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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"

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[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 1529: Adding tools to fetch microsatellites and esti...
by greg＠scofield.bx.psu.edu 25 Sep '08

25 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 1527: Some metadata updates.
by greg＠scofield.bx.psu.edu 25 Sep '08

25 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 1528: Eliminate enable_beta_features ( and the conce...
by greg＠scofield.bx.psu.edu 25 Sep '08

25 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 25 Sep '08

25 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 25 Sep '08

25 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 25 Sep '08

25 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 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 3777227 fr1.chrUn 343707053 343707336 283 122 0.4311 +hg17.chrX 3760375 3760468 fr1.chrUn 343706399 343706492 93 20 0.2151 +hg17.chrX 3733405 3733881 fr1.chrUn 303515824 303516268 444 186 0.4189 +hg17.chrX 3731355 3731463 fr1.chrUn 303515724 303515815 91 36 0.3956 +hg17.chrX 3730591 3731038 fr1.chrUn 303515378 303515724 346 126 0.3642 +hg17.chrX 3729219 3729457 fr1.chrUn 343703525 343703763 238 57 0.2395 +hg17.chrX 3700391 3700698 fr1.chrUn 241017738 241018068 307 112 0.3648 +hg17.chrX 3639441 3639646 fr1.chrUn 333536350 333536563 205 66 0.3220 diff -r 05974294cbf1 -r dabed25dfbaf test-data/subs.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subs.out Sun Sep 21 17:36:28 2008 -0400 @@ -0,0 +1,1379 @@ +#Chr Start End +hg17.chrX 3816460 3816460 +fr1.chrUn 343715249 343715249 +hg17.chrX 3816462 3816463 +fr1.chrUn 343715251 343715252 +hg17.chrX 3816466 3816466 +fr1.chrUn 343715255 343715255 +hg17.chrX 3816471 3816471 +fr1.chrUn 343715260 343715260 +hg17.chrX 3816473 3816474 +fr1.chrUn 343715262 343715263 +hg17.chrX 3816478 3816479 +fr1.chrUn 343715267 343715268 +hg17.chrX 3816484 3816485 +fr1.chrUn 343715273 343715274 +hg17.chrX 3816493 3816494 +fr1.chrUn 343715284 343715285 +hg17.chrX 3816496 3816499 +fr1.chrUn 343715287 343715290 +hg17.chrX 3816502 3816502 +fr1.chrUn 343715293 343715293 +hg17.chrX 3816504 3816505 +fr1.chrUn 343715295 343715296 +hg17.chrX 3816507 3816507 +fr1.chrUn 343715298 343715298 +hg17.chrX 3816511 3816511 +fr1.chrUn 343715302 343715302 +hg17.chrX 3816515 3816516 +fr1.chrUn 343715306 343715307 +hg17.chrX 3816518 3816518 +fr1.chrUn 343715312 343715312 +hg17.chrX 3816521 3816522 +fr1.chrUn 343715315 343715316 +hg17.chrX 3816524 3816524 +fr1.chrUn 343715318 343715318 +hg17.chrX 3816531 3816531 +fr1.chrUn 343715324 343715324 +hg17.chrX 3816534 3816542 +fr1.chrUn 343715327 343715335 +hg17.chrX 3816544 3816544 +fr1.chrUn 343715337 343715337 +hg17.chrX 3816547 3816549 +fr1.chrUn 343715340 343715342 +hg17.chrX 3816551 3816554 +fr1.chrUn 343715344 343715347 +hg17.chrX 3816556 3816558 +fr1.chrUn 343715349 343715351 +hg17.chrX 3816561 3816561 +fr1.chrUn 343715354 343715354 +hg17.chrX 3816564 3816564 +fr1.chrUn 343715357 343715357 +hg17.chrX 3816568 3816568 +fr1.chrUn 343715361 343715361 +hg17.chrX 3816570 3816571 +fr1.chrUn 343715363 343715364 +hg17.chrX 3816578 3816579 +fr1.chrUn 343715367 343715368 +hg17.chrX 3816582 3816582 +fr1.chrUn 343715371 343715371 +hg17.chrX 3816586 