:1:112:1280 +GTTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTGTC +>HWI-EAS91_1_306UPAAXX:6:1:891:381 +GACCAGGGCGAGCGCCAGAACGTTTTTTACCTTTAG +>HWI-EAS91_1_306UPAAXX:6:1:1348:958 +GATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTT +>HWI-EAS91_1_306UPAAXX:6:1:1785:1915 +GCCCCGAAGGGGACNANAAATGGTTTTTAGAGAACG +>HWI-EAS91_1_306UPAAXX:6:1:1418:42 +GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTT +>HWI-EAS91_1_306UPAAXX:6:1:1421:743 +GGTCAACGCTACCTGTAGGAAGTGTCCGCATAAAAT +>HWI-EAS91_1_306UPAAXX:6:1:1079:790 +GCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGT +>HWI-EAS91_1_306UPAAXX:6:1:663:740 +GGTATTAAGGATGAGTGTTCAAGATTGCTGGATGCC +>HWI-EAS91_1_306UPAAXX:6:1:1245:413 +GTTTGAATGTTGACGGGATGAACATAATAAGCAATG +>HWI-EAS91_1_306UPAAXX:6:1:1378:1035 +GCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGG +>HWI-EAS91_1_306UPAAXX:6:1:903:1746 +GTACGGGGAAGGACGTCAATAGTCACACAGTCCTTG +>HWI-EAS91_1_306UPAAXX:6:1:1713:1134 +GGCGTACGGGGAAGGACGTCAATAGTCACACAGTCC +>HWI-EAS91_1_306UPAAXX:6:1:1246:1887 +GCTCTAATCTCTGGGCATCTGGCTATGATGTTGATG +>HWI-EAS91_1_306UPAAXX:6:1:872:1731 +GGGCGGCCTCATCAGGGTTAGGAACATTAGAGCCTT +>HWI-EAS91_1_306UPAAXX:6:1:1714:1582 +GCTTTCCTGCTCCTGTTGAGTTTATTGCTTCCGTCT +>HWI-EAS91_1_306UPAAXX:6:1:1785:763 +GNCGAGAAATAAAANNNTGAAACATGATTAAANTCC +>HWI-EAS91_1_306UPAAXX:6:1:1684:542 +GAAAAGACAGAATCTCTTCCAAGAGCTTGATGCGGT +>HWI-EAS91_1_306UPAAXX:6:1:1581:1665 +GACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATT +>HWI-EAS91_1_306UPAAXX:6:1:901:1581 +GTGCTGATATTGCTTTTGATGCCGACCCTAAATTTT +>HWI-EAS91_1_306UPAAXX:6:1:1128:239 +GGTTATTATACCGTCAAGGACTGTGTGACTATTGAC +>HWI-EAS91_1_306UPAAXX:6:1:969:441 +GGTAAGAAATCATGAGTCAAGTTACTGAACAATCCG +>HWI-EAS91_1_306UPAAXX:6:1:630:1087 +GCCACCATGATTATGACCAGTGTTTCCAGTCCGTTC +>HWI-EAS91_1_306UPAAXX:6:1:606:1852 +GGAGACAAATAATCTCTTTAATAACCTGATTCAGCG +>HWI-EAS91_1_306UPAAXX:6:1:489:1315 +GAAAGCTCAGTCTCAGGAGGAAGCGGAGCAGTCCAC +>HWI-EAS91_1_306UPAAXX:6:1:465:1983 +GAGCCAATACCATCAGCTTTACCGTCTTTCCAGAAA +>HWI-EAS91_1_306UPAAXX:6:1:559:1028 +GAGTGCTTAATCCAACTTACCAAGCTGGGTTACGAC +>HWI-EAS91_1_306UPAAXX:6:1:1655:1413 +GTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCG +>HWI-EAS91_1_306UPAAXX:6:1:980:605 +GCCGTTTGAATGTTGACGGGATGAACATAATAAGCA +>HWI-EAS91_1_306UPAAXX:6:1:1629:1865 +GAAAAGCGGCATGGTCAATATAACCAGTAGTGTTAT +>HWI-EAS91_1_306UPAAXX:6:1:1180:1920 +GCACTCCGTGGACAGATTTGTCATTGTGAGCATTTT +>HWI-EAS91_1_306UPAAXX:6:1:1116:383 +GCGCAGGAAACACTGACGTTCTTACTGACGCAGAAG +>HWI-EAS91_1_306UPAAXX:6:1:906:2041 +GTCACGTTTATGGTGAACAGTGGATTAAGTTCATGA +>HWI-EAS91_1_306UPAAXX:6:1:1514:157 +GTCAATAGATGTGGTAGAAGTCGTCATTTGGCGTGG +>HWI-EAS91_1_306UPAAXX:6:1:1032:1857 +GCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGT +>HWI-EAS91_1_306UPAAXX:6:1:638:609 +GATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAT +>HWI-EAS91_1_306UPAAXX:6:1:74:750 +GATAATCACGAGTATCCTTTCCTTTATCATCTTCAT +>HWI-EAS91_1_306UPAAXX:6:1:486:822 +GTTGACGATGTAGCTTTAGGTGTCTTTAAAACAGGT +>HWI-EAS91_1_306UPAAXX:6:1:899:473 +GAACAGCATCGGACTCAGATAGTAATCCACGCTCTT +>HWI-EAS91_1_306UPAAXX:6:1:1613:197 +GTGACATTCAGAAGGGTAATAAGAACGAACCATAAA +>HWI-EAS91_1_306UPAAXX:6:1:326:1747 +GTTGAGGCTTTCGTTTATTGTACGCTTTGCTTTTTT +>HWI-EAS91_1_306UPAAXX:6:1:1487:526 +GCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +>HWI-EAS91_1_306UPAAXX:6:1:629:665 +GAAATGCAGCAGCAAGATAATCACGAGTATCCTTTC +>HWI-EAS91_1_306UPAAXX:6:1:766:744 +GGCCGTCAACATACATATCACCATTATCGAACTCAA +>HWI-EAS91_1_306UPAAXX:6:1:391:1771 +GTGGTTGATATTTTTCATGGTATTGATAAATCTTTT +>HWI-EAS91_1_306UPAAXX:6:1:591:1102 +GCTTTGCGTGACTATTTTCGTGATATTGTTCGTTTG +>HWI-EAS91_1_306UPAAXX:6:1:917:664 +GCCATGATGGTGGTTATTATACCGTCAAGGACTGTG +>HWI-EAS91_1_306UPAAXX:6:1:217:737 +GTTCAGTTGTTGCATTGGAATATTCAGTTTAAATTT +>HWI-EAS91_1_306UPAAXX:6:1:1047:839 +GACCATTCAAAGGATAAACATCATAGGCAGTCGGGG +>HWI-EAS91_1_306UPAAXX:6:1:558:1040 +GCCACCAGCAAGAGCAGAAGCAATACCGCCAGCAAT +>HWI-EAS91_1_306UPAAXX:6:1:1207:524 +GCCAATACCATCAGCTTTACCGTCTTTCCAGAAATT +>HWI-EAS91_1_306UPAAXX:6:1:708:1634 +GCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAG +>HWI-EAS91_1_306UPAAXX:6:1:576:1851 +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAG +>HWI-EAS91_1_306UPAAXX:6:1:906:460 +GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC +>HWI-EAS91_1_306UPAAXX:6:1:693:1260 +GCGAAAGGTCGCAAAGTAAGAGCTTCTCGAGCTGCG +>HWI-EAS91_1_306UPAAXX:6:1:1373:286 +GGACACTTCCTACAGGTAGCGTTGACCCTAATTTTG +>HWI-EAS91_1_306UPAAXX:6:1:762:41 +GATACTTGGAACAATTTCTGGAAAGACGGTAAAGCT +>HWI-EAS91_1_306UPAAXX:6:1:475:1091 +GTCACACAGTCCTTGACGGTATAATAACCACCATCT +>HWI-EAS91_1_306UPAAXX:6:1:791:627 +GCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACC +>HWI-EAS91_1_306UPAAXX:6:1:336:1791 +GAAGGAGTCGCCAGCGATAACCGGAGTAGTTGAAAT +>HWI-EAS91_1_306UPAAXX:6:1:1483:943 +GCACGTAATTTTTGACGCACGTTTTCTTCTGCGTCT +>HWI-EAS91_1_306UPAAXX:6:1:641:1071 +GATGGGCATACTGTAACCATAAGGCCACGTATTTTG +>HWI-EAS91_1_306UPAAXX:6:1:196:755 +GAACGCCCTCTTAAGGATATTCGCGATGAGTATAAT +>HWI-EAS91_1_306UPAAXX:6:1:463:1398 +GTCATAAGAGGTTTTACCTCCAAATGAAGAAATAAC +>HWI-EAS91_1_306UPAAXX:6:1:1559:460 +GCTCACAATGACAAATCTGTCCACGGAGTGCTTAAT +>HWI-EAS91_1_306UPAAXX:6:1:1625:1561 +GAGGAGTGGCATTAACACCATCCTTCATGAACTTAC +>HWI-EAS91_1_306UPAAXX:6:1:1729:1588 +GCTGATAAAGGAAAGGATACTCGTGATTATCTTGCT +>HWI-EAS91_1_306UPAAXX:6:1:945:393 +GGCCTCATCAGGGTTAGGAACATTAGAGCCTTGAAT +>HWI-EAS91_1_306UPAAXX:6:1:298:1391 +GTAAAGTTAGACCAAACCATGAAACCAACATAAACA +>HWI-EAS91_1_306UPAAXX:6:1:1270:1500 +GAATTACTACTGCTTGTTTACGAATTAAATATATGT +>HWI-EAS91_1_306UPAAXX:6:1:481:1546 +GCTGGCATTCAGTCGGCGACTTCACGCCAGAATACG +>HWI-EAS91_1_306UPAAXX:6:1:473:1729 +GTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAT +>HWI-EAS91_1_306UPAAXX:6:1:801:1831 +GCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAAT +>HWI-EAS91_1_306UPAAXX:6:1:536:639 +GCCGACCCTAAATTTTTTGCCTGTTTGGTTCTCTTT +>HWI-EAS91_1_306UPAAXX:6:1:259:938 +GTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTG +>HWI-EAS91_1_306UPAAXX:6:1:907:1513 +GGCATGGGTGATGCTGGTATTAAATCTGCCATTCAC +>HWI-EAS91_1_306UPAAXX:6:1:372:1409 +GATGAGTATAATTACCCCAAAAAGAAAGGTATTAAG +>HWI-EAS91_1_306UPAAXX:6:1:485:1626 +GATGGCAGCAACGGAAACCATAACGAGCATCATCTT +>HWI-EAS91_1_306UPAAXX:6:1:583:1679 +GCTCAAAGTCAAAATAATCAGCGTGACATTCAGAAG +>HWI-EAS91_1_306UPAAXX:6:1:690:1610 +GACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTT +>HWI-EAS91_1_306UPAAXX:6:1:257:918 +GCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTTCT +>HWI-EAS91_1_306UPAAXX:6:1:818:33 +GTGTTAATGCCACTCCTCTCCCGACTGTTAACTCTG +>HWI-EAS91_1_306UPAAXX:6:1:541:1242 +GGGATTATCATAAAACGCCTCTAATCGGTCGTCAGC +>HWI-EAS91_1_306UPAAXX:6:1:1014:279 +GTAAAAATGTCTACAGTAGAGTCAATAGCAAGGCCC +>HWI-EAS91_1_306UPAAXX:6:1:672:1790 +GGCCGTTTGAATGTTGACGGGATGAACATAATAAGC +>HWI-EAS91_1_306UPAAXX:6:1:708:464 +GGAGACAAATAATCTCTTTAATAACCTGATTCAGCG +>HWI-EAS91_1_306UPAAXX:6:1:633:1486 +GGGAAAGGTCATGCGGCATACGCTCGGCGCCAGTTT +>HWI-EAS91_1_306UPAAXX:6:1:328:696 +GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT +>HWI-EAS91_1_306UPAAXX:6:1:259:1389 +GCGTACTTATTCGCCACCATGATTATTACCAGTGTT +>HWI-EAS91_1_306UPAAXX:6:1:1315:41 +GCTTTCCGTGATGTCACAGCCTGCTTTGATGTGTCG +>HWI-EAS91_1_306UPAAXX:6:1:1647:549 +GCTTAATCCAACTTACCAAGCTGGGTTACGACGCGC +>HWI-EAS91_1_306UPAAXX:6:1:300:886 +GTTCTTGGTCAGTATGCAAATTAGCATAAGCAGCTT +>HWI-EAS91_1_306UPAAXX:6:1:317:1411 +GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCTT +>HWI-EAS91_1_306UPAAXX:6:1:321:1819 +GGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGT +>HWI-EAS91_1_306UPAAXX:6:1:631:70 +GTGGATTACTATCTGAGTCCGATGCTGTTCAACCAC +>HWI-EAS91_1_306UPAAXX:6:1:624:1040 +GCTGGCGACTCCTTCGAGATGGACGCCGTTTGCGCT +>HWI-EAS91_1_306UPAAXX:6:1:662:1187 +GGGAGAGGAGTGGCATTAACACCATCCTTCATGACC +>HWI-EAS91_1_306UPAAXX:6:1:1440:1959 +GAATCAGCGGTATGGCTCCTCTCCTATTTTTGCTTC +>HWI-EAS91_1_306UPAAXX:6:1:458:1629 +GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT +>HWI-EAS91_1_306UPAAXX:6:1:216:790 +GGGATGAAAATGCTCACAATGACAAATCTGTCCACG +>HWI-EAS91_1_306UPAAXX:6:1:1407:1174 +TTACCTATTAGTGGTTGAACAGCATCGGACTCAGAT +>HWI-EAS91_1_306UPAAXX:6:1:999:1790 +GTCCTGCGTGTAGCGAACTGCGATGGGCATACTGTC +>HWI-EAS91_1_306UPAAXX:6:1:141:1994 +GGCTTTTTTATGGTTCGTTCTTATTACCCTTCTTAT +>HWI-EAS91_1_306UPAAXX:6:1:225:465 +GTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGC +>HWI-EAS91_1_306UPAAXX:6:1:649:1760 +GACCCATAATGTCAATAGATGTGGTAGAAGTCGTCT +>HWI-EAS91_1_306UPAAXX:6:1:300:986 +GTTGAACACGACCAGAAAACTGGCCTAACGACGTTT +>HWI-EAS91_1_306UPAAXX:6:1:478:605 +GAGACTGAGCTTTCTCGCCAAATGACGACTTCTACC +>HWI-EAS91_1_306UPAAXX:6:1:622:395 +GGTAGCTTTAAGCGGCTCACCTTTAGCATCAACAGG +>HWI-EAS91_1_306UPAAXX:6:1:1701:574 +GTAAAGCCTCTACGCGATTTCATAGTGGAGGCCTCC +>HWI-EAS91_1_306UPAAXX:6:1:646:59 +GGAAGTGTCCGCATAAAATGCACCGCATGGAAATGT +>HWI-EAS91_1_306UPAAXX:6:1:284:2031 +GACAGAATCGTTAGTTGATGGCGAAAGGTCGCAAAG +>HWI-EAS91_1_306UPAAXX:6:1:22:1009 +GATGGATACATCTGTCAACGCCGCTAATCAGGTTGT +>HWI-EAS91_1_306UPAAXX:6:1:47:1826 +GCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCG +>HWI-EAS91_1_306UPAAXX:6:1:1025:1236 +TGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGT +>HWI-EAS91_1_306UPAAXX:6:1:773:591 +GAGCAGGAAAGCGAGGGTATCCCACAAAGTCCAGCG +>HWI-EAS91_1_306UPAAXX:6:1:1753:527 +GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAAC +>HWI-EAS91_1_306UPAAXX:6:1:426:1717 +GTAGCGCCAATATGAGAAGAGCCATACCGCTGATTC +>HWI-EAS91_1_306UPAAXX:6:1:959:818 +TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC +>HWI-EAS91_1_306UPAAXX:6:1:459:1344 +GCCTATGATGTTTATCCTTTGAATGGTCGCCATGAT +>HWI-EAS91_1_306UPAAXX:6:1:973:1367 +TTCGTGATGAGTTTGTATCTGTTACTGATAAGTTAT +>HWI-EAS91_1_306UPAAXX:6:1:201:871 +GATTAGAGGCGTTTTATGATAATCCCAATGCTTTTC +>HWI-EAS91_1_306UPAAXX:6:1:713:1672 +GGCGTACGGGGAAGGACGTCAATAGTCACACAGTCC +>HWI-EAS91_1_306UPAAXX:6:1:444:1435 +TTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGTG +>HWI-EAS91_1_306UPAAXX:6:1:288:1136 +GCCTTCCATGATGAGACAGGCCGTTTTAATTTTTTC +>HWI-EAS91_1_306UPAAXX:6:1:1653:225 +GCAAGGCCACGACGCAATGGAGAAAGACGGAGAGCG +>HWI-EAS91_1_306UPAAXX:6:1:537:1764 +GCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAA +>HWI-EAS91_1_306UPAAXX:6:1:196:1854 +GTATCGAGGCTCTTAAACCTGCTATTTAGGCTTTTT +>HWI-EAS91_1_306UPAAXX:6:1:312:1707 +GCGTCATAAGAGGTTTTACCTCCAAATGAAGAAATA +>HWI-EAS91_1_306UPAAXX:6:1:651:183 +GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT +>HWI-EAS91_1_306UPAAXX:6:1:295:694 +GTGATTACTTCATGCAGCGTTACCGTGATGTTATTT +>HWI-EAS91_1_306UPAAXX:6:1:330:1895 +GCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTG +>HWI-EAS91_1_306UPAAXX:6:1:590:331 +GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT +>HWI-EAS91_1_306UPAAXX:6:1:481:1687 +GCAGATTGCGATAAACGGTCACATTAAATTTAACCT +>HWI-EAS91_1_306UPAAXX:6:1:1112:1279 +TGTGCATATACCTGGTCTTTCGTATTCTGTCGTGAT +>HWI-EAS91_1_306UPAAXX:6:1:1099:1216 +TTAGAGCGCATGACAAGTAAAGGACGGTTGTCAGCG +>HWI-EAS91_1_306UPAAXX:6:1:221:1238 +GTATCCTTTCCTTTATCATCGGCAGACTTTTCACCT +>HWI-EAS91_1_306UPAAXX:6:1:1015:364 +GCCAGCGATAACCGGAGTAGTTGAAATGGTAATAAG +>HWI-EAS91_1_306UPAAXX:6:1:735:1806 +TGTTATTAATATCAAGTTGGGGGAGCACATTGTAGC +>HWI-EAS91_1_306UPAAXX:6:1:320:411 +GCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGTG +>HWI-EAS91_1_306UPAAXX:6:1:1273:1031 +TTAAGGATATTCGCGATGAGTATAATTACCCCAAAA +>HWI-EAS91_1_306UPAAXX:6:1:1456:1088 +AATAATCAGCGTGACATTCAGAAGGGTAATAAGAAC +>HWI-EAS91_1_306UPAAXX:6:1:1365:307 +GACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAG +>HWI-EAS91_1_306UPAAXX:6:1:478:252 +GATGCGGTTATCCATCTGCTTATTGAAGCCAAGCAT +>HWI-EAS91_1_306UPAAXX:6:1:915:1232 +TATTAATAACACTATAGACCACCGCCCCGAAGGGGC +>HWI-EAS91_1_306UPAAXX:6:1:680:1357 +TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGC +>HWI-EAS91_1_306UPAAXX:6:1:238:1279 +GCCGAAGCCCCTGCAATTAAAATTGTTGACCACCTA +>HWI-EAS91_1_306UPAAXX:6:1:1583:35 +GCAAATTAGCATAAGCAGCTTGCAGACCCATAATGT +>HWI-EAS91_1_306UPAAXX:6:1:502:283 +GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT +>HWI-EAS91_1_306UPAAXX:6:1:418:1730 +GAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGT +>HWI-EAS91_1_306UPAAXX:6:1:596:647 +GCCTCAACGCAGCGACGAGCACGAGAGCGGTCAGTA +>HWI-EAS91_1_306UPAAXX:6:1:92:1591 +GTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCC +>HWI-EAS91_1_306UPAAXX:6:1:430:1938 +GCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGTCC +>HWI-EAS91_1_306UPAAXX:6:1:212:527 +GGTATTGATAAAGCTGTTGCCGATACTTGTAACAAT +>HWI-EAS91_1_306UPAAXX:6:1:594:942 +GACGACATTAGAAATATCCTTTGCAGTAGCGCCAAT +>HWI-EAS91_1_306UPAAXX:6:1:169:1774 +GCCTTCCATGATGAGACAGGCCGTTTTAATTTTTAC +>HWI-EAS91_1_306UPAAXX:6:1:1090:210 +GGAGAGCGCCAACGGCGTCCATCTCGAAGGAGTCGC +>HWI-EAS91_1_306UPAAXX:6:1:589:96 +GGCGGCCCCATCAGGGTTAGGAACATTAGAGCCTTG +>HWI-EAS91_1_306UPAAXX:6:1:1477:1231 +TAGGAACATTAGAGCCTTGAATGGCAGATTTAATAC +>HWI-EAS91_1_306UPAAXX:6:1:707:1076 +TCTGACGTTCGTGATGAGTTTGTATCTTTTTCTTTG +>HWI-EAS91_1_306UPAAXX:6:1:749:1715 +GAACATAATAAGCAATGACGGCAGCAATAAACTCAA +>HWI-EAS91_1_306UPAAXX:6:1:1738:1884 +GCTCACCTTTAGCATCAACAGGCCACAACCAACCAG +>HWI-EAS91_1_306UPAAXX:6:1:1160:1088 +TCACATTTTGTTCATGGTAGAGATTCTCTTGTTGAC +>HWI-EAS91_1_306UPAAXX:6:1:517:119 +GCAAGGCTAATGATTCACACGCCGACTGCTATCAGT +>HWI-EAS91_1_306UPAAXX:6:1:1472:716 +TGGTAATGGTGGTTTTCTTCATTTCATTCAGTTTTT +>HWI-EAS91_1_306UPAAXX:6:1:281:441 +GAGCAGTAGACTCCTTCTGTTGATAAGCAAGCATCT +>HWI-EAS91_1_306UPAAXX:6:1:1101:324 +AATACCATCAGCTTTACCGTCTTTCCAGAAATTGTT +>HWI-EAS91_1_306UPAAXX:6:1:1225:1494 +TTCTCAAATCCGGCGTCAACCATACCAGCAGAGGAA +>HWI-EAS91_1_306UPAAXX:6:1:1509:1025 +TTCTTGCTGCCGAGGGTCGCAAGGCTATTGTTTCAC +>HWI-EAS91_1_306UPAAXX:6:1:592:510 +GATACCAATAAAATCCCTAAGCATTTGTTTCTGGTT +>HWI-EAS91_1_306UPAAXX:6:1:324:1729 +GAACAAAGAAACGCGGCACAGAATGTTTATAGGTCT +>HWI-EAS91_1_306UPAAXX:6:1:128:1925 +GGAACAACTCACTAAAAACCAAGCTGTCGCTACTTC +>HWI-EAS91_1_306UPAAXX:6:1:786:893 +TACGGGGAAGGACGTCAATAGTCACACAGTCCTTGC +>HWI-EAS91_1_306UPAAXX:6:1:248:955 +GCTACAATGTGCTCCCCCAACTTGATATTAATAACA +>HWI-EAS91_1_306UPAAXX:6:1:388:1127 +GATATTGGTCGTATGGTTCTTGCTGCCTAGTGTCTC +>HWI-EAS91_1_306UPAAXX:6:1:721:1156 +TCTGGTTGGTTGTGGCCTTTTTATGCTAAATGTTAG +>HWI-EAS91_1_306UPAAXX:6:1:1564:1468 +TTACTTTTTATGTCCCTCATCGTCACGTTTATGTTG +>HWI-EAS91_1_306UPAAXX:6:1:750:77 +GGCTCATTCTGATTCTGAACAGCTTCTTGGGAAGTA +>HWI-EAS91_1_306UPAAXX:6:1:405:487 +GTTGGATTAAGCACTCCGTGGACAGATTTGTCATTT +>HWI-EAS91_1_306UPAAXX:6:1:836:1204 +TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT +>HWI-EAS91_1_306UPAAXX:6:1:224:1548 +GCTGCCGTCATTGCTTATTATGTTCATCCCTTCAAC +>HWI-EAS91_1_306UPAAXX:6:1:931:1015 +TTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGT +>HWI-EAS91_1_306UPAAXX:6:1:329:579 +GTCCCTCATCGTCACGTTTATGGTGAACAGTGGATT +>HWI-EAS91_1_306UPAAXX:6:1:260:1145 +GCTTGCGTTTATGGTACGCTGGACTTTTTGTGATAC +>HWI-EAS91_1_306UPAAXX:6:1:1523:1253 +TTGGTAAAATACTGACCAGCCGTTTGAGCTTGAGTA +>HWI-EAS91_1_306UPAAXX:6:1:326:1271 +GACCACTCGCGATTCAATCATGACTTCGTGATAAAT +>HWI-EAS91_1_306UPAAXX:6:1:213:622 +GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA +>HWI-EAS91_1_306UPAAXX:6:1:274:712 +GCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTG +>HWI-EAS91_1_306UPAAXX:6:1:1549:627 +TATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGT +>HWI-EAS91_1_306UPAAXX:6:1:1714:737 +TCTTTCGTATTCTGGCGTGAAGTCGCCGACTGAATG +>HWI-EAS91_1_306UPAAXX:6:1:760:1217 +TACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTT +>HWI-EAS91_1_306UPAAXX:6:1:174:768 +GTTGGCTGACGACCGATTAGAGGCGTTTTTTTATAT +>HWI-EAS91_1_306UPAAXX:6:1:172:1412 +GGTCGGCAGATTGCGATAAACGTTCACATTAAATTT +>HWI-EAS91_1_306UPAAXX:6:1:1393:869 +TTCATCCCGTCAACATTCAAACGGCCTGTCTCATCT +>HWI-EAS91_1_306UPAAXX:6:1:301:481 +GTTATAGATATTCAAATAACCCTGAAACAAATGCTT +>HWI-EAS91_1_306UPAAXX:6:1:648:1093 +TAACGCTGCATGAAGTAATCACGTTCTTGGTCAGTT +>HWI-EAS91_1_306UPAAXX:6:1:1233:591 +TTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCT +>HWI-EAS91_1_306UPAAXX:6:1:540:1415 +TTATTAAAGAGATTATTTTTCTCCAGCCACTTATGT +>HWI-EAS91_1_306UPAAXX:6:1:151:1792 +GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA +>HWI-EAS91_1_306UPAAXX:6:1:748:1378 +TGGATTACTATCTGAGTCCGATGCTGTTCAACCACT +>HWI-EAS91_1_306UPAAXX:6:1:1526:1479 +TGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCC +>HWI-EAS91_1_306UPAAXX:6:1:985:1093 +TAACCGTCTTCTCGTTCTCTAAAAACCATTTTTCTT +>HWI-EAS91_1_306UPAAXX:6:1:480:1378 +TCAACCTCAGCACTAACCTTGCGAGTCATTTCTTTG +>HWI-EAS91_1_306UPAAXX:6:1:903:753 +TGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAG +>HWI-EAS91_1_306UPAAXX:6:1:1697:1737 +GGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGT +>HWI-EAS91_1_306UPAAXX:6:1:803:1037 +TGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCTACT +>HWI-EAS91_1_306UPAAXX:6:1:1727:1244 +TTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCT +>HWI-EAS91_1_306UPAAXX:6:1:253:1162 +GCATTTAGTAGCGGTAAAGTTTGACCAAACCATTAT +>HWI-EAS91_1_306UPAAXX:6:1:216:856 +GTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCT +>HWI-EAS91_1_306UPAAXX:6:1:825:886 +TCCCACAAAGTCCAGCGTACCATAAACGCAAGCCTC +>HWI-EAS91_1_306UPAAXX:6:1:1699:962 +TGATTTCGATTTTCTGACGAGTAACAAAGTTTGGAT +>HWI-EAS91_1_306UPAAXX:6:1:1210:625 +TCAGATAGTAATCCACGCTCTTTTAAAATGTCAACA +>HWI-EAS91_1_306UPAAXX:6:1:538:616 +TAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGT +>HWI-EAS91_1_306UPAAXX:6:1:184:1849 +GCTCACCTTTAGCATCAACAGGCCACAACCAACCAG +>HWI-EAS91_1_306UPAAXX:6:1:1636:1103 +TATCTGACTTTTTGTTAACGTATTTAGCCACATAGA +>HWI-EAS91_1_306UPAAXX:6:1:605:223 +GGTTATTTGAATATCTATAACAACTATTTTAAATCG +>HWI-EAS91_1_306UPAAXX:6:1:256:1052 +GGTAAAGGACTTCTTGAAGGTACGTTGCAGTCTGGC +>HWI-EAS91_1_306UPAAXX:6:1:300:1515 +GCCATGATGGTGGTTATTATACCGTCAAGGACTTTT +>HWI-EAS91_1_306UPAAXX:6:1:1684:1320 +TGCTTGGCTTCCATAAGCAGATGGATAACCGCATCA +>HWI-EAS91_1_306UPAAXX:6:1:1186:895 +TCAGATGGATACATCTGTCAACGCCGCTAATCAGGT +>HWI-EAS91_1_306UPAAXX:6:1:1463:754 +TCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTT +>HWI-EAS91_1_306UPAAXX:6:1:808:1053 +TGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGG +>HWI-EAS91_1_306UPAAXX:6:1:960:1218 +TTTCTAATGTCGTCACTGATGCTGCTTCTGTTGTTT +>HWI-EAS91_1_306UPAAXX:6:1:521:1646 +GGAAAACGAACAAGCGCAAGAGTAAACATAGTGCCA +>HWI-EAS91_1_306UPAAXX:6:1:289:1885 +GCCAGCGATAACCGGAGTAGTTGAAATGGTAATAAG +>HWI-EAS91_1_306UPAAXX:6:1:471:170 +GGTCAGTTCCATCAACATCATAGCCAGATGCCCAGA +>HWI-EAS91_1_306UPAAXX:6:1:828:754 +TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT +>HWI-EAS91_1_306UPAAXX:6:1:924:1679 +TTTAATGTGACCGTTTATCGCAATCTGCCGACCACT +>HWI-EAS91_1_306UPAAXX:6:1:837:901 +TGCATTTTAGTAAGCTCTTTTTGATTCTCAAATCCG +>HWI-EAS91_1_306UPAAXX:6:1:543:16 +GCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTC +>HWI-EAS91_1_306UPAAXX:6:1:1482:578 +TCTTTAGCTCCTAGACCTTTAGCAGCAAGGTCCATA +>HWI-EAS91_1_306UPAAXX:6:1:1254:1668 +TTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCT +>HWI-EAS91_1_306UPAAXX:6:1:1402:898 +TCATGAGTCAAGTTACTGAACAATCCGTACGTTTCC +>HWI-EAS91_1_306UPAAXX:6:1:764:1534 +TTATACCGTCAAGGACTGTGTGACTATTGACGTCCT +>HWI-EAS91_1_306UPAAXX:6:1:681:1079 +TGGCGAATAAGTACGCGTTCTTGCAAATCACCAGAA +>HWI-EAS91_1_306UPAAXX:6:1:672:1350 +TTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTT +>HWI-EAS91_1_306UPAAXX:6:1:1266:493 +TGACCAGCCGTTTGAGCTTGAGTAAGCATTTGGCGC +>HWI-EAS91_1_306UPAAXX:6:1:118:238 +GACGGTATAATAACCACCATCATGGCGACCATTCAA +>HWI-EAS91_1_306UPAAXX:6:1:699:433 +TTATTGCCCGGCGTACGGGGAAGGACGTCAATAGTC +>HWI-EAS91_1_306UPAAXX:6:1:708:1387 +TGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTAC +>HWI-EAS91_1_306UPAAXX:6:1:498:1085 +TTATGATAATCCCAATGCTTTGCGTGACTATTTTCT +>HWI-EAS91_1_306UPAAXX:6:1:1101:1301 +TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAT +>HWI-EAS91_1_306UPAAXX:6:1:261:213 +GAATGGTCGCCATGATGGTGGTTATTATACCGTCAC +>HWI-EAS91_1_306UPAAXX:6:1:1287:1267 +TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGT +>HWI-EAS91_1_306UPAAXX:6:1:744:331 +TTAATGGATGAATTGGCACAATGCTACAATGTGCTC +>HWI-EAS91_1_306UPAAXX:6:1:614:814 +TGTCAGCGTCATAAGAGGTTTTACCTCCAAATGAAG +>HWI-EAS91_1_306UPAAXX:6:1:1362:1063 +TAAACGCAAGCCTCAACGCAGCGACGAGCACGAGAG +>HWI-EAS91_1_306UPAAXX:6:1:1238:1508 +TCAACTAACGATTCTGTCAAAAACTGACGCGTTGGT +>HWI-EAS91_1_306UPAAXX:6:1:904:1130 +TTATCGCAATCTGCCGACCACTCGCGATTCAATCAT +>HWI-EAS91_1_306UPAAXX:6:1:465:216 +GACCATGCCGCTTTTCTTGGCACGATTAACCCTTAT +>HWI-EAS91_1_306UPAAXX:6:1:844:628 +TAATGTCAATAGATGTGGTAGAAGTCGTCATTTGGC +>HWI-EAS91_1_306UPAAXX:6:1:684:1444 +TATCCCACAAAGTCCAGCGTACCATAAACGCAAGCC +>HWI-EAS91_1_306UPAAXX:6:1:515:1373 +TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCT +>HWI-EAS91_1_306UPAAXX:6:1:764:1667 +TTGAGTTCGATAATGGTGATATGTATGTTGACGTCC +>HWI-EAS91_1_306UPAAXX:6:1:1722:598 +TGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCT +>HWI-EAS91_1_306UPAAXX:6:1:670:1188 +TTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGT +>HWI-EAS91_1_306UPAAXX:6:1:1682:1705 +TAGCCACATAGAAACCAACAGCCATATAACTGGTAG +>HWI-EAS91_1_306UPAAXX:6:1:1008:1616 +TCCTTTACTTGTCATGCGCTCTAATCTCTGTGCATC +>HWI-EAS91_1_306UPAAXX:6:1:490:1220 +TAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCT +>HWI-EAS91_1_306UPAAXX:6:1:891:1437 +TAATGGTGATATGTATGTTTACGTCCATAAGGCTGT +>HWI-EAS91_1_306UPAAXX:6:1:1310:321 +TCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGT +>HWI-EAS91_1_306UPAAXX:6:1:827:1597 +TGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTC +>HWI-EAS91_1_306UPAAXX:6:1:1062:1158 +TAGAGTCAATAGCAAGGCCACGACGCAATGGAGAAA +>HWI-EAS91_1_306UPAAXX:6:1:1419:208 +TGGCGCATAATCTCGGAAACCTGCTGTTGCTTGGAA +>HWI-EAS91_1_306UPAAXX:6:1:691:1018 +AAATATCAACCACACCAGAAGCAGCATCAGTGACGA +>HWI-EAS91_1_306UPAAXX:6:1:374:113 +GATAAAGCTGTTGCCGATACTTGGAACAATTTCTGT +>HWI-EAS91_1_306UPAAXX:6:1:1720:784 +TGAGGATAAATTATGTCTAATATTCAAACTGGCGCC +>HWI-EAS91_1_306UPAAXX:6:1:1424:1394 +ATAAAAATGATTGGCGTATCCAACCTGCAGAGTTTT +>HWI-EAS91_1_306UPAAXX:6:1:1063:1760 +TAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCT +>HWI-EAS91_1_306UPAAXX:6:1:1235:729 +TTTTTATGTCCCTCATCGTCACGTTTATGGTGAACA +>HWI-EAS91_1_306UPAAXX:6:1:167:1507 +TAGTGTTATTAATATCAAGTTTTTGGAGCACATTGT +>HWI-EAS91_1_306UPAAXX:6:1:717:1569 +TCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGT +>HWI-EAS91_1_306UPAAXX:6:1:610:765 +TTCAGCGCCTTCCATGATGAGACAGGCCGTTTGAAT +>HWI-EAS91_1_306UPAAXX:6:1:663:380 +TAAACATTCTGTGCCGCGTTTCTTTGTTCCTTATCT +>HWI-EAS91_1_306UPAAXX:6:1:790:1358 +TTATCACCTTATTGAAGGCTTATCATTCATTTAGGT +>HWI-EAS91_1_306UPAAXX:6:1:965:1633 +TAGATGTGGTAGAAGTCGTCATTTGGCGAGAAAGCT +>HWI-EAS91_1_306UPAAXX:6:1:673:319 +TTCTTGCAAATCACCAGAAGGCGGTTCCTGAATGAT +>HWI-EAS91_1_306UPAAXX:6:1:684:371 +TAGCGGTAAAGTTAGACCAAACCATGAAACCAACAT +>HWI-EAS91_1_306UPAAXX:6:1:1147:1444 +ATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGC +>HWI-EAS91_1_306UPAAXX:6:1:983:678 +ATACCTGGTCTTTCGTATTCTGGCGTGAAGTCGCCG +>HWI-EAS91_1_306UPAAXX:6:1:1608:1119 +TCACGCGGCGGCAAGTTGCCATACAAAACAGGGTCG +>HWI-EAS91_1_306UPAAXX:6:1:1048:1193 +TAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAT +>HWI-EAS91_1_306UPAAXX:6:1:1265:1429 +ATATTTTTCATGGTATTGATAAAGCTGTTGCCGATT +>HWI-EAS91_1_306UPAAXX:6:1:1607:1677 +TGTTGCTTGGAAAGATTGGTGTTTTCCATAATAGAC +>HWI-EAS91_1_306UPAAXX:6:1:1087:1421 +ACGAACGTCAGAAGCAGCCTTATGGCCGTCAACATC +>HWI-EAS91_1_306UPAAXX:6:1:324:490 +GCACCAAACATAAATCACCTCACTTAAGTGGCTGGG +>HWI-EAS91_1_306UPAAXX:6:1:1596:614 +TTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGT +>HWI-EAS91_1_306UPAAXX:6:1:343:83 +GTTACGCAGTTTTGCCGCAAGCTGGCTGCTGTACGC +>HWI-EAS91_1_306UPAAXX:6:1:203:667 +GCATGAATGTGCTTAATAGAGGCCAAGGCGGTCTAG +>HWI-EAS91_1_306UPAAXX:6:1:34:480 +GGCAAGTTGCCATACAAAACAGGGTCGCCAGCAATT +>HWI-EAS91_1_306UPAAXX:6:1:606:1743 +TAGCGACAGCTTGGTTTTTAGTGAGTTGTTCCATTC +>HWI-EAS91_1_306UPAAXX:6:1:254:1391 +TATAATTACCCCAAAAAGAAAGGTATTAAGGATGAG +>HWI-EAS91_1_306UPAAXX:6:1:1568:1750 +TAACCAGTAGTGTTAACAGTCGGGAGAGGAGTGGCT +>HWI-EAS91_1_306UPAAXX:6:1:1538:869 +TACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCA +>HWI-EAS91_1_306UPAAXX:6:1:255:38 +GTCAGGATTGACACCCTCCCAATTGTATGTTTTCAT +>HWI-EAS91_1_306UPAAXX:6:1:1543:1555 +TAAAACGCCTCTAATCGGTCGTCAGCCAACGTGAGG +>HWI-EAS91_1_306UPAAXX:6:1:1365:733 +AGAATCAGCGGTATGGCTCTTCTCCTTTTTTCGCTT +>HWI-EAS91_1_306UPAAXX:6:1:1604:943 +TACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCT +>HWI-EAS91_1_306UPAAXX:6:1:1574:1632 +TCAGTATGCAAATTAGCATAAGCAGCTTGCAGACCC +>HWI-EAS91_1_306UPAAXX:6:1:565:1799 +TCTTGGTCAGTATGCAAATTAGCATAAGCAGCTTGC +>HWI-EAS91_1_306UPAAXX:6:1:1004:380 +TATTGACTCTACTGTAGACATTTTTACTTTTTATTT +>HWI-EAS91_1_306UPAAXX:6:1:1345:965 +ATTCAAAGGATAAACATCATAGGCAGTCGGGAGGGT +>HWI-EAS91_1_306UPAAXX:6:1:1704:756 +TGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGG +>HWI-EAS91_1_306UPAAXX:6:1:310:1346 +TATAACGTTGACGATGTAGCTTTAGTTTTCTTTAAA +>HWI-EAS91_1_306UPAAXX:6:1:900:1858 +TTTACCGCTTCGGCGTTATAACCTCACACTCAATCT +>HWI-EAS91_1_306UPAAXX:6:1:1250:1741 +TAAATCCAAAACGGCAGAAGCCTGAATGAGCTTAAT +>HWI-EAS91_1_306UPAAXX:6:1:1170:1317 +TCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTC +>HWI-EAS91_1_306UPAAXX:6:1:149:1896 +GCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATC +>HWI-EAS91_1_306UPAAXX:6:1:1504:494 +TGTCTACAGTAGAGTCAATAGCAAGGCCACGACGCC +>HWI-EAS91_1_306UPAAXX:6:1:395:256 +GTCCATATCTGACTTTTTGTTAACGTATTTATCCAC +>HWI-EAS91_1_306UPAAXX:6:1:1110:1109 +ACCGCTTCGGCGTTATAACCTCACACTCAATCTTTT +>HWI-EAS91_1_306UPAAXX:6:1:895:649 +TTCTGCACGTAATTTTTGACGCACGTTTTCTTCTGC +>HWI-EAS91_1_306UPAAXX:6:1:827:1378 +TGCAAGCTGCTTATGCTAATTTGCATACTGACCAAG +>HWI-EAS91_1_306UPAAXX:6:1:1051:1587 +TTTGACACTCTCACGTTGGCTGACGACCGATTAGAG +>HWI-EAS91_1_306UPAAXX:6:1:1656:1549 +AACCTGCTGTTGCTTGGAAAGATTGGTGTTTTCCAT +>HWI-EAS91_1_306UPAAXX:6:1:366:150 +GGTCAGTAGCAATCCAAACTTTGTTACTCGTCAGAA +>HWI-EAS91_1_306UPAAXX:6:1:955:1792 +ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA +>HWI-EAS91_1_306UPAAXX:6:1:1340:1403 +ATAAAATGCACCGCATGGAAATGAAGACGGCCATTA +>HWI-EAS91_1_306UPAAXX:6:1:1693:1017 +TGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGT +>HWI-EAS91_1_306UPAAXX:6:1:1099:1572 +AATTTTTACCGCTTCGGCGTTATAACCTCACACTCA +>HWI-EAS91_1_306UPAAXX:6:1:218:1148 +TATGCAAATTAGCATAAGCAGCTTGCAGACCCATAT +>HWI-EAS91_1_306UPAAXX:6:1:403:614 +TGGTGCTGATGCTTCCTCTGCTGGTATGGTTTACGC +>HWI-EAS91_1_306UPAAXX:6:1:1651:646 +TCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGC +>HWI-EAS91_1_306UPAAXX:6:1:1566:499 +TGCGGTGCATTTTATGCGGACACTTCCTACAGGTAG +>HWI-EAS91_1_306UPAAXX:6:1:825:951 +ACAGGCCGTTTGAATGTTTACGGGGTGTACATAATA +>HWI-EAS91_1_306UPAAXX:6:1:1745:1865 +TTAACTTCTGCGTCATGGAAGCGATAAAACTCTGCG +>HWI-EAS91_1_306UPAAXX:6:1:973:1992 +TAGTAATTCCTGCTTTATCAAGATAATTTTTCGACT +>HWI-EAS91_1_306UPAAXX:6:1:171:1653 +TAATAATGTTTTCCGTAAATTCAGCGCCTTCCATGT +>HWI-EAS91_1_306UPAAXX:6:1:397:363 +TGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGT +>HWI-EAS91_1_306UPAAXX:6:1:1336:1155 +ATATGTATGTTGACGGCCATAAGGCTGCTTCTGACG +>HWI-EAS91_1_306UPAAXX:6:1:685:629 +AGTATGCAAATTAGCATAAGCAGCTTGCAGACCCAT +>HWI-EAS91_1_306UPAAXX:6:1:1409:510 +ACATAATAAGCAATGACGGCAGCAATAAACTCAACA +>HWI-EAS91_1_306UPAAXX:6:1:1631:998 +AACCATCAGCATGAGCCTGTCGCATTGCATTCATCC +>HWI-EAS91_1_306UPAAXX:6:1:260:1698 +TTATTATGTTCATCCCGTCAACATTCAAACTGCCTT +>HWI-EAS91_1_306UPAAXX:6:1:578:971 +TTAACGCTACTAAATTCCGCGGATTGGTTTCGTTGT +>HWI-EAS91_1_306UPAAXX:6:1:1613:642 +ATAGAAATTTCACGCGGCGGCAAGTTGCCATACAAA +>HWI-EAS91_1_306UPAAXX:6:1:237:650 +GACGGTATAATAACCACCATCATGGCGACCATTCAA +>HWI-EAS91_1_306UPAAXX:6:1:1100:1875 +TTATGGTTCGTTCTTATTACCCTTCTGAATGTCACG +>HWI-EAS91_1_306UPAAXX:6:1:352:32 +GTACCATAAACGCAAGCCTCAACGCAGCGACGAGCC +>HWI-EAS91_1_306UPAAXX:6:1:443:229 +GCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAAC +>HWI-EAS91_1_306UPAAXX:6:1:1131:731 +AGCAGTCGGCGTGTGAATCATTAGCCTTGCGACCCT +>HWI-EAS91_1_306UPAAXX:6:1:133:1089 +AAGGTTAGTGCTGAGGTTGACTTAGTTCATCATCAA +>HWI-EAS91_1_306UPAAXX:6:1:65:1307 +TGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTT +>HWI-EAS91_1_306UPAAXX:6:1:905:1493 +TCAGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTT +>HWI-EAS91_1_306UPAAXX:6:1:733:540 +TGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAT +>HWI-EAS91_1_306UPAAXX:6:1:161:1707 +TAATGTCGTCACTGATGCTGCTTCTGTTGTTGTTTT +>HWI-EAS91_1_306UPAAXX:6:1:380:1861 +TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC +>HWI-EAS91_1_306UPAAXX:6:1:1761:566 +TATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAT +>HWI-EAS91_1_306UPAAXX:6:1:1486:651 +TGGCGGTATTTCTTCTTCTCTTTCTTGTTGCGCCCT +>HWI-EAS91_1_306UPAAXX:6:1:508:1380 +TCCATCAACATCATAGCCAGATGCCCAGAGATTAGA +>HWI-EAS91_1_306UPAAXX:6:1:1763:855 +TGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTC +>HWI-EAS91_1_306UPAAXX:6:1:1553:553 +TAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAA +>HWI-EAS91_1_306UPAAXX:6:1:1424:507 +TCCACTGCAACAACTGAACGGACTGGAAACACTGGT +>HWI-EAS91_1_306UPAAXX:6:1:988:135 +TAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTC +>HWI-EAS91_1_306UPAAXX:6:1:810:1918 +TTTTCATCCCGAAGTTGCGGCTCATTCTGATTCTGT +>HWI-EAS91_1_306UPAAXX:6:1:588:559 +TCTGGTTGAACGGCGTCGCGTCGTAACCCAGCTTGG +>HWI-EAS91_1_306UPAAXX:6:1:1264:1214 +ATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC +>HWI-EAS91_1_306UPAAXX:6:1:1000:1475 +TCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTG +>HWI-EAS91_1_306UPAAXX:6:1:1389:160 +TTATTCGCCACCATGATTATGACCAGTGTTTCCAGT +>HWI-EAS91_1_306UPAAXX:6:1:422:1296 +TTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGT +>HWI-EAS91_1_306UPAAXX:6:1:1273:856 +TAGCCATAGCACCAGAAACAAAACTAGGGGCGGCCT +>HWI-EAS91_1_306UPAAXX:6:1:450:969 +TGTTTTCCATAATAGACGCAACGCGAGCAGTAGACT +>HWI-EAS91_1_306UPAAXX:6:1:1202:828 +ATCGTCAACGTTATATTTTGATAGTTTGACGTTTAT +>HWI-EAS91_1_306UPAAXX:6:1:1721:1800 +GGGTTAGGGACATTAGAGCCTTGACTGACTGAGTTT +>HWI-EAS91_1_306UPAAXX:6:1:228:2019 +TTGAGTAAGCATTTGGCGCATAATCTCGGAAACCTG +>HWI-EAS91_1_306UPAAXX:6:1:1579:1214 +ACGTTTGGTCAGTTCCATCAACATCATAGCCAGATG +>HWI-EAS91_1_306UPAAXX:6:1:429:1055 +TTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCTTT +>HWI-EAS91_1_306UPAAXX:6:1:1359:1689 +AAGAGCAGAAGCAATACCGCCAGCAATAGCACCAAA +>HWI-EAS91_1_306UPAAXX:6:1:1474:1056 +TCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGAC +>HWI-EAS91_1_306UPAAXX:6:1:105:1818 +TTGGGGATTGAGAAAGAGTAGAAATGCCACAAGCCT +>HWI-EAS91_1_306UPAAXX:6:1:208:1538 +TAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +>HWI-EAS91_1_306UPAAXX:6:1:1361:1623 +AATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTA +>HWI-EAS91_1_306UPAAXX:6:1:595:1670 +TGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACA +>HWI-EAS91_1_306UPAAXX:6:1:6:1885 +TCTAATGTCGTCACTGATGCTGCTTCTGGTGTGTTT +>HWI-EAS91_1_306UPAAXX:6:1:706:1085 +TGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTG +>HWI-EAS91_1_306UPAAXX:6:1:1307:825 +AGCGGTAAAGTTAGACCAAACCATGAAACCAACATA +>HWI-EAS91_1_306UPAAXX:6:1:762:802 +TGGCATTAACACCATCCTTCATGAACTTAATCCACT +>HWI-EAS91_1_306UPAAXX:6:1:1657:506 +TTGCGACCCTCGGCAGCAAGAACCATACGACCAATT +>HWI-EAS91_1_306UPAAXX:6:1:184:811 +TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC +>HWI-EAS91_1_306UPAAXX:6:1:1469:1718 +TGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTT +>HWI-EAS91_1_306UPAAXX:6:1:815:1640 +TGGCGGCGATTGCGTACCCGACGACCCAAATTAGGG +>HWI-EAS91_1_306UPAAXX:6:1:1580:1388 +AAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTG +>HWI-EAS91_1_306UPAAXX:6:1:1617:1554 +TACGGGGAAGGACGTCAATAGTCACACAGTCCTTGA +>HWI-EAS91_1_306UPAAXX:6:1:1544:431 +TGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTA +>HWI-EAS91_1_306UPAAXX:6:1:1604:1541 +TCAGTGACGACATTAGAAATATCCTTTGCAGTAGCG +>HWI-EAS91_1_306UPAAXX:6:1:1485:741 +ATCAAACGCTGAATAGTAAAGCCTCTACGCGATTTC +>HWI-EAS91_1_306UPAAXX:6:1:1226:393 +TGCCACAAGCCTCAATAGCAGGTTTAAGAGCCTCGA +>HWI-EAS91_1_306UPAAXX:6:1:1506:973 +ATTAGGGTCAACGCTACCTGTAGGAAGTGTCCGCAT +>HWI-EAS91_1_306UPAAXX:6:1:890:1838 +TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC +>HWI-EAS91_1_306UPAAXX:6:1:453:1527 +TAAGAGGGCGTTCAGCAGCCAGCTTGCGGCAAAACT +>HWI-EAS91_1_306UPAAXX:6:1:1056:570 +ACATTGTAGCATTGTGCCAATTCATCCATTAACTTC +>HWI-EAS91_1_306UPAAXX:6:1:1736:74 +TATCCGAAAGTGTTAACTTCTGCGTCATGGAAGCGT +>HWI-EAS91_1_306UPAAXX:6:1:169:1896 +GTATGCAAATTAGCATAAGCAGCTTGCAGACCCATA +>HWI-EAS91_1_306UPAAXX:6:1:259:949 +TGAGGATAAATTATGTCTAATATTCAAACTTGCTCC +>HWI-EAS91_1_306UPAAXX:6:1:1205:893 +ATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCT +>HWI-EAS91_1_306UPAAXX:6:1:732:1335 +TACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCT +>HWI-EAS91_1_306UPAAXX:6:1:667:664 +TCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAG +>HWI-EAS91_1_306UPAAXX:6:1:535:587 +TTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGT +>HWI-EAS91_1_306UPAAXX:6:1:412:446 +GTGTGGTTGATATTTTTCATGGTATTGATAAAGCTT +>HWI-EAS91_1_306UPAAXX:6:1:507:1599 +TTGCTGGCGGTTTTTCTTTTTTTTTTTTTTTTTTTT +>HWI-EAS91_1_306UPAAXX:6:1:575:1818 +TAAAATGCACCGCATGGAAATGAAGACGGCCATTAG +>HWI-EAS91_1_306UPAAXX:6:1:1568:1428 +ACCAGTTATATGGCTGGTTGTTTTTTTTTTTTTTTT +>HWI-EAS91_1_306UPAAXX:6:1:1417:982 +AACAAGAGAATCTCTACCATGAACAAAATGTGACTC +>HWI-EAS91_1_306UPAAXX:6:1:280:1340 +GGCCAAACCAGTGGCGATGGCCGCGCTGGAGGTTTT +>HWI-EAS91_1_306UPAAXX:6:1:966:144 +TACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGT +>HWI-EAS91_1_306UPAAXX:6:1:1391:1987 +TAATAATGTTTTCCGTAAATTCAGCGCCTTCCATGT +>HWI-EAS91_1_306UPAAXX:6:1:1280:278 +ATGGAAATGAAGACGGCCATTAGCTGTACCATACTC +>HWI-EAS91_1_306UPAAXX:6:1:631:858 +TGATATTGGTCGTATGGTTCTTGCTTCCGTGGGTCT +>HWI-EAS91_1_306UPAAXX:6:1:518:573 +TTAGGTGTCTGTAAAACAGGTGCCGAAGAAGCTGGT +>HWI-EAS91_1_306UPAAXX:6:1:54:981 +TTGACATTTTAAAAGAGCGTGGATTACTATCTGATT +>HWI-EAS91_1_306UPAAXX:6:1:218:1165 +TATTGACTCTACTGTAGACATTTTTACTTTTTATTT +>HWI-EAS91_1_306UPAAXX:6:1:1727:1530 +TCAACGCAGCGACGAGCACGAGAGCGGTCAGTAGCA +>HWI-EAS91_1_306UPAAXX:6:1:519:657 +TGAACAGCATCGGACTCAGATAGTAATCCACGCTCT +>HWI-EAS91_1_306UPAAXX:6:1:939:967 +ATACCGTCAAGGACTGTGTGACTATTGACGTCCTTC +>HWI-EAS91_1_306UPAAXX:6:1:299:1060 +TATAACTGGTAGCTTTAAGCGGCTCACCTTTAGCAT +>HWI-EAS91_1_306UPAAXX:6:1:438:665 +TAATTCGTAAACAAGCAGTAGTAATTCCTGCTTTAT +>HWI-EAS91_1_306UPAAXX:6:1:1303:1971 +AGCATTGTGCCAATTCATCCATTAACTTCTCAGTAA +>HWI-EAS91_1_306UPAAXX:6:1:214:1264 +TCAGCACCAACAGAAACAACCTGATTAGCGGCGTTG +>HWI-EAS91_1_306UPAAXX:6:1:1454:1423 +AACGGAAAACATCCTTCATAGAAATTTCACGCGGCG +>HWI-EAS91_1_306UPAAXX:6:1:1633:340 +TTCCATAATAGACGCAACGCGAGCAGTAGACTCCTT +>HWI-EAS91_1_306UPAAXX:6:1:671:1196 +ATACGAAAAGACAGAATCTCTTCCAAGAGCTTGATG diff -r b6ff467f4522 -r 26825f08d362 test-data/phiX.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX.fa Sun Sep 14 14:58:50 2008 -0400 @@ -0,0 +1,79 @@ +>phiX +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA +

1 0

dynamic_options
by Ross 15 Sep '08

15 Sep '08

I see from the parameters code that dynamic_options are to be replaced with options as part of workflow buildout. I'm finding lots of use cases where the dynamic_options returned by code from an included module makes some complicated things really easy for users. For example. In the new gene expression tools, each expression experiment is stored as a new Galaxy datatype based on the Bioconductor representation (affybatch, eset etc). Each of those structures has (optional!) accompanying experimental metadata (phenodata) which at the time the affybatch is being created, is in the form of a tab delimited file with a header row. For constructing design and contrast matrices for analyses, the user has to choose one or more of those phenodata columns for that experiment - and the choice typically might be limited to those columns containing *exactly* two values - ie dichotomous contrasts. I have code working that allows the user to choose an input (eg affybatch) experiment file from their history, then to choose from among *only* the dichotomous phenotype columns, and run the analysis - you cannot imagine what a big deal this is compared with trying to teach people to generate design and contrast matrices interactively in R! But of course, these miracles all rely on dynamic_options calling some code included with the tool. What's the best way forward for a situation where we need to obtain this kind of drop down list for a tool, that depends on the choice on a previous page, that will be compatible with workflows in the long-haul? I guess one approach is that when generating the (eg affybatch) metadata, I guess I could create all the option lists I'm going to ever need as additional metadata datastructures that could be used like the options from files are used elsewhere - the catch is that they'd all have to be precomputed rather than being computed on the fly by the tool - is that reasonable or is there some way to allow dynamic computing on the metadata (and it's a little complex, involving parsing the phenodata and constructing a concordance of the values in each column and eg returning only the columns with exactly two values) -- python -c "foo = map(None,'moc.liamg(a)surazal.ssor'); foo.reverse(); print ''.join(foo)"

1 0

[hg] galaxy 1503: Lastz with additional short read changes
by Nate Coraor 12 Sep '08

