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commit/galaxy-central: dannon: page controller: fix invalid error syntax, remove unused import.
by Bitbucket 15 Jan '13

15 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ec543816a2a2/ changeset: ec543816a2a2 user: dannon date: 2013-01-15 16:34:58 summary: page controller: fix invalid error syntax, remove unused import. affected #: 1 file diff -r 8d2fe975c13c33439167903653c6c06217cab764 -r ec543816a2a2b6fea98e3353e65f9e9c30d62cbe lib/galaxy/webapps/galaxy/controllers/page.py --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -6,7 +6,6 @@ from galaxy.web.framework.helpers import time_ago, grids from galaxy import util from galaxy.util.sanitize_html import sanitize_html, _BaseHTMLProcessor -from galaxy.util.odict import odict from galaxy.util.json import from_json_string def format_bool( b ): @@ -716,7 +715,7 @@ id = trans.security.decode_id( id ) page = trans.sa_session.query( model.Page ).get( id ) if not page: - err+msg( "Page not found" ) + error( "Page not found" ) else: return self.security_check( trans, page, check_ownership, check_accessible ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Remove tipsy classes from base css.
by Bitbucket 15 Jan '13

15 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8d2fe975c13c/ changeset: 8d2fe975c13c user: jgoecks date: 2013-01-15 03:07:11 summary: Remove tipsy classes from base css. affected #: 2 files diff -r 311b636a72988f339f6b81837d5341a6505917a0 -r 8d2fe975c13c33439167903653c6c06217cab764 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -1480,37 +1480,6 @@ padding: 0; } -.tipsy { - padding: 5px; - font-size: 10px; - filter: alpha(opacity=80); - background-repeat: no-repeat; - background-image: url(../images/tipsy.gif); -} -.tipsy-inner { - padding: 5px 8px 4px 8px; - background-color: black; - color: white; - max-width: 200px; - text-align: center; -} - -.tipsy-north { - background-position: top center; -} - -.tipsy-south { - background-position: bottom center; -} - -.tipsy-east { - background-position: right center; -} - -.tipsy-west { - background-position: left center; -} - .editable-text { cursor:pointer; } diff -r 311b636a72988f339f6b81837d5341a6505917a0 -r 8d2fe975c13c33439167903653c6c06217cab764 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -1047,12 +1047,6 @@ .text-content th,.text-content td{border-bottom:1px solid #ddd;border-right:1px solid #ccc;} .text-content th,.text-content td{padding:.8em;} .icon-button{width:16px;height:16px;display:block;float:left;margin-left:2px;text-indent:20px;background-repeat:no-repeat;background-position:0px 0px;padding:0;} -.tipsy{padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);} -.tipsy-inner{padding:5px 8px 4px 8px;background-color:black;color:white;max-width:200px;text-align:center;} -.tipsy-north{background-position:top center;} -.tipsy-south{background-position:bottom center;} -.tipsy-east{background-position:right center;} -.tipsy-west{background-position:left center;} .editable-text{cursor:pointer;} .editable-text:hover{cursor:text;border:dotted #999999 1px;} .icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: clements: Update Sphinx RST structural doc to reflect recent code changes.
by Bitbucket 15 Jan '13

15 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/311b636a7298/ changeset: 311b636a7298 user: clements date: 2013-01-15 02:01:17 summary: Update Sphinx RST structural doc to reflect recent code changes. affected #: 4 files diff -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 -r 311b636a72988f339f6b81837d5341a6505917a0 doc/source/lib/galaxy.jobs.runners.rst --- a/doc/source/lib/galaxy.jobs.runners.rst +++ b/doc/source/lib/galaxy.jobs.runners.rst @@ -72,4 +72,5 @@ galaxy.jobs.runners.cli_job galaxy.jobs.runners.cli_shell + galaxy.jobs.runners.lwr_client diff -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 -r 311b636a72988f339f6b81837d5341a6505917a0 doc/source/lib/galaxy.util.rst --- a/doc/source/lib/galaxy.util.rst +++ b/doc/source/lib/galaxy.util.rst @@ -159,4 +159,5 @@ .. toctree:: galaxy.util.backports + galaxy.util.log diff -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 -r 311b636a72988f339f6b81837d5341a6505917a0 doc/source/lib/galaxy.webapps.community.controllers.rst --- a/doc/source/lib/galaxy.webapps.community.controllers.rst +++ b/doc/source/lib/galaxy.webapps.community.controllers.rst @@ -65,11 +65,3 @@ :undoc-members: :show-inheritance: -:mod:`workflow` Module ----------------------- - -.. automodule:: galaxy.webapps.community.controllers.workflow - :members: - :undoc-members: - :show-inheritance: - diff -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 -r 311b636a72988f339f6b81837d5341a6505917a0 doc/source/lib/galaxy.webapps.community.util.rst --- a/doc/source/lib/galaxy.webapps.community.util.rst +++ b/doc/source/lib/galaxy.webapps.community.util.rst @@ -25,3 +25,11 @@ :undoc-members: :show-inheritance: +:mod:`workflow_util` Module +--------------------------- + +.. automodule:: galaxy.webapps.community.util.workflow_util + :members: + :undoc-members: + :show-inheritance: + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: clements: Replaced "query" with "dataset" in a number of tool definition XML files.