3816591 +fr1.chrUn 343715375 343715380 +hg17.chrX 3816595 3816597 +fr1.chrUn 343715384 343715386 +hg17.chrX 3816600 3816602 +fr1.chrUn 343715389 343715391 +hg17.chrX 3816604 3816604 +fr1.chrUn 343715393 343715393 +hg17.chrX 3816607 3816607 +fr1.chrUn 343715396 343715396 +hg17.chrX 3816611 3816611 +fr1.chrUn 343715402 343715402 +hg17.chrX 3816614 3816616 +fr1.chrUn 343715405 343715407 +hg17.chrX 3816619 3816621 +fr1.chrUn 343715410 343715412 +hg17.chrX 3816625 3816625 +fr1.chrUn 343715416 343715416 +hg17.chrX 3816627 3816628 +fr1.chrUn 343715418 343715419 +hg17.chrX 3816632 3816635 +fr1.chrUn 343715423 343715426 +hg17.chrX 3816639 3817164 +fr1.chrUn 343715430 343715959 +hg17.chrX 3816645 3816646 +fr1.chrUn 343715441 343715442 +hg17.chrX 3816649 3816650 +fr1.chrUn 343715445 343715446 +hg17.chrX 3816662 3816662 +fr1.chrUn 343715467 343715467 +hg17.chrX 3816665 3816665 +fr1.chrUn 343715470 343715470 +hg17.chrX 3816667 3816668 +fr1.chrUn 343715472 343715473 +hg17.chrX 3816670 3816670 +fr1.chrUn 343715475 343715475 +hg17.chrX 3816672 3816672 +fr1.chrUn 343715477 343715477 +hg17.chrX 3816674 3816678 +fr1.chrUn 343715479 343715483 +hg17.chrX 3816680 3816682 +fr1.chrUn 343715485 343715487 +hg17.chrX 3816684 3816684 +fr1.chrUn 343715489 343715489 +hg17.chrX 3816687 3816687 +fr1.chrUn 343715492 343715492 +hg17.chrX 3816690 3816690 +fr1.chrUn 343715495 343715495 +hg17.chrX 3816693 3816693 +fr1.chrUn 343715498 343715498 +hg17.chrX 3816695 3816695 +fr1.chrUn 343715500 343715500 +hg17.chrX 3816698 3816699 +fr1.chrUn 343715503 343715504 +hg17.chrX 3816714 3816714 +fr1.chrUn 343715519 343715519 +hg17.chrX 3816720 3816720 +fr1.chrUn 343715525 343715525 +hg17.chrX 3816726 3816727 +fr1.chrUn 343715531 343715532 +hg17.chrX 3816736 3816736 +fr1.chrUn 343715541 343715541 +hg17.chrX 3816741 3816741 +fr1.chrUn 343715546 343715546 +hg17.chrX 3816748 3816750 +fr1.chrUn 343715553 343715555 +hg17.chrX 3816752 3816753 +fr1.chrUn 343715557 343715558 +hg17.chrX 3816756 3816757 +fr1.chrUn 343715561 343715562 +hg17.chrX 3816771 3816772 +fr1.chrUn 343715576 343715577 +hg17.chrX 3816777 3816778 +fr1.chrUn 343715582 343715583 +hg17.chrX 3816780 3816781 +fr1.chrUn 343715585 343715586 +hg17.chrX 3816784 3816784 +fr1.chrUn 343715589 343715589 +hg17.chrX 3816786 3816786 +fr1.chrUn 343715591 343715591 +hg17.chrX 3816789 3816790 +fr1.chrUn 343715594 343715595 +hg17.chrX 3816796 3816797 +fr1.chrUn 343715597 343715598 +hg17.chrX 3816800 3816800 +fr1.chrUn 343715601 343715601 +hg17.chrX 3816805 3816808 +fr1.chrUn 343715606 343715609 +hg17.chrX 3816810 3816811 +fr1.chrUn 343715611 343715612 +hg17.chrX 3816814 3816814 +fr1.chrUn 343715615 343715615 +hg17.chrX 3816818 3816819 +fr1.chrUn 343715619 343715620 +hg17.chrX 3816835 3816835 +fr1.chrUn 343715625 343715625 +hg17.chrX 3816837 3816837 +fr1.chrUn 343715627 343715627 +hg17.chrX 3816841 3816842 +fr1.chrUn 343715631 343715632 +hg17.chrX 3816844 3816846 +fr1.chrUn 343715634 343715636 +hg17.chrX 3816849 3816849 +fr1.chrUn 343715639 343715639 +hg17.chrX 3816853 3816853 +fr1.chrUn 343715643 343715643 +hg17.chrX 3816868 3816868 +fr1.chrUn 343715661 343715661 +hg17.chrX 3816870 3816870 +fr1.chrUn 343715663 343715663 +hg17.chrX 3816878 3816879 +fr1.chrUn 343715671 343715672 +hg17.chrX 3816882 3816882 +fr1.chrUn 343715675 343715675 +hg17.chrX 3816891 3816891 +fr1.chrUn 343715684 