12 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/777e41dbdf1f changeset: 1503:777e41dbdf1f user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Fri Sep 12 15:14:20 2008 -0400 description: Lastz with additional short read changes 10 file(s) affected in this change: test-data/lastz_census.txt test-data/lastz_diffs.txt test-data/lastz_diffs_ref_name.txt test-data/lastz_maf.txt tool_conf.xml.sample tools/metag_tools/blat_wrapper.xml tools/metag_tools/megablast_wrapper.xml tools/sr_mapping/fastq_statistics.xml tools/sr_mapping/lastz_code.py tools/sr_mapping/lastz_wrapper.xml diffs (truncated from 7931 to 3000 lines): diff -r 6bb33bc9903f -r 777e41dbdf1f test-data/lastz_census.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lastz_census.txt Fri Sep 12 15:14:20 2008 -0400 @@ -0,0 +1,5386 @@ +phiX 1 255 +phiX 2 255 +phiX 3 255 +phiX 4 255 +phiX 5 255 +phiX 6 255 +phiX 7 255 +phiX 8 255 +phiX 9 255 +phiX 10 255 +phiX 11 255 +phiX 12 255 +phiX 13 255 +phiX 14 255 +phiX 15 255 +phiX 16 255 +phiX 17 255 +phiX 18 255 +phiX 19 255 +phiX 20 255 +phiX 21 255 +phiX 22 255 +phiX 23 255 +phiX 24 255 +phiX 25 255 +phiX 26 255 +phiX 27 255 +phiX 28 255 +phiX 29 255 +phiX 30 255 +phiX 31 255 +phiX 32 255 +phiX 33 255 +phiX 34 255 +phiX 35 255 +phiX 36 255 +phiX 37 255 +phiX 38 255 +phiX 39 255 +phiX 40 255 +phiX 41 255 +phiX 42 255 +phiX 43 255 +phiX 44 255 +phiX 45 255 +phiX 46 255 +phiX 47 255 +phiX 48 255 +phiX 49 255 +phiX 50 255 +phiX 51 255 +phiX 52 255 +phiX 53 255 +phiX 54 255 +phiX 55 255 +phiX 56 255 +phiX 57 255 +phiX 58 255 +phiX 59 255 +phiX 60 255 +phiX 61 255 +phiX 62 255 +phiX 63 255 +phiX 64 255 +phiX 65 255 +phiX 66 255 +phiX 67 255 +phiX 68 255 +phiX 69 255 +phiX 70 255 +phiX 71 255 +phiX 72 255 +phiX 73 255 +phiX 74 255 +phiX 75 255 +phiX 76 255 +phiX 77 255 +phiX 78 255 +phiX 79 255 +phiX 80 255 +phiX 81 255 +phiX 82 255 +phiX 83 255 +phiX 84 255 +phiX 85 255 +phiX 86 255 +phiX 87 255 +phiX 88 255 +phiX 89 255 +phiX 90 255 +phiX 91 255 +phiX 92 255 +phiX 93 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1 0

[hg] galaxy 1502: Prevent workflow editor form loading in IE6 an...
by Nate Coraor 12 Sep '08

12 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/6bb33bc9903f changeset: 1502:6bb33bc9903f user: James Taylor <james(a)jamestaylor.org> date: Fri Sep 12 07:13:09 2008 -0400 description: Prevent workflow editor form loading in IE6 and print a message 1 file(s) affected in this change: templates/workflow/editor.mako diffs (25 lines): diff -r 362a1c02da3d -r 6bb33bc9903f templates/workflow/editor.mako --- a/templates/workflow/editor.mako Thu Sep 11 12:22:32 2008 -0400 +++ b/templates/workflow/editor.mako Fri Sep 12 07:13:09 2008 -0400 @@ -28,9 +28,21 @@ <script type='text/javascript' src="/static/scripts/galaxy.workflow_editor.canvas.js"> </script> +  + <script type='text/javascript'> $( function() { + if ( window.lt_ie_7 ) { + show_modal( + "Browser not supported", + "Sorry, the workflow editor is not supported for IE6 and below." + ); + return; + } // Initialize workflow state reset(); // Load the datatype info

1 0

[hg] galaxy 1500: Allow complete logging configuration to be spe...
by Nate Coraor 11 Sep '08

11 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/30f4ab3cc266 changeset: 1500:30f4ab3cc266 user: James Taylor <james(a)jamestaylor.org> date: Wed Sep 10 09:58:29 2008 -0400 description: Allow complete logging configuration to be specified in the ini file, in which case this is used instead of the "log_level" and "log_format" keys under the app configuration. PasteScript actually handles this, so we just do nothing related to logging config if the ini file contains a "[loggers]" section. For example, you could add this to the end of your universe_wsgi.ini to include SQLAlchemy debugging and include the thread name with every log message. # Logger overrides [loggers] keys = root, sqlalchemy.engine, sqlalchemy.orm.unitofwork, paste.httpserver.ThreadPool [logger_root] level = DEBUG handlers = console [logger_sqlalchemy.engine] level = INFO handlers = console qualname = sqlalchemy.engine [logger_sqlalchemy.orm.unitofwork] level = DEBUG handlers = console qualname = sqlalchemy.orm.unitofwork [logger_paste.httpserver.ThreadPool] level = INFO handlers = console qualname = paste.httpserver.ThreadPool [handlers] keys = console [handler_console] class = StreamHandler args = (sys.stderr,) level = NOTSET formatter = generic [formatters] keys = generic [formatter_generic] format = %(threadName)s %(name)s %(levelname)s %(asctime)s %(message)s 1 file(s) affected in this change: lib/galaxy/config.py diffs (28 lines): diff -r f9d00dbefdec -r 30f4ab3cc266 lib/galaxy/config.py --- a/lib/galaxy/config.py Mon Sep 08 16:00:49 2008 -0400 +++ b/lib/galaxy/config.py Wed Sep 10 09:58:29 2008 -0400 @@ -64,9 +64,10 @@ self.bugs_email = kwargs.get( 'bugs_email', None ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) - #Parse global_conf + # Parse global_conf and save the parser global_conf = kwargs.get( 'global_conf', None ) global_conf_parser = ConfigParser.ConfigParser() + self.global_conf_parser = global_conf_parser if global_conf and "__file__" in global_conf: global_conf_parser.read(global_conf['__file__']) #Store per-tool runner config @@ -118,6 +119,12 @@ Allow some basic logging configuration to be read from the cherrpy config. """ + # PasteScript will have already configured the logger if the appropriate + # sections were found in the config file, so we do nothing if the + # config has a loggers section, otherwise we do some simple setup + # using the 'log_*' values from the config. + if config.global_conf_parser.has_section( "loggers" ): + return format = config.get( "log_format", "%(name)s %(levelname)s %(asctime)s %(message)s" ) level = logging._levelNames[ config.get( "log_level", "DEBUG" ) ] destination = config.get( "log_destination", "stdout" )

1 0

[hg] galaxy 1501: Upgrade bx-python to r448.
by Nate Coraor 11 Sep '08

11 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/362a1c02da3d changeset: 1501:362a1c02da3d user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Sep 11 12:22:32 2008 -0400 description: Upgrade bx-python to r448. 1 file(s) affected in this change: eggs.ini diffs (18 lines): diff -r 30f4ab3cc266 -r 362a1c02da3d eggs.ini --- a/eggs.ini Wed Sep 10 09:58:29 2008 -0400 +++ b/eggs.ini Thu Sep 11 12:22:32 2008 -0400 @@ -55,12 +55,12 @@ MySQL_python = _5.0.51a_static python_lzo = _static flup = .dev_r2311 -bx_python = _dev_r427 +bx_python = _dev_r448 nose = .dev_r101 ; source location, necessary for scrambling [source] -bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r427.tar.bz2 +bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r448.tar.bz2 Cheetah = http://umn.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar.gz DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://mysql.mirrors.pair.com/Downloads/MySQL-5.0/mysql-5.0.51a.tar.gz

1 0

[hg] galaxy 1497: Fix for scatterplot.py: Handling an uncaught e...
by Nate Coraor 11 Sep '08

11 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/a17b2cd3d9a4 changeset: 1497:a17b2cd3d9a4 user: guru date: Mon Sep 08 14:36:37 2008 -0400 description: Fix for scatterplot.py: Handling an uncaught exception. 1 file(s) affected in this change: tools/plotting/scatterplot.py diffs (15 lines): diff -r 2a361ee9ce3e -r a17b2cd3d9a4 tools/plotting/scatterplot.py --- a/tools/plotting/scatterplot.py Mon Sep 08 11:15:58 2008 -0400 +++ b/tools/plotting/scatterplot.py Mon Sep 08 14:36:37 2008 -0400 @@ -44,7 +44,10 @@ skipped_lines += 1 if not first_invalid_line: first_invalid_line = i + 1 - invalid_value = fields[column] + try: + invalid_value = fields[column] + except: + invalid_value = '' invalid_column = column + 1 break else:

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[hg] galaxy 1496: The interval to BED converter will now use the...
by Nate Coraor 11 Sep '08

11 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/2a361ee9ce3e changeset: 1496:2a361ee9ce3e user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Sep 08 11:15:58 2008 -0400 description: The interval to BED converter will now use the name field specified via metadata, if available. 2 file(s) affected in this change: lib/galaxy/datatypes/converters/interval_to_bed_converter.py lib/galaxy/datatypes/converters/interval_to_bed_converter.xml diffs (48 lines): diff -r 49fe600b9499 -r 2a361ee9ce3e lib/galaxy/datatypes/converters/interval_to_bed_converter.py --- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.py Mon Sep 08 09:47:37 2008 -0400 +++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.py Mon Sep 08 11:15:58 2008 -0400 @@ -31,18 +31,28 @@ strandCol = int( sys.argv[6] ) - 1 except: strandCol = -1 + try: + nameCol = int( sys.argv[7] ) - 1 + except: + nameCol = -1 skipped_lines = 0 first_skipped_line = 0 - count = 0 out = open( output_name,'w' ) - for region in bx.intervals.io.NiceReaderWrapper( open( input_name, 'r' ), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False ): + for count, region in enumerate( bx.intervals.io.NiceReaderWrapper( open( input_name, 'r' ), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False ) ): try: - out.write( region.chrom + "\t" + str( region.start ) + "\t" + str( region.end ) + "\tregion_" + str( count ) + "\t" + "0\t" + region.strand + "\n" ) + if nameCol >= 0: + name = region.fields[nameCol] + else: + raise IndexError + except: + name = "region_%i" % count + try: + + out.write( "%s\t%i\t%i\t%s\t%i\t%s\n" % ( region.chrom, region.start, region.end, name, 0, region.strand ) ) except: skipped_lines += 1 if not first_skipped_line: first_skipped_line = count + 1 - count += 1 out.close() info_msg = "%i regions converted to BED." % ( count - skipped_lines ) if skipped_lines > 0: diff -r 49fe600b9499 -r 2a361ee9ce3e lib/galaxy/datatypes/converters/interval_to_bed_converter.xml --- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml Mon Sep 08 09:47:37 2008 -0400 +++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml Mon Sep 08 11:15:58 2008 -0400 @@ -1,7 +1,7 @@ <tool id="CONVERTER_interval_to_bed_0" name="Convert Genomic Intervals To BED">   - <command interpreter="python">interval_to_bed_converter.py $output1 $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol}</command> + <command interpreter="python">interval_to_bed_converter.py $output1 $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol}</command> <inputs> <page> <param format="interval" name="input1" type="data" label="Choose intervals"/>

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[hg] galaxy 1498: Fix for grouping.py: New line character append...
by Nate Coraor 11 Sep '08

11 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/ad69f789d1cd changeset: 1498:ad69f789d1cd user: guru date: Mon Sep 08 14:54:40 2008 -0400 description: Fix for grouping.py: New line character appended when grouping by the last column will now be trimmed. 1 file(s) affected in this change: tools/stats/grouping.py diffs (11 lines): diff -r a17b2cd3d9a4 -r ad69f789d1cd tools/stats/grouping.py --- a/tools/stats/grouping.py Mon Sep 08 14:36:37 2008 -0400 +++ b/tools/stats/grouping.py Mon Sep 08 14:54:40 2008 -0400 @@ -90,6 +90,7 @@ for ii, line in enumerate( file( tmpfile.name )): if line and not line.startswith( '#' ): + line = line.strip() try: fields = line.split("\t") item = fields[group_col]

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[hg] galaxy 1499: Update GMAJ tool to allow the specifying of an...
by Nate Coraor 11 Sep '08