by Bitbucket 15 Jan '13

15 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1e6f086d98d2/ changeset: 1e6f086d98d2 user: clements date: 2013-01-15 01:13:54 summary: Replaced "query" with "dataset" in a number of tool definition XML files. I got tired of coming across "query" when doing workshops. affected #: 7 files diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/extract/liftOver_wrapper.xml --- a/tools/extract/liftOver_wrapper.xml +++ b/tools/extract/liftOver_wrapper.xml @@ -39,8 +39,8 @@ <param name="minChainT" type="hidden" value="0" /></when><when value="1"> - <param name="minSizeQ" size="10" type="integer" value="0" label="Minimum matching region size in query" help="Recommended value: set to >= 300 bases for complete transcripts"/> - <param name="minChainQ" size="10" type="integer" value="500" label="Minimum chain size in query"/> + <param name="minSizeQ" size="10" type="integer" value="0" label="Minimum matching region size in dataset" help="Recommended value: set to >= 300 bases for complete transcripts"/> + <param name="minChainQ" size="10" type="integer" value="500" label="Minimum chain size in dataset"/><param name="minChainT" size="10" type="integer" value="500" label="Minimum chain size in target"/></when></conditional> diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/filters/bed2gff.xml --- a/tools/filters/bed2gff.xml +++ b/tools/filters/bed2gff.xml @@ -2,7 +2,7 @@ <description>converter</description><command interpreter="python">bed_to_gff_converter.py $input $out_file1</command><inputs> - <param format="bed" name="input" type="data" label="Convert this query"/> + <param format="bed" name="input" type="data" label="Convert this dataset"/></inputs><outputs><data format="gff" name="out_file1" /> diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/filters/condense_characters.xml --- a/tools/filters/condense_characters.xml +++ b/tools/filters/condense_characters.xml @@ -12,7 +12,7 @@ <option value="U">Underscores</option><option value="P">Pipes</option></param> - <param format="txt" name="input" type="data" label="in this Query"/> + <param format="txt" name="input" type="data" label="in this Dataset"/></inputs><outputs><data format="input" name="out_file1" metadata_source="input" /> diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/filters/convert_characters.xml --- a/tools/filters/convert_characters.xml +++ b/tools/filters/convert_characters.xml @@ -13,7 +13,7 @@ <option value="P">Pipes</option><option value="Co">Colons</option></param> - <param format="txt" name="input" type="data" label="in Query"/> + <param format="txt" name="input" type="data" label="in Dataset"/></inputs><outputs><data format="tabular" name="out_file1" /> diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/filters/gff2bed.xml --- a/tools/filters/gff2bed.xml +++ b/tools/filters/gff2bed.xml @@ -2,7 +2,7 @@ <description>converter</description><command interpreter="python">gff_to_bed_converter.py $input $out_file1</command><inputs> - <param format="gff" name="input" type="data" label="Convert this query"/> + <param format="gff" name="input" type="data" label="Convert this dataset"/></inputs><outputs><data format="bed" name="out_file1" /> diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/filters/sorter.xml --- a/tools/filters/sorter.xml +++ b/tools/filters/sorter.xml @@ -14,7 +14,7 @@ #end for </command><inputs> - <param format="tabular" name="input" type="data" label="Sort Query" /> + <param format="tabular" name="input" type="data" label="Sort Dataset" /><param name="column" label="on column" type="data_column" data_ref="input" accept_default="true"/><param name="style" type="select" label="with flavor"><option value="num">Numerical sort</option> diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/new_operations/get_flanks.xml --- a/tools/new_operations/get_flanks.xml +++ b/tools/new_operations/get_flanks.xml @@ -50,11 +50,11 @@ **Example 1** -- For the following query:: +- For the following dataset:: chr22 1000 7000 NM_174568 0 + -- running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Query positive strand; Blue: Flanks output)**:: +- running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Dataset positive strand; Blue: Flanks output)**:: chr22 500 800 NM_174568 0 + @@ -62,11 +62,11 @@ **Example 2** -- For the following query:: +- For the following dataset:: chr22 1000 7000 NM_028946 0 - -- running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Query negative strand; Magenta: Flanks output)**:: +- running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Dataset negative strand; Magenta: Flanks output)**:: chr22 500 800 NM_028946 0 - @@ -75,4 +75,4 @@ </help> -</tool> \ No newline at end of file +</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fixes for discovering repository dependencies when resinstalling a tool shed repository when the repository dependencies were added to updated revisions of a repository after it was uninstalled.