343715684 +hg17.chrX 3816894 3816894 +fr1.chrUn 343715687 343715687 +hg17.chrX 3816903 3816903 +fr1.chrUn 343715696 343715696 +hg17.chrX 3816906 3816906 +fr1.chrUn 343715699 343715699 +hg17.chrX 3816909 3816909 +fr1.chrUn 343715702 343715702 +hg17.chrX 3816912 3816912 +fr1.chrUn 343715705 343715705 +hg17.chrX 3816915 3816915 +fr1.chrUn 343715708 343715708 +hg17.chrX 3816918 3816920 +fr1.chrUn 343715711 343715713 +hg17.chrX 3816924 3816924 +fr1.chrUn 343715717 343715717 +hg17.chrX 3816930 3816931 +fr1.chrUn 343715723 343715724 +hg17.chrX 3816935 3816935 +fr1.chrUn 343715728 343715728 +hg17.chrX 3816939 3816939 +fr1.chrUn 343715732 343715732 +hg17.chrX 3816952 3816952 +fr1.chrUn 343715745 343715745 +hg17.chrX 3816958 3816958 +fr1.chrUn 343715751 343715751 +hg17.chrX 3816961 3816961 +fr1.chrUn 343715754 343715754 +hg17.chrX 3816964 3816964 +fr1.chrUn 343715757 343715757 +hg17.chrX 3816966 3816968 +fr1.chrUn 343715759 343715761 +hg17.chrX 3816972 3816972 +fr1.chrUn 343715765 343715765 +hg17.chrX 3816974 3816974 +fr1.chrUn 343715767 343715767 +hg17.chrX 3816976 3816977 +fr1.chrUn 343715769 343715770 +hg17.chrX 3816979 3816980 +fr1.chrUn 343715772 343715773 +hg17.chrX 3795168 3795168 +fr1.chrUn 343710815 343710815 +hg17.chrX 3795170 3795170 +fr1.chrUn 343710817 343710817 +hg17.chrX 3795175 3795175 +fr1.chrUn 343710822 343710822 +hg17.chrX 3795188 3795188 +fr1.chrUn 343710827 343710827 +hg17.chrX 3795192 3795194 +fr1.chrUn 343710831 343710833 +hg17.chrX 3795196 3795198 +fr1.chrUn 343710835 343710837 +hg17.chrX 3795207 3795208 +fr1.chrUn 343710846 343710847 +hg17.chrX 3795210 3795211 +fr1.chrUn 343710849 343710850 +hg17.chrX 3795218 3795222 +fr1.chrUn 343710861 343710865 +hg17.chrX 3795225 3795226 +fr1.chrUn 343710868 343710869 +hg17.chrX 3795229 3795230 +fr1.chrUn 343710874 343710875 +hg17.chrX 3795235 3795235 +fr1.chrUn 343710887 343710887 +hg17.chrX 3795239 3795239 +fr1.chrUn 343710891 343710891 +hg17.chrX 3795241 3795242 +fr1.chrUn 343710893 343710894 +hg17.chrX 3795245 3795251 +fr1.chrUn 343710897 343710903 +hg17.chrX 3795254 3795259 +fr1.chrUn 343710906 343710911 +hg17.chrX 3795265 3795265 +fr1.chrUn 343710917 343710917 +hg17.chrX 3795268 3795268 +fr1.chrUn 343710920 343710920 +hg17.chrX 3795272 3795272 +fr1.chrUn 343710924 343710924 +hg17.chrX 3795274 3795275 +fr1.chrUn 343710926 343710927 +hg17.chrX 3795284 3795284 +fr1.chrUn 343710940 343710940 +hg17.chrX 3795312 3795312 +fr1.chrUn 343710968 343710968 +hg17.chrX 3795317 3795317 +fr1.chrUn 343710973 343710973 +hg17.chrX 3795326 3795326 +fr1.chrUn 343710982 343710982 +hg17.chrX 3795332 3795332 +fr1.chrUn 343710988 343710988 +hg17.chrX 3795336 3795336 +fr1.chrUn 343710992 343710992 +hg17.chrX 3795338 3795338 +fr1.chrUn 343710994 343710994 +hg17.chrX 3795344 3795344 +fr1.chrUn 343711000 343711000 +hg17.chrX 3795350 3795350 +fr1.chrUn 343711006 343711006 +hg17.chrX 3795353 3795353 +fr1.chrUn 343711009 343711009 +hg17.chrX 3795356 3795356 +fr1.chrUn 343711012 343711012 +hg17.chrX 3795359 3795359 +fr1.chrUn 343711015 343711015 +hg17.chrX 3795377 3795377 +fr1.chrUn 343711033 343711033 +hg17.chrX 3795380 3795380 +fr1.chrUn 343711036 343711036 +hg17.chrX 3795383 3795383 +fr1.chrUn 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-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

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