11 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/f9d00dbefdec changeset: 1499:f9d00dbefdec user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Sep 08 16:00:49 2008 -0400 description: Update GMAJ tool to allow the specifying of annotations in two styles. 1 file(s) affected in this change: tools/visualization/GMAJ.xml diffs (144 lines): diff -r ad69f789d1cd -r f9d00dbefdec tools/visualization/GMAJ.xml --- a/tools/visualization/GMAJ.xml Mon Sep 08 14:54:40 2008 -0400 +++ b/tools/visualization/GMAJ.xml Mon Sep 08 16:00:49 2008 -0400 @@ -1,21 +1,40 @@ -<tool id="gmaj_1" name="GMAJ" Version="2.0.0"> +<tool id="gmaj_1" name="GMAJ" Version="2.0.1"> <description>Multiple Alignment Viewer</description> <command interpreter="python">GMAJ.py $out_file1 $maf_input $gmaj_file $filenames_file</command> <inputs> <param name="maf_input" type="data" format="maf" label="Alignment File" optional="False"/> <param name="refseq" label="Reference Sequence" value="" type="text" help="Leave empty to allow interactive selection."/> <repeat name="annotations" title="Annotations"> - <param name="species" type="select" label="Species of Annotation" multiple="False"> - <options> - <filter type="data_meta" ref="maf_input" key="species" /> - </options> - </param> - <param name="exons_file" type="data" format="bed,gff" label="Exons File" optional="True"/> - <param name="highlights_file" type="data" format="bed,gff" label="Highlights File" optional="True"/> - <param name="underlays_file" type="data" format="bed,gff" label="Underlays File" optional="True"/> - <param name="repeats_file" type="data" format="bed,gff" label="Repeats File" optional="True"/> - <param name="links_file" type="data" format="bed,gff" label="Links File" optional="True"/> - <param name="offset" label="Offset" value="0" type="integer"/> + <conditional name="annotation_style"> + <param name="style" type="select" label="Annotation Style" help="If your data is not in a style similar to what is available from Galaxy (and the UCSC table browser), choose 'Basic'."> + <option value="galaxy" selected="true">Galaxy</option> + <option value="basic">Basic</option> + </param> + <when value="galaxy"> + <param name="species" type="select" label="Species of Annotation" multiple="False"> + <options> + <filter type="data_meta" ref="maf_input" key="species" /> + </options> + </param> + <param name="exons_file" type="data" format="bed,gff" label="Exons File" optional="True"/> + <param name="highlights_file" type="data" format="bed,gff" label="Highlights File" optional="True"/> + <param name="underlays_file" type="data" format="bed,gff" label="Underlays File" optional="True"/> + <param name="repeats_file" type="data" format="bed,gff" label="Repeats File" optional="True"/> + <param name="links_file" type="data" format="bed,gff" label="Links File" optional="True"/> + <param name="offset" label="Offset" value="0" type="integer"/> + </when> + <when value="basic"> + <param name="seq_name" label="Full Sequence Name" value="" type="text"> + <validator type="empty_field" message="You must supply the sequence name"/> + </param> + <param name="exons_file" type="data" format="bed,gff" label="Exons File" optional="True"/> + <param name="highlights_file" type="data" format="bed,gff" label="Highlights File" optional="True"/> + <param name="underlays_file" type="data" format="bed,gff" label="Underlays File" optional="True"/> + <param name="repeats_file" type="data" format="bed,gff" label="Repeats File" optional="True"/> + <param name="links_file" type="data" format="bed,gff" label="Links File" optional="True"/> + <param name="offset" label="Offset" value="0" type="integer"/> + </when> + </conditional> </repeat> <param name="nowarn" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true" label="Choose Warnings to Suppress" separator=" " help="These do not affect behavior, only suppress warning messages."> <options> @@ -81,52 +100,59 @@ #end if #set $seq_count = 0 -#for $spec_count, $annotation in $enumerate( $annotations ): -#if $maf_input.metadata.species_chromosomes and $annotation['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation['species'].value]: -#set $seq_names = [ "%s.%s" % ( $annotation['species'].value, $chrom ) for $chrom in $maf_input.metadata.species_chromosomes[$annotation['species'].value]] -#else -#set $seq_names = [$annotation['species'].value] +#for $annotation_count, $annotation in $enumerate( $annotations ): +#if $annotation.annotation_style.style == "galaxy": +#if $maf_input.metadata.species_chromosomes and $annotation.annotation_style['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]: +#set $seq_names = [ "%s.%s" % ( $annotation.annotation_style['species'].value, $chrom ) for $chrom in $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]] +#set $aliases = [ " %s" % $chrom for $chrom in $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]] +#else: +#set $seq_names = [$annotation.annotation_style['species']] +#set $aliases = [""] #end if -#for $seq_name in $seq_names: +#else: +#set $seq_names = [$annotation.annotation_style['seq_name']] +#set $aliases = [""] +#end if +#for $seq_name, $alias in $zip( $seq_names, $aliases ): seq ${seq_count}: seqname = $seq_name -#if $annotation['exons_file'].dataset: -exons = ${spec_count}.exons.${annotation['exons_file'].extension} +#if $annotation.annotation_style['exons_file'].dataset: +exons = ${annotation_count}.exons.${annotation.annotation_style['exons_file'].extension}$alias #end if -#if $annotation['repeats_file'].dataset: -repeats = ${spec_count}.repeats.${annotation['repeats_file'].extension} +#if $annotation.annotation_style['repeats_file'].dataset: +repeats = ${annotation_count}.repeats.${annotation.annotation_style['repeats_file'].extension}$alias #end if -#if $annotation['links_file'].dataset: -links = ${spec_count}.links.${annotation['links_file'].extension} +#if $annotation.annotation_style['links_file'].dataset: +links = ${annotation_count}.links.${annotation.annotation_style['links_file'].extension}$alias #end if -#if $annotation['underlays_file'].dataset: -underlays = ${spec_count}.underlays.${annotation['underlays_file'].extension} +#if $annotation.annotation_style['underlays_file'].dataset: +underlays = ${annotation_count}.underlays.${annotation.annotation_style['underlays_file'].extension}$alias #end if -#if $annotation['highlights_file'].dataset: -highlights = ${spec_count}.highlights.${annotation['highlights_file'].extension} +#if $annotation.annotation_style['highlights_file'].dataset: +highlights = ${annotation_count}.highlights.${annotation.annotation_style['highlights_file'].extension}$alias #end if -offset = $annotation['offset'] +offset = $annotation.annotation_style['offset'] #set $seq_count = $seq_count + 1 #end for #end for </configfile> <configfile name="filenames_file"> -#for $spec_count, $annotation in $enumerate( $annotations ): -#if $annotation['exons_file'].dataset: -$annotation['exons_file'] = ${spec_count}.exons.${annotation['exons_file'].extension} +#for $annotation_count, $annotation in $enumerate( $annotations ): +#if $annotation.annotation_style['exons_file'].dataset: +$annotation.annotation_style['exons_file'] = ${annotation_count}.exons.${annotation.annotation_style['exons_file'].extension} #end if -#if $annotation['repeats_file'].dataset: -$annotation['repeats_file'] = ${spec_count}.repeats.${annotation['repeats_file'].extension} +#if $annotation.annotation_style['repeats_file'].dataset: +$annotation.annotation_style['repeats_file'] = ${annotation_count}.repeats.${annotation.annotation_style['repeats_file'].extension} #end if -#if $annotation['links_file'].dataset: -$annotation['links_file'] = ${spec_count}.links.${annotation['links_file'].extension} +#if $annotation.annotation_style['links_file'].dataset: +$annotation.annotation_style['links_file'] = ${annotation_count}.links.${annotation.annotation_style['links_file'].extension} #end if -#if $annotation['underlays_file'].dataset: -$annotation['underlays_file'] = ${spec_count}.underlays.${annotation['underlays_file'].extension} +#if $annotation.annotation_style['underlays_file'].dataset: +$annotation.annotation_style['underlays_file'] = ${annotation_count}.underlays.${annotation.annotation_style['underlays_file'].extension} #end if -#if $annotation['highlights_file'].dataset: -$annotation['highlights_file'] = ${spec_count}.highlights.${annotation['highlights_file'].extension} +#if $annotation.annotation_style['highlights_file'].dataset: +$annotation.annotation_style['highlights_file'] = ${annotation_count}.highlights.${annotation.annotation_style['highlights_file'].extension} #end if #end for </configfile>

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Main is at rev 1495:49fe600b9499
by Greg Von Kuster 08 Sep '08

08 Sep '08

1 0

[hg] galaxy 1491: Fix for GMAJ tool when species chromosomes are...
by greg＠scofield.bx.psu.edu 08 Sep '08

08 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/9b8d06eea5b7 changeset: 1491:9b8d06eea5b7 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Sep 03 12:06:33 2008 -0400 description: Fix for GMAJ tool when species chromosomes are not specified. Error appears in paster.log as 'TypeError: iterable argument required' 1 file(s) affected in this change: tools/visualization/GMAJ.xml diffs (12 lines): diff -r cefbb71490a2 -r 9b8d06eea5b7 tools/visualization/GMAJ.xml --- a/tools/visualization/GMAJ.xml Sun Aug 31 21:14:06 2008 -0400 +++ b/tools/visualization/GMAJ.xml Wed Sep 03 12:06:33 2008 -0400 @@ -82,7 +82,7 @@ #set $seq_count = 0 #for $spec_count, $annotation in $enumerate( $annotations ): -#if $annotation['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation['species'].value]: +#if $maf_input.metadata.species_chromosomes and $annotation['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation['species'].value]: #set $seq_names = [ "%s.%s" % ( $annotation['species'].value, $chrom ) for $chrom in $maf_input.metadata.species_chromosomes[$annotation['species'].value]] #else #set $seq_names = [$annotation['species'].value]

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[hg] galaxy 1492: Fix for save link of history items.
by greg＠scofield.bx.psu.edu 08 Sep '08

08 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/d7e7804572fd changeset: 1492:d7e7804572fd user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Sep 04 12:19:32 2008 -0400 description: Fix for save link of history items. 1 file(s) affected in this change: templates/root/history_common.mako diffs (12 lines): diff -r 9b8d06eea5b7 -r d7e7804572fd templates/root/history_common.mako --- a/templates/root/history_common.mako Wed Sep 03 12:06:33 2008 -0400 +++ b/templates/root/history_common.mako Thu Sep 04 12:19:32 2008 -0400 @@ -57,7 +57,7 @@ <div class="info">Info: ${data.display_info()} </div> <div> %if data.has_data: - <a href="${h.url_for( action='display', id=data.id, tofile='yes', toext='data.ext' )}" target="_blank">save</a> + <a href="${h.url_for( action='display', id=data.id, tofile='yes', toext=data.ext )}" target="_blank">save</a> %for display_app in data.datatype.get_display_types(): <% display_links = data.datatype.get_display_links( data, display_app, app, request.base ) %> %if len( display_links ) > 0:

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[hg] galaxy 1493: More fixes for twill 0.9, the annotation profi...
by greg＠scofield.bx.psu.edu 08 Sep '08