by Bitbucket 14 Jan '13

14 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/76a8795d3a7e/ changeset: 76a8795d3a7e user: greg date: 2013-01-14 23:15:46 summary: Fixes for discovering repository dependencies when resinstalling a tool shed repository when the repository dependencies were added to updated revisions of a repository after it was uninstalled. affected #: 3 files diff -r b94fbc70b5be12b56852f811843092eeca6b2f98 -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -952,12 +952,16 @@ update_dict = encoding_util.tool_shed_decode( encoded_update_dict ) changeset_revision = update_dict[ 'changeset_revision' ] ctx_rev = update_dict[ 'ctx_rev' ] + includes_tools = update_dict.get( 'includes_tools', False ) + has_repository_dependencies = update_dict.get( 'has_repository_dependencies', False ) response.close() except Exception, e: log.debug( "Error getting change set revision for update from the tool shed for repository '%s': %s" % ( repository.name, str( e ) ) ) + includes_tools = False + has_repository_dependencies = False changeset_revision = None ctx_rev = None - return changeset_revision, ctx_rev + return changeset_revision, ctx_rev, includes_tools, has_repository_dependencies def handle_missing_data_table_entry( app, relative_install_dir, tool_path, repository_tools_tups ): """ Inspect each tool to see if any have input parameters that are dynamically generated select lists that require entries in the diff -r b94fbc70b5be12b56852f811843092eeca6b2f98 -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1256,6 +1256,21 @@ @web.expose def get_changeset_revision_and_ctx_rev( self, trans, **kwd ): """Handle a request from a local Galaxy instance to retrieve the changeset revision hash to which an installed repository can be updated.""" + def has_tools_and_repository_dependencies( repository_metadata ): + includes_tools = False + has_repository_dependencies = False + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + if 'tools' in metadata: + includes_tools = True + else: + includes_tools = False + if 'repository_dependencies' in metadata: + has_repository_dependencies = True + else: + has_repository_dependencies = False + return includes_tools, has_repository_dependencies params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -1264,20 +1279,24 @@ owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans, name, owner ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + trans.security.encode_id( repository.id ), + changeset_revision ) + includes_tools, has_repository_dependencies = has_tools_and_repository_dependencies( repository_metadata ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) # Default to the received changeset revision and ctx_rev. update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) ctx_rev = str( update_to_ctx.rev() ) latest_changeset_revision = changeset_revision - update_dict = dict( changeset_revision=changeset_revision, ctx_rev=ctx_rev ) + update_dict = dict( changeset_revision=changeset_revision, + ctx_rev=ctx_rev, + includes_tools=includes_tools, + has_repository_dependencies=has_repository_dependencies ) if changeset_revision == repository.tip( trans.app ): # If changeset_revision is the repository tip, there are no additional updates. return encoding_util.tool_shed_encode( update_dict ) else: - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, - trans.security.encode_id( repository.id ), - changeset_revision ) if repository_metadata: # If changeset_revision is in the repository_metadata table for this repository, there are no additional updates. return encoding_util.tool_shed_encode( update_dict ) @@ -1286,10 +1305,16 @@ # repository was installed. We need to find the changeset_revision to which we need to update. update_to_changeset_hash = None for changeset in repo.changelog: + includes_tools = False + has_repository_dependencies = False changeset_hash = str( repo.changectx( changeset ) ) ctx = suc.get_changectx_for_changeset( repo, changeset_hash ) if update_to_changeset_hash: - if suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_hash ): + update_to_repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + trans.security.encode_id( repository.id ), + changeset_hash ) + if update_to_repository_metadata: + includes_tools, has_repository_dependencies = has_tools_and_repository_dependencies( update_to_repository_metadata ) # We found a RepositoryMetadata record. if changeset_hash == repository.tip( trans.app ): # The current ctx is the repository tip, so use it. @@ -1302,6 +1327,8 @@ elif not update_to_changeset_hash and changeset_hash == changeset_revision: # We've found the changeset in the changelog for which we need to get the next update. update_to_changeset_hash = changeset_hash + update_dict[ 'includes_tools' ] = includes_tools + update_dict[ 'has_repository_dependencies' ] = has_repository_dependencies update_dict[ 'changeset_revision' ] = str( latest_changeset_revision ) update_dict[ 'ctx_rev' ] = str( update_to_ctx.rev() ) return encoding_util.tool_shed_encode( update_dict ) diff -r b94fbc70b5be12b56852f811843092eeca6b2f98 -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -372,27 +372,15 @@ if operation == "activate or reinstall": repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) if repository.uninstalled: - # Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated so that we + # Since we're reinstalling the repository we need to find the latest changeset revision to which it can be updated so that we # can reset the metadata if necessary. This will ensure that information about repository dependencies and tool dependencies # will be current. - current_changeset_revision, current_ctx_rev = shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, repository ) - if current_ctx_rev != repository.ctx_rev: - repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( repository.repo_path( trans.app ) ) ) - repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, repository ) - shed_util.pull_repository( repo, repository_clone_url, current_changeset_revision ) - suc.update_repository( repo, ctx_rev=current_ctx_rev ) - shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) - shed_config_dict = trans.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) - metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app, - repository=repository, - repository_clone_url=repository_clone_url, - shed_config_dict=shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=True, - persist=True ) - if repository.includes_tools or repository.has_repository_dependencies: + current_changeset_revision, current_ctx_rev, includes_tools, has_repository_dependencies = \ + shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, repository ) + if current_ctx_rev == repository.ctx_rev: + includes_tools = repository.includes_tools + has_repository_dependencies = repository.has_repository_dependencies + if includes_tools or has_repository_dependencies: # Only allow selecting a different section in the tool panel if the repository was uninstalled. return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='reselect_tool_panel_section', @@ -859,12 +847,12 @@ if cloned_ok: if reinstalling: # Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated. - current_changeset_revision, current_ctx_rev = shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository ) + current_changeset_revision, current_ctx_rev, includes_tools, has_repository_dependencies = \ + shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository ) if current_ctx_rev != ctx_rev: repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( install_dir ) ) shed_util.pull_repository( repo, repository_clone_url, current_changeset_revision ) suc.update_repository( repo, ctx_rev=current_ctx_rev ) - self.handle_repository_contents( trans, tool_shed_repository=tool_shed_repository, tool_path=tool_path, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Get updates to the latest changset revision and reset metadata when reinstalling an uninstalled tool shed repository in Galaxy.
by Bitbucket 14 Jan '13

14 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b94fbc70b5be/ changeset: b94fbc70b5be user: greg date: 2013-01-14 21:16:06 summary: Get updates to the latest changset revision and reset metadata when reinstalling an uninstalled tool shed repository in Galaxy. affected #: 2 files diff -r dc575517a5f2d3081e1795c5d5e91c77e4488bc5 -r b94fbc70b5be12b56852f811843092eeca6b2f98 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -46,9 +46,9 @@ """ for dependency_key, requirements_dict in tool_dependencies.items(): if dependency_key not in [ 'set_environment' ]: - repository_name = requirements_dict[ 'repository_name' ] - repository_owner = requirements_dict[ 'repository_owner' ] - changeset_revision = requirements_dict[ 'changeset_revision' ] + repository_name = requirements_dict.get( 'repository_name', 'unknown' ) + repository_owner = requirements_dict.get( 'repository_owner', 'unknown' ) + changeset_revision = requirements_dict.get( 'changeset_revision', 'unknown' ) dependency_name = requirements_dict[ 'name' ] version = requirements_dict[ 'version' ] type = requirements_dict[ 'type' ] diff -r dc575517a5f2d3081e1795c5d5e91c77e4488bc5 -r b94fbc70b5be12b56852f811843092eeca6b2f98 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -372,6 +372,26 @@ if operation == "activate or reinstall": repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) if repository.uninstalled: + # Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated so that we + # can reset the metadata if necessary. This will ensure that information about repository dependencies and tool dependencies + # will be current. + current_changeset_revision, current_ctx_rev = shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, repository ) + if current_ctx_rev != repository.ctx_rev: + repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( repository.repo_path( trans.app ) ) ) + repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, repository ) + shed_util.pull_repository( repo, repository_clone_url, current_changeset_revision ) + suc.update_repository( repo, ctx_rev=current_ctx_rev ) + shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) + shed_config_dict = trans.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) + metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app, + repository=repository, + repository_clone_url=repository_clone_url, + shed_config_dict=shed_config_dict, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=True, + persist=True ) if repository.includes_tools or repository.has_repository_dependencies: # Only allow selecting a different section in the tool panel if the repository was uninstalled. return trans.response.send_redirect( web.url_for( controller='admin_toolshed', @@ -811,6 +831,7 @@ @web.require_admin def install_tool_shed_repositories( self, trans, tool_shed_repositories, reinstalling=False, **kwd ): """Install specified tool shed repositories.""" + shed_tool_conf = kwd.get( 'shed_tool_conf', '' ) tool_path = kwd[ 'tool_path' ] includes_tool_dependencies = util.string_as_bool( kwd[ 'includes_tool_dependencies' ] ) install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) ) @@ -843,6 +864,7 @@ repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( install_dir ) ) shed_util.pull_repository( repo, repository_clone_url, current_changeset_revision ) suc.update_repository( repo, ctx_rev=current_ctx_rev ) + self.handle_repository_contents( trans, tool_shed_repository=tool_shed_repository, tool_path=tool_path, @@ -850,7 +872,7 @@ relative_install_dir=relative_install_dir, tool_shed=tool_shed_repository.tool_shed, tool_section=tool_section, - shed_tool_conf=kwd.get( 'shed_tool_conf', '' ), + shed_tool_conf=shed_tool_conf, reinstalling=reinstalling ) trans.sa_session.refresh( tool_shed_repository ) metadata = tool_shed_repository.metadata @@ -1389,12 +1411,12 @@ repository_id=repository_id, repository_name=tool_shed_repository.name, repository_owner=tool_shed_repository.owner, - changeset_revision=tool_shed_repository.installed_changeset_revision ) + changeset_revision=tool_shed_repository.changeset_revision ) else: repository_dependencies = None repo_info_dict = suc.create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.installed_changeset_revision, + changeset_revision=tool_shed_repository.changeset_revision, ctx_rev=ctx_rev, repository_owner=tool_shed_repository.owner, repository_name=tool_shed_repository.name, @@ -1475,7 +1497,7 @@ repository_id=repository_id, repository_name=tool_shed_repository.name, repository_owner=tool_shed_repository.owner, - changeset_revision=tool_shed_repository.installed_changeset_revision ) + changeset_revision=tool_shed_repository.changeset_revision ) if repository_dependencies: includes_repository_dependencies = True else: @@ -1483,7 +1505,7 @@ includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies repo_info_dict = suc.create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.installed_changeset_revision, + changeset_revision=tool_shed_repository.changeset_revision, ctx_rev=ctx_rev, repository_owner=tool_shed_repository.owner, repository_name=tool_shed_repository.name, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Add tool id for when clause warnings that are output when tool XML is parsed.