08 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/e85d660c46ee changeset: 1493:e85d660c46ee user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Sep 05 16:36:51 2008 -0400 description: More fixes for twill 0.9, the annotation profiler tests do not yet pass, but all else should work now, more tests coming soon. 7 file(s) affected in this change: test/base/twilltestcase.py test/functional/__init__.py test/functional/test_metadata_editing.py tools/annotation_profiler/annotation_profiler.xml tools/filters/joiner.xml tools/new_operations/intersect.xml tools/new_operations/subtract.xml diffs (289 lines): diff -r d7e7804572fd -r e85d660c46ee test/base/twilltestcase.py --- a/test/base/twilltestcase.py Thu Sep 04 12:19:32 2008 -0400 +++ b/test/base/twilltestcase.py Fri Sep 05 16:36:51 2008 -0400 @@ -1,8 +1,7 @@ import pkg_resources -pkg_resources.require('twill') +pkg_resources.require( "twill==0.9" ) -import StringIO -import os, sys, random, filecmp, time, unittest, urllib, logging, difflib, zipfile +import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, zipfile from itertools import * import twill @@ -18,7 +17,7 @@ # Dial ClientCookie logging down (very noisy) logging.getLogger( "ClientCookie.cookies" ).setLevel( logging.WARNING ) -#log = logging.getLogger( __name__ ) +log = logging.getLogger( __name__ ) class TwillTestCase( unittest.TestCase ): @@ -244,8 +243,14 @@ self.assertEqual(len(elems), 1) self.visit_page( "delete?id=%s" % elems[0].get('id') ) - def edit_metadata( self, hid=None, form=1, **kwd ): - """Edits the metadata associated with a history item. There are currently 3 forms on the edit page.""" + def edit_metadata( self, hid=None, form_no=0, **kwd ): + """ + Edits the metadata associated with a history item.""" + # There are currently 4 forms on the edit page: + # 0. name="edit_attributes" + # 1. name="auto_detect" + # 2. name="convert_data" + # 3. name="change_datatype" data_list = self.get_history() self.assertTrue( data_list ) if hid is None: # take last hid @@ -253,12 +258,16 @@ hid = elem.get('hid') self.assertTrue( hid ) self.visit_page( 'edit?hid=%d' % hid ) - if form == 1: button = "save" #Edit Attributes form - elif form == 2: button = "detect" #Auto-detect Metadata Attributes - elif form == 3: button = "convert_data" #Convert to new format form - elif form == 4: button = "change" #Change data type form + if form_no == 0: + button = "save" #Edit Attributes form + elif form_no == 1: + button = "detect" #Auto-detect Metadata Attributes + elif form_no == 2: + button = "convert_data" #Convert to new format form + elif form_no == 3: + button = "change" #Change data type form if kwd: - self.submit_form(form=form, button=button, **kwd) + self.submit_form( form_no=form_no, button=button, **kwd) def get_dataset_ids_in_history( self ): """Returns the ids of datasets in a history""" @@ -406,23 +415,24 @@ def showforms( self ): """Shows form, helpful for debugging new tests""" - return tc.browser.showforms() + return tc.showforms() - def submit_form( self, form=1, button="runtool_btn", **kwd ): - """Populates and submits a form from the keyword arguments""" - #Check for onchange attribute, submit a change if required - for i, f in enumerate( tc.showforms() ): - if i == form - 1: + def submit_form( self, form_no=0, button="runtool_btn", **kwd ): + """Populates and submits a form from the keyword arguments.""" + for i, f in enumerate( self.showforms() ): + if i == form_no: break + # An HTMLForm contains a sequence of Controls. Supported control classes are: + # TextControl, FileControl, ListControl, RadioControl, CheckboxControl, SelectControl, + # SubmitControl, ImageControl for i, control in enumerate( f.controls ): try: + # Check for refresh_on_change attribute, submit a change if required if 'refresh_on_change' in control.attrs.keys(): changed = False for elem in kwd[control.name]: - """ - For DataToolParameter, control.value is the index of the DataToolParameter select list, - but elem is the filename. The following loop gets the filename of that index. - """ + # For DataToolParameter, control.value is the index of the DataToolParameter select list, + # but elem is the filename. The following loop gets the filename of that index. param_text = '' for param in tc.show().split('<select'): param = ('<select' + param.split('select>')[0] + 'select>').replace('selected', 'selected="yes"') @@ -433,52 +443,56 @@ param_text = option.text.strip() break break - if elem not in control.value and param_text.find(elem) == -1 : changed = True break if changed: - # Clear Control and set to proper value - the command: - # formvalue <formnum> <fieldname> <value> - # sets the given field in the given form to the given value. - # For read-only form widgets/controls, the click may be recorded for use by submit, - # but the value is not changed unless the 'config' command has changed the default behavior. + # Clear Control and set to proper value control.clear() - for elem in kwd[control.name]: - tc.formvalue(str(form), str(i+1), str(elem) ) - #Create a new submit control, allows form to refresh, instead of going to next page - control = ClientForm.SubmitControl('SubmitControl','___refresh_grouping___',{'name':'refresh_grouping'}) + # kwd[control.name] should be a singlelist + for elem in kwd[ control.name ]: + tc.fv( f.name, control.name, str( elem ) ) + # Create a new submit control, allows form to refresh, instead of going to next page + control = ClientForm.SubmitControl( 'SubmitControl', '___refresh_grouping___', {'name':'refresh_grouping'} ) control.add_to_form( f ) control.fixup() - #submit for refresh - tc.submit('___refresh_grouping___') - #start over submit_form() - return self.submit_form(form, button, **kwd) + # Submit for refresh + tc.submit( '___refresh_grouping___' ) + return self.submit_form( form_no=form_no, button=button, **kwd ) except Exception, e: - # Log.debug("In submit_form, caught exception: %s" %str( e )) + log.debug( "In submit_form, continuing, but caught exception: %s" % str( e ) ) continue - for key, value in kwd.items(): - # needs to be able to handle multiple values per key - if not isinstance(value, list): - value = [ value ] - for i, control in enumerate( f.controls ): - if control.name == key: - control.clear() - if control.is_of_kind("text"): - # set the given field in the given form to the given value. - tc.formvalue(str(form), str(i+1), ",".join(value) ) - else: - try: - for elem in value: - tc.formvalue(str(form), str(i+1), str(elem) ) - except Exception, exc: - errmsg = "Attempting to set field '%s' to value '%s' threw exception: '%s'\n" % ( str( key ), str( elem ), str( exc ) ) - errmsg += "control: %s\n" % str( control ) - errmsg += "If the above control is a DataToolparameter whose data type class does not include a sniff() method,\n" - errmsg += "make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.\n" - raise AssertionError( errmsg ) - break - tc.submit(button) + # No refresh_on_change attribute found in current form, so process as usual + for control_name, control_value in kwd.items(): + if not isinstance( control_value, list ): + control_value = [ control_value ] + try: + control = f.find_control( name=control_name ) + except: + # This assumes we always want the first control of the given name, + # which may not be ideal... + control = f.find_control( name=control_name, nr=0 ) + control.clear() + if control.is_of_kind( "text" ): + tc.fv( f.name, control.name, ",".join( control_value ) ) + elif control.is_of_kind( "list" ): + try: + if control.is_of_kind( "multilist" ): + for elem in control_value: + control.get( name=elem ).selected = True + else: # control.is_of_kind( "singlelist" ) + for elem in control_value: + tc.fv( f.name, control.name, str( elem ) ) + except Exception, exc: + errmsg = "Attempting to set field '%s' to value '%s' in form '%s' threw exception: %s\n" % ( control_name, str( control_value ), f.name, str( exc ) ) + errmsg += "control: %s\n" % str( control ) + errmsg += "If the above control is a DataToolparameter whose data type class does not include a sniff() method,\n" + errmsg += "make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.\n" + raise AssertionError( errmsg ) + else: + # Add conditions for other control types here when necessary. + pass + tc.submit( button ) def visit_page( self, page ): tc.go("./%s" % page) @@ -493,8 +507,8 @@ tool_id = tool_id.replace(" ", "+") """Runs the tool 'tool_id' and passes it the key/values from the *kwd""" self.visit_url( "%s/tool_runner/index?tool_id=%s" % (self.url, tool_id) ) - tc.find('runtool_btn') - self.submit_form(**kwd) + tc.find( 'runtool_btn' ) + self.submit_form( **kwd ) def wait( self, maxiter=20 ): """Waits for the tools to finish""" diff -r d7e7804572fd -r e85d660c46ee test/functional/__init__.py --- a/test/functional/__init__.py Thu Sep 04 12:19:32 2008 -0400 +++ b/test/functional/__init__.py Fri Sep 05 16:36:51 2008 -0400 @@ -2,7 +2,7 @@ import pkg_resources -pkg_resources.require( "twill==0.8.3" ) +pkg_resources.require( "twill==0.9" ) pkg_resources.require( "Paste" ) pkg_resources.require( "PasteDeploy" ) pkg_resources.require( "Cheetah" ) diff -r d7e7804572fd -r e85d660c46ee test/functional/test_metadata_editing.py --- a/test/functional/test_metadata_editing.py Thu Sep 04 12:19:32 2008 -0400 +++ b/test/functional/test_metadata_editing.py Fri Sep 05 16:36:51 2008 -0400 @@ -9,17 +9,17 @@ self.check_history_for_string('\? bed') self.check_metadata_for_string('1.bed uploaded file unspecified (\?) chromCol value="1" selected endCol value="3" is_strandCol value="true" checked', hid=1) """test editing attributes""" - self.edit_metadata(hid=1, form=1, name='Testdata', info="Uploaded my file", dbkey='hg16', startCol='6') + self.edit_metadata(hid=1, form_no=0, name='Testdata', info="Uploaded my file", dbkey='hg16', startCol='6') self.check_metadata_for_string('Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="6" selected', hid=1) """test Auto-detecting attributes""" - self.edit_metadata(hid=1, form=2) + self.edit_metadata(hid=1, form_no=1) self.check_metadata_for_string('Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="2" selected', hid=1) """test converting formats""" - self.edit_metadata(hid=1, form=3, target_type='gff') + self.edit_metadata(hid=1, form_no=2, target_type='gff') self.check_history_for_string('hg16 Testdata Convert BED to GFF') self.check_metadata_for_string('"gff" selected="yes"', hid=1) """test changing data type""" - self.edit_metadata(hid=1, form=4, datatype='gff3') + self.edit_metadata(hid=1, form_no=3, datatype='gff3') self.check_history_for_string('hg16 Testdata Convert BED to GFF format: gff3') self.delete_history_item( 1 ) def test_9999_clean_up( self ): diff -r d7e7804572fd -r e85d660c46ee tools/annotation_profiler/annotation_profiler.xml --- a/tools/annotation_profiler/annotation_profiler.xml Thu Sep 04 12:19:32 2008 -0400 +++ b/tools/annotation_profiler/annotation_profiler.xml Fri Sep 05 16:36:51 2008 -0400 @@ -30,7 +30,7 @@ <test> <param name="input1" value="3.bed" dbkey="hg18"/> <param name="keep_empty" value=""/> - <param name="summary" value="-S"/> + <param name="summary" value="Summary"/> <param name="table_names" value="acembly,affyGnf1h,affyHuEx1,knownAlt,knownGene,mrna,multiz17way,multiz28way,refGene,snp126"/> <output name="out_file1" file="annotation_profiler_2.out" /> </test> diff -r d7e7804572fd -r e85d660c46ee tools/filters/joiner.xml --- a/tools/filters/joiner.xml Thu Sep 04 12:19:32 2008 -0400 +++ b/tools/filters/joiner.xml Fri Sep 05 16:36:51 2008 -0400 @@ -33,8 +33,8 @@ <param name="input2" value="2.bed"/> <param name="field1" value="2"/> <param name="field2" value="2"/> - <param name="unmatched" value="-u"/> - <param name="partial" value="-p"/> + <param name="unmatched" value="Yes"/> + <param name="partial" value="Yes"/> <output name="out_file1" file="joiner_out2.bed"/> </test> </tests> diff -r d7e7804572fd -r e85d660c46ee tools/new_operations/intersect.xml --- a/tools/new_operations/intersect.xml Thu Sep 04 12:19:32 2008 -0400 +++ b/tools/new_operations/intersect.xml Fri Sep 05 16:36:51 2008 -0400 @@ -33,7 +33,7 @@ <param name="input1" value="1.bed" /> <param name="input2" value="2.bed" /> <param name="min" value="10" /> - <param name="returntype" value="-p" /> + <param name="returntype" value="Overlapping pieces of Intervals" /> <output name="output" file="gops_intersect_p_out.bed" /> </test> <test> diff -r d7e7804572fd -r e85d660c46ee tools/new_operations/subtract.xml --- a/tools/new_operations/subtract.xml Thu Sep 04 12:19:32 2008 -0400 +++ b/tools/new_operations/subtract.xml Fri Sep 05 16:36:51 2008 -0400 @@ -43,7 +43,7 @@ <param name="input1" value="1.bed" /> <param name="input2" value="2.bed" /> <param name="min" value="10" /> - <param name="returntype" value="-p" /> + <param name="returntype" value="Non-overlapping pieces of intervals" /> <output name="output" file="gops-subtract-p.dat" /> </test> </tests>

1 0

[hg] galaxy 1494: Fix functional test for count tool and correct...
by greg＠scofield.bx.psu.edu 08 Sep '08

08 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/d427760f8fec changeset: 1494:d427760f8fec user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Sep 08 09:16:32 2008 -0400 description: Fix functional test for count tool and correct spelling errors in template. 1 file(s) affected in this change: tools/filters/uniq.xml diffs (33 lines): diff -r e85d660c46ee -r d427760f8fec tools/filters/uniq.xml --- a/tools/filters/uniq.xml Fri Sep 05 16:36:51 2008 -0400 +++ b/tools/filters/uniq.xml Mon Sep 08 09:16:32 2008 -0400 @@ -1,9 +1,9 @@ <tool id="Count1" name="Count"> - <description>occurences of each record</description> + <description>occurrences of each record</description> <command interpreter="python">uniq.py -i $input -o $out_file1 -c "$column" -d $delim</command> <inputs> <param name="input" type="data" format="tabular" label="from query" help="Query missing? See TIP below"/> - <param name="column" type="data_column" data_ref="input" multiple="True" numerical="False" label="Count occurencies of values in column(s)" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" /> + <param name="column" type="data_column" data_ref="input" multiple="True" numerical="False" label="Count occurrences of values in column(s)" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" /> <param name="delim" type="select" label="Delimited by"> <option value="T">Tab</option> <option value="Sp">Whitespace</option> @@ -21,7 +21,7 @@ <test> <param name="input" value="1.bed"/> <output name="out_file1" file="uniq_out.dat"/> - <param name="column" value="c1"/> + <param name="column" value="1"/> <param name="delim" value="T"/> </test> </tests> @@ -35,7 +35,7 @@ **Syntax** -This tool counts occurences of unique values in selected column(s). +This tool counts occurrences of unique values in selected column(s). - If multiple columns are selected, counting is performed on each unique group of all values in the selected columns. - The first column of the resulting query will be the count of unique values in the selected column(s) and will be followed by each value.

1 0

[hg] galaxy 1495: Update packed version of workflow editor scrip...
by greg＠scofield.bx.psu.edu 08 Sep '08