by Bitbucket 14 Jan '13

14 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dc575517a5f2/ changeset: dc575517a5f2 user: jgoecks date: 2013-01-14 20:14:41 summary: Add tool id for when clause warnings that are output when tool XML is parsed. affected #: 1 file diff -r 7b30a0fd0a042eb6db92e43e005ccd6634184e66 -r dc575517a5f2d3081e1795c5d5e91c77e4488bc5 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1600,9 +1600,11 @@ try: possible_cases.remove( case.value ) except: - log.warning( "A when tag has been defined for '%s (%s) --> %s', but does not appear to be selectable." % ( group.name, group.test_param.name, case.value ) ) + log.warning( "Tool %s: a when tag has been defined for '%s (%s) --> %s', but does not appear to be selectable." % + ( self.id, group.name, group.test_param.name, case.value ) ) for unspecified_case in possible_cases: - log.warning( "A when tag has not been defined for '%s (%s) --> %s', assuming empty inputs." % ( group.name, group.test_param.name, unspecified_case ) ) + log.warning( "Tool %s: a when tag has not been defined for '%s (%s) --> %s', assuming empty inputs." % + ( self.id, group.name, group.test_param.name, unspecified_case ) ) case = ConditionalWhen() case.value = unspecified_case case.inputs = odict() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Remove unused test parameter.
by Bitbucket 14 Jan '13

14 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7b30a0fd0a04/ changeset: 7b30a0fd0a04 user: jgoecks date: 2013-01-14 20:00:21 summary: Remove unused test parameter. affected #: 1 file diff -r 58e3f00d02b8c09da2f1172fcadb7c8e65493ee3 -r 7b30a0fd0a042eb6db92e43e005ccd6634184e66 tools/rgenetics/rgGRR.xml --- a/tools/rgenetics/rgGRR.xml +++ b/tools/rgenetics/rgGRR.xml @@ -28,7 +28,6 @@ <param name='title' value='rgGRRtest1' /><param name='n' value='100' /><param name='Z' value='6' /> - <param name='force' value='true' /><output name='out_file1' file='rgtestouts/rgGRR/rgGRRtest1.html' ftype='html' compare="diff" lines_diff='350'><extra_files type="file" name='Log_rgGRRtest1.txt' value="rgtestouts/rgGRR/Log_rgGRRtest1.txt" compare="diff" lines_diff="170"/><extra_files type="file" name='rgGRRtest1.svg' value="rgtestouts/rgGRR/rgGRRtest1.svg" compare="diff" lines_diff="1000" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 14 Jan '13

14 Jan '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/46fc972bb869/ changeset: 46fc972bb869 user: jgoecks date: 2013-01-14 19:56:50 summary: Improve error message for test parameters that could not be added. affected #: 1 file diff -r f57b2bfb2365bef93b7974d990d663a0660a67d9 -r 46fc972bb869a4d3807bc11dcad7f279efc3a878 lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py +++ b/lib/galaxy/tools/test.py @@ -35,11 +35,13 @@ value = new_value break if not found_parameter: - raise ValueError( "Unable to determine parameter type of test input '%s'. Ensure that the parameter exists and that any container groups are defined first." % name ) + raise ValueError( "Unable to determine parameter type of test input '%s'. " + "Ensure that the parameter exists and that any container groups are defined first." + % name ) elif isinstance( self.tool.inputs[name], basic.DataToolParameter ): value = self.__add_uploaded_dataset( name, value, extra, self.tool.inputs[name] ) except Exception, e: - log.debug( "Error in add_param for %s: %s" % ( name, e ) ) + log.debug( "Error for tool %s: could not add test parameter %s. %s" % ( self.tool.id, name, e ) ) self.inputs.append( ( name, value, extra ) ) def add_output( self, name, file, extra ): self.outputs.append( ( name, file, extra ) ) https://bitbucket.org/galaxy/galaxy-central/commits/58e3f00d02b8/ changeset: 58e3f00d02b8 user: jgoecks date: 2013-01-14 19:57:19 summary: Fix issues in Tophat color wrapper tests. affected #: 1 file diff -r 46fc972bb869a4d3807bc11dcad7f279efc3a878 -r 58e3f00d02b8c09da2f1172fcadb7c8e65493ee3 tools/ngs_rna/tophat_color_wrapper.xml --- a/tools/ngs_rna/tophat_color_wrapper.xml +++ b/tools/ngs_rna/tophat_color_wrapper.xml @@ -503,7 +503,7 @@ <test> @@ -564,7 +564,7 @@  @@ -591,7 +591,10 @@ <param name="max_insertion_length" value="3"/><param name="max_deletion_length" value="3"/><param name="use_junctions" value="No" /> - <param name="use_search" value="No" /> + <param name="use_search" value="Yes" /> + <param name="min_closure_exon" value="50" /> + <param name="min_closure_intron" value="50" /> + <param name="max_closure_intron" value="5000" /><param name="use_search" value="Yes" /><param name="min_coverage_intron" value="50" /><param name="max_coverage_intron" value="20000" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Ensure each repository dependency container contains only unique entries.