08 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/49fe600b9499 changeset: 1495:49fe600b9499 user: James Taylor <james(a)jamestaylor.org> date: Mon Sep 08 09:47:37 2008 -0400 description: Update packed version of workflow editor script (fix z-index problem again?) 1 file(s) affected in this change: static/scripts/packed/galaxy.workflow_editor.canvas.js diffs (8 lines): diff -r d427760f8fec -r 49fe600b9499 static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js Mon Sep 08 09:16:32 2008 -0400 +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js Mon Sep 08 09:47:37 2008 -0400 @@ -1,1 +1,1 @@ -function Terminal(A){this.element=A;this.connectors=[]}Terminal.prototype={connect:function(A){this.connectors.push(A);if(this.node){this.node.changed()}},disconnect:function(A){this.connectors.splice($.inArray(A,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(A,B){B.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(A,B){B.destroy()})}};function OutputTerminal(A,B){Terminal.call(this,A);this.datatype=B}OutputTerminal.prototype=new Terminal;function InputTerminal(A,B){Terminal.call(this,A);this.datatypes=B}InputTerminal.prototype=new Terminal;$.extend(InputTerminal.prototype,{can_accept:function(A){if(this.connectors.length<1){for(t in this.datatypes){if(A.datatype=="input"){return true}if(issubtype(A.datatype,this.datatypes[t])){return true}}}return false}});function Connector(B,A){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365"}$.extend(Connector.prototy pe,{connect:function(B,A){this.handle1=B;this.handle1.connect(this);this.handle2=A;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var C=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}C.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var L=function(S){return $(S).offset().left-C.offset().left};var G=function(S){return $(S).offset().top-C.offset().top};var F=L(this.handle1.element)+5;var E=G(this.handle1.element)+5;var N=L(this.handle2.element)+5;var K=G(this.handle2.element)+5;var D=100;var I=Math.min(F,N);var A=Math.max(F,N);var H=Math.min(E,K);var R=Math.max(E,K);var B=Math.min(Math.max(Math.abs(R-H)/2,100),300);var M=I-D;var Q=H-D;var O=A-I+2*D;var J=R-H+2*D;this.canvas.style.left=M+"px";this.canvas.styl e.top=Q+"px";this.canvas.setAttribute("width",O);this.canvas.setAttribute("height",J);F-=M;E-=Q;N-=M;K-=Q;var P=this.canvas.getContext("2d");P.lineCap="round";P.strokeStyle=this.outer_color;P.lineWidth=7;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke();P.strokeStyle=this.inner_color;P.lineWidth=5;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke()}});function Node(A){this.element=A;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new InputTerminal(this,B);D.node=node;D.name=A;$(this).droppable({tolerance:"intersect",accept:function(E){E=E.get(0);return(E.terminal)&&(D.can_accept(E.terminal))},activeClass:"input-terminal-active",over:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#BBFFBB"},out:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#FFFFFF"},drop:function(I ,G){var E=$(this).data("droppable");var F=G.draggable.get(0).terminal;var H=E.element.get(0).terminal;var J=new Connector();J.connect(F,H);J.redraw()}});$(this).hoverIntent(function(){if(D.connectors.length>0){var E=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(D.connectors,function(G,F){F.destroy()});E.remove()}))).bind("mouseleave",function(){$(this).remove()});E.css({top:$(this).offset().top-2,left:$(this).offset().left-E.width(),"padding-right":$(this).width()}).show()}},function(){});node.input_terminals[A]=D})},enable_output_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new OutputTerminal(this,B);D.node=node;D.name=A;$(this).draggable({scrollPanel:true,panel:$("#canvas-container"),helper:function(){var E=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container"). get(0);E.terminal=new OutputTerminal(E);var F=new Connector();this.drag_temp_connector=F;F.dragging=true;F.connect(this.terminal,E.terminal);return E},drag:function(F,E){h=E.helper.get(0);h.terminal.redraw()},stop:function(F,E){this.drag_temp_connector.destroy()}});node.output_terminals[A]=D})},redraw:function(){$.each(this.input_terminals,function(A,B){B.redraw()});$.each(this.output_terminals,function(A,B){B.redraw()})},destroy:function(){$.each(this.input_terminals,function(A,B){B.destroy();$(B.element).droppable("destroy")});$.each(this.output_terminals,function(A,B){B.destroy();$(B.element).draggable("destroy")});$(this.element).draggable("destroy").remove();workflow.remove_node(this)},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){$(this.element).removeClass("toolForm-active")},init_field_data:function(D){var C=this.element;if(D.type){this.type=D.type}this.form_html=D.form_html;this.tool_state=D.tool_state;this.tool_errors= D.tool_errors;if(this.tool_errors){C.addClass("tool-node-error")}else{C.removeClass("tool-node-error")}var B=this;var A=C.find(".toolFormBody");A.find("div").remove();var E=$("<div class='inputs'></div>").appendTo(A);$.each(D.data_inputs,function(H,F){var G=$("<div class='terminal input-terminal'></div>");B.enable_input_terminal(G,F.name,F.extensions);E.append($("<div class='form-row dataRow input-data-row' name='"+F.name+"'>"+F.label+"</div>").prepend(G))});if((D.data_inputs.length>0)&&(D.data_outputs.length>0)){A.append($("<div class='rule'></div>"))}$.each(D.data_outputs,function(I,F){var H=$("<div class='terminal output-terminal'></div>");B.enable_output_terminal(H,F.name,F.extension);var G=F.name;if(F.extension!="input"){G=G+" ("+F.extension+")"}A.append($("<div class='form-row dataRow'>"+G+"</div>").append(H))});workflow.node_changed(this)},update_field_data:function(E){var C=$(this.element),D=this;this.tool_state=E.tool_state;this.form_html=E.form_html;this.tool_error s=E.tool_errors;if(this.tool_errors){C.addClass("tool-node-error")}else{C.removeClass("tool-node-error")}var F=C.find("div.inputs");var B=$("<div class='inputs'></div>");var A=F.find("div.input-data-row");$.each(E.data_inputs,function(I,G){var H=$("<div class='terminal input-terminal'></div>");D.enable_input_terminal(H,G.name,G.extensions);F.find("div[name="+G.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var J=this.terminal.connectors[0];if(J){H[0].terminal.connectors[0]=J;J.handle2=H[0].terminal}});$(this).remove()});B.append($("<div class='form-row dataRow input-data-row' name='"+G.name+"'>"+G.label+"</div>").prepend(H))});F.replaceWith(B);F.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(C){var A=$(this.element).find(".toolFormBody");A.find("div").remove();var B="<div style='color: red; text-style: italic;'>"+C+"</div>";this.form_html=B;A.html(B);workflow.node_change d(this)},changed:function(){workflow.node_changed(this)}});function Workflow(){this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(A){A.id=this.id_counter;this.id_counter++;this.nodes[A.id]=A;this.has_changes=true;A.workflow=this},remove_node:function(A){if(this.active_node==A){this.clear_active_node()}delete this.nodes[A.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(B,A){A.destroy();wf.remove_node(A)})},to_simple:function(){var A={};$.each(this.nodes,function(B,D){var E={};$.each(D.input_terminals,function(F,G){E[G.name]=null;$.each(G.connectors,function(H,I){E[G.name]={id:I.handle1.node.id,output_name:I.handle1.name}})});var C={id:D.id,type:D.type,tool_id:D.tool_id,tool_state:D.tool_state,tool_errors:D.tool_errors,input_connections:E,position:$(D.element).position()};A[D.id]=C});return{steps:A}},from_simple:function(A){wf=this;var B=0;wf.name=A.name;$.each(A.steps,functio n(E,D){var C=prebuild_node("tool",D.name,D.tool_id);C.init_field_data(D);if(D.position){C.element.css({top:D.position.top,left:D.position.left})}C.id=D.id;wf.nodes[C.id]=C;B=Math.max(B,parseInt(E))});wf.id_counter=B+1;$.each(A.steps,function(E,D){var C=wf.nodes[E];$.each(D.input_connections,function(G,F){if(F){var H=wf.nodes[F.id];var I=new Connector();I.connect(H.output_terminals[F.output_name],C.input_terminals[G]);I.redraw()}})})},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive()}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(A){this.clear_active_node();parent.show_form_for_tool(A.form_html,A);A.make_active();this.active_node=A},node_changed:function(A){this.has_changes=true;if(this.active_node==A){this.activate_node(A)}}});function prebuild_node(H,F,K){var E=$("<div class='toolForm toolFormInCanvas'></div>");var C=new Node(E);C.type=H;if(H=="tool"){C.tool_id=K}var J=$("<div class='toolFormTitle unselectab le'>"+F+"</div>");E.append(J);E.css("left",$(window).scrollLeft()+20);E.css("top",$(window).scrollTop()+20);var I=$("<div class='toolFormBody'></div>");var D="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";I.append(D);C.form_html=D;E.append(I);var G=$("<div class='buttons' style='float: right;'></div>");G.append($("<img src='../images/delete_icon.png' />").click(function(L){C.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));zmax=$("#canvas-container").data("zmax");if(!zmax){zmax=0}E.css("zIndex",zmax+1);$("#canvas-container").data("zmax",zmax+1);E.appendTo("#canvas-container");var B=$("#canvas-container").position();E.css({left:(-B.left)+10,top:(-B.top)+10});var A=E.width();G.prependTo(J);A+=(G.width()+10);E.css("width",A);$(E).draggable({cursor:"move",scrollPanel:true,panel:$("#canvas-container"),scrollSensitivity:10, scrollSpeed:20,click:function(M,L){zmax=$("#canvas-container").data("zmax");$(this).css("zIndex",zmax+1);$("#canvas-container").data("zmax",zmax+1);workflow.activate_node(C)},start:function(M,L){workflow.activate_node(C);$(this).css("z-index",$("#canvas-container").data("zmax")+1000)},drag:function(M,L){$(this).find(".terminal").each(function(){this.terminal.redraw()})},stop:function(M,L){zmax=$("#canvas-container").data("zmax");$(this).css("zIndex",zmax+1);$("#canvas-container").data("zmax",zmax+1);$(this).find(".terminal").each(function(){this.terminal.redraw()});workflow.node_changed(this)}});return C}var ext_to_type=null;var type_to_type=null;function issubtype(B,A){B=ext_to_type[B];A=ext_to_type[A];return(A in type_to_type[B])}function populate_datatype_info(A){ext_to_type=A.ext_to_class_name;type_to_type=A.class_to_classes}; \ No newline at end of file +function Terminal(A){this.element=A;this.connectors=[]}Terminal.prototype={connect:function(A){this.connectors.push(A);if(this.node){this.node.changed()}},disconnect:function(A){this.connectors.splice($.inArray(A,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(A,B){B.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(A,B){B.destroy()})}};function OutputTerminal(A,B){Terminal.call(this,A);this.datatype=B}OutputTerminal.prototype=new Terminal;function InputTerminal(A,B){Terminal.call(this,A);this.datatypes=B}InputTerminal.prototype=new Terminal;$.extend(InputTerminal.prototype,{can_accept:function(A){if(this.connectors.length<1){for(t in this.datatypes){if(A.datatype=="input"){return true}if(issubtype(A.datatype,this.datatypes[t])){return true}}}return false}});function Connector(B,A){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365"}$.extend(Connector.prototy pe,{connect:function(B,A){this.handle1=B;this.handle1.connect(this);this.handle2=A;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var C=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}C.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var L=function(S){return $(S).offset().left-C.offset().left};var G=function(S){return $(S).offset().top-C.offset().top};var F=L(this.handle1.element)+5;var E=G(this.handle1.element)+5;var N=L(this.handle2.element)+5;var K=G(this.handle2.element)+5;var D=100;var I=Math.min(F,N);var A=Math.max(F,N);var H=Math.min(E,K);var R=Math.max(E,K);var B=Math.min(Math.max(Math.abs(R-H)/2,100),300);var M=I-D;var Q=H-D;var O=A-I+2*D;var J=R-H+2*D;this.canvas.style.left=M+"px";this.canvas.styl e.top=Q+"px";this.canvas.setAttribute("width",O);this.canvas.setAttribute("height",J);F-=M;E-=Q;N-=M;K-=Q;var P=this.canvas.getContext("2d");P.lineCap="round";P.strokeStyle=this.outer_color;P.lineWidth=7;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke();P.strokeStyle=this.inner_color;P.lineWidth=5;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke()}});function Node(A){this.element=A;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new InputTerminal(this,B);D.node=node;D.name=A;$(this).droppable({tolerance:"intersect",accept:function(E){E=E.get(0);return(E.terminal)&&(D.can_accept(E.terminal))},activeClass:"input-terminal-active",over:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#BBFFBB"},out:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#FFFFFF"},drop:function(I ,G){var E=$(this).data("droppable");var F=G.draggable.get(0).terminal;var H=E.element.get(0).terminal;var J=new Connector();J.connect(F,H);J.redraw()}});$(this).hoverIntent(function(){if(D.connectors.length>0){var E=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(D.connectors,function(G,F){F.destroy()});E.remove()}))).bind("mouseleave",function(){$(this).remove()});E.css({top:$(this).offset().top-2,left:$(this).offset().left-E.width(),"padding-right":$(this).width()}).show()}},function(){});node.input_terminals[A]=D})},enable_output_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new OutputTerminal(this,B);D.node=node;D.name=A;$(this).draggable({scrollPanel:true,panel:$("#canvas-container"),helper:function(){var E=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container"). get(0);E.terminal=new OutputTerminal(E);var F=new Connector();this.drag_temp_connector=F;F.dragging=true;F.connect(this.terminal,E.terminal);return E},drag:function(F,E){h=E.helper.get(0);h.terminal.redraw()},stop:function(F,E){this.drag_temp_connector.destroy()}});node.output_terminals[A]=D})},redraw:function(){$.each(this.input_terminals,function(A,B){B.redraw()});$.each(this.output_terminals,function(A,B){B.redraw()})},destroy:function(){$.each(this.input_terminals,function(A,B){B.destroy();$(B.element).droppable("destroy")});$.each(this.output_terminals,function(A,B){B.destroy();$(B.element).draggable("destroy")});workflow.remove_node(this);$(this.element).draggable("destroy").remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var A=this.element.get(0);(function(B){B.removeChild(A);B.appendChild(A)})(A.parentNode);$(A).removeClass("toolForm-active")},init_field_data:function(D){var C=this.element;if(D.type){this.type=D. type}this.form_html=D.form_html;this.tool_state=D.tool_state;this.tool_errors=D.tool_errors;if(this.tool_errors){C.addClass("tool-node-error")}else{C.removeClass("tool-node-error")}var B=this;var A=C.find(".toolFormBody");A.find("div").remove();var E=$("<div class='inputs'></div>").appendTo(A);$.each(D.data_inputs,function(H,F){var G=$("<div class='terminal input-terminal'></div>");B.enable_input_terminal(G,F.name,F.extensions);E.append($("<div class='form-row dataRow input-data-row' name='"+F.name+"'>"+F.label+"</div>").prepend(G))});if((D.data_inputs.length>0)&&(D.data_outputs.length>0)){A.append($("<div class='rule'></div>"))}$.each(D.data_outputs,function(I,F){var H=$("<div class='terminal output-terminal'></div>");B.enable_output_terminal(H,F.name,F.extension);var G=F.name;if(F.extension!="input"){G=G+" ("+F.extension+")"}A.append($("<div class='form-row dataRow'>"+G+"</div>").append(H))});workflow.node_changed(this)},update_field_data:function(E){var C=$(this.element), D=this;this.tool_state=E.tool_state;this.form_html=E.form_html;this.tool_errors=E.tool_errors;if(this.tool_errors){C.addClass("tool-node-error")}else{C.removeClass("tool-node-error")}var F=C.find("div.inputs");var B=$("<div class='inputs'></div>");var A=F.find("div.input-data-row");$.each(E.data_inputs,function(I,G){var H=$("<div class='terminal input-terminal'></div>");D.enable_input_terminal(H,G.name,G.extensions);F.find("div[name="+G.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var J=this.terminal.connectors[0];if(J){H[0].terminal.connectors[0]=J;J.handle2=H[0].terminal}});$(this).remove()});B.append($("<div class='form-row dataRow input-data-row' name='"+G.name+"'>"+G.label+"</div>").prepend(H))});F.replaceWith(B);F.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(C){var A=$(this.element).find(".toolFormBody");A.find("div").remove();var B="<div style='color: red; tex t-style: italic;'>"+C+"</div>";this.form_html=B;A.html(B);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(){this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(A){A.id=this.id_counter;this.id_counter++;this.nodes[A.id]=A;this.has_changes=true;A.workflow=this},remove_node:function(A){if(this.active_node==A){this.clear_active_node()}delete this.nodes[A.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(B,A){A.destroy();wf.remove_node(A)})},to_simple:function(){var A={};$.each(this.nodes,function(B,D){var E={};$.each(D.input_terminals,function(F,G){E[G.name]=null;$.each(G.connectors,function(H,I){E[G.name]={id:I.handle1.node.id,output_name:I.handle1.name}})});var C={id:D.id,type:D.type,tool_id:D.tool_id,tool_state:D.tool_state,tool_errors:D.tool_errors,input_connections:E,position:$(D.element).position()};A[D.id]=C});return{steps:A}} ,from_simple:function(A){wf=this;var B=0;wf.name=A.name;$.each(A.steps,function(E,D){var C=prebuild_node("tool",D.name,D.tool_id);C.init_field_data(D);if(D.position){C.element.css({top:D.position.top,left:D.position.left})}C.id=D.id;wf.nodes[C.id]=C;B=Math.max(B,parseInt(E))});wf.id_counter=B+1;$.each(A.steps,function(E,D){var C=wf.nodes[E];$.each(D.input_connections,function(G,F){if(F){var H=wf.nodes[F.id];var I=new Connector();I.connect(H.output_terminals[F.output_name],C.input_terminals[G]);I.redraw()}})})},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(A){if(this.active_node!=A){this.clear_active_node();parent.show_form_for_tool(A.form_html,A);A.make_active();this.active_node=A}},node_changed:function(A){this.has_changes=true;if(this.active_node==A){parent.show_form_for_tool(A.form_html,A)}}});function prebuild_node(H,F,K){var E=$("<d iv class='toolForm toolFormInCanvas'></div>");var C=new Node(E);C.type=H;if(H=="tool"){C.tool_id=K}var J=$("<div class='toolFormTitle unselectable'>"+F+"</div>");E.append(J);E.css("left",$(window).scrollLeft()+20);E.css("top",$(window).scrollTop()+20);var I=$("<div class='toolFormBody'></div>");var D="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";I.append(D);C.form_html=D;E.append(I);var G=$("<div class='buttons' style='float: right;'></div>");G.append($("<img src='../images/delete_icon.png' />").click(function(L){C.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));E.appendTo("#canvas-container");var B=$("#canvas-container").position();E.css({left:(-B.left)+10,top:(-B.top)+10});var A=E.width();G.prependTo(J);A+=(G.width()+10);E.css("width",A);$(E).draggable({cursor:"move",scrollPanel:true,panel:$("#canvas-container"),s crollSensitivity:10,scrollSpeed:20,click:function(M,L){workflow.activate_node(C)},start:function(M,L){workflow.activate_node(C)},drag:function(M,L){$(this).find(".terminal").each(function(){this.terminal.redraw()})},stop:function(M,L){$(this).find(".terminal").each(function(){this.terminal.redraw()});workflow.node_changed(this)}});return C}var ext_to_type=null;var type_to_type=null;function issubtype(B,A){B=ext_to_type[B];A=ext_to_type[A];return(A in type_to_type[B])}function populate_datatype_info(A){ext_to_type=A.ext_to_class_name;type_to_type=A.class_to_classes}; \ No newline at end of file

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