by Bitbucket 14 Jan '13

14 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f57b2bfb2365/ changeset: f57b2bfb2365 user: greg date: 2013-01-14 17:22:07 summary: Ensure each repository dependency container contains only unique entries. affected #: 1 file diff -r 937966b77a10fb229ee265f2a85eac6634fb7d08 -r f57b2bfb2365bef93b7974d990d663a0660a67d9 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -235,11 +235,8 @@ for name, repo_info_tuple in repo_info_dict.items(): description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ suc.get_repo_info_tuple_contents( repo_info_tuple ) - clone_dir = os.path.join( tool_path, generate_tool_path( repository_clone_url, changeset_revision ) ) - relative_install_dir = os.path.join( clone_dir, name ) # Make sure the repository was not already installed. - installed_tool_shed_repository, installed_changeset_revision = \ - repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple, clone_dir ) + installed_tool_shed_repository, installed_changeset_revision = repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple ) if installed_tool_shed_repository: tool_section, new_tool_panel_section, tool_panel_section_key = handle_tool_panel_selection( trans=trans, metadata=installed_tool_shed_repository.metadata, @@ -602,8 +599,7 @@ installed_rd, missing_rd = \ get_installed_and_missing_repository_dependencies( trans, repository ) else: - installed_rd, missing_rd = \ - get_installed_and_missing_repository_dependencies_for_new_install( trans, repository_dependencies ) + installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple ) # Discover all repository dependencies and retrieve information for installing them. required_repo_info_dicts = get_required_repo_info_dicts( tool_shed_url, util.listify( repo_info_dict ) ) # Display tool dependencies defined for each of the repository dependencies. @@ -697,7 +693,7 @@ missing_repository_dependencies[ root_key ] = missing_rd_tups missing_repository_dependencies[ 'description' ] = description return installed_repository_dependencies, missing_repository_dependencies -def get_installed_and_missing_repository_dependencies_for_new_install( trans, repository_dependencies ): +def get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple ): """ Parse the received repository_dependencies dictionary that is associated with a repository being installed into Galaxy for the first time and attempt to determine repository dependencies that are already installed and those that are not. @@ -706,28 +702,32 @@ installed_repository_dependencies = {} missing_rd_tups = [] installed_rd_tups = [] - description = repository_dependencies[ 'description' ] - root_key = repository_dependencies[ 'root_key' ] - # The repository dependencies container will include only the immediate repository dependencies of this repository, so the container will be - # only a single level in depth. - for key, rd_tups in repository_dependencies.items(): - if key in [ 'description', 'root_key' ]: - continue - for rd_tup in rd_tups: - tool_shed, name, owner, changeset_revision = rd_tup - # This is tricky because updates to installed repository revisions may have occurred making it difficult to discover installed repository - # revisions. If installed repositories are not discovered in this method, they will be returned in the list of missing_repository_dependencies, - # but should be discovered later during the installation process since that process inspects all appropriate changeset revisions. - repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed, name, owner, changeset_revision ) - if repository: - new_rd_tup = [ tool_shed, name, owner, changeset_revision, repository.id, repository.status ] - if repository.status == trans.model.ToolShedRepository.installation_status.INSTALLED: - installed_rd_tups.append( new_rd_tup ) + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td = \ + suc.get_repo_info_tuple_contents( repo_info_tuple ) + if repository_dependencies: + description = repository_dependencies[ 'description' ] + root_key = repository_dependencies[ 'root_key' ] + # The repository dependencies container will include only the immediate repository dependencies of this repository, so the container will be + # only a single level in depth. + for key, rd_tups in repository_dependencies.items(): + if key in [ 'description', 'root_key' ]: + continue + for rd_tup in rd_tups: + tool_shed, name, owner, changeset_revision = rd_tup + # Updates to installed repository revisions may have occurred, so make sure to locate the appropriate repository revision if one exists. + repository, current_changeset_revision = repository_was_previously_installed( trans, tool_shed, name, repo_info_tuple ) + if repository: + new_rd_tup = [ tool_shed, name, owner, changeset_revision, repository.id, repository.status ] + if repository.status == trans.model.ToolShedRepository.installation_status.INSTALLED: + if new_rd_tup not in installed_rd_tups: + installed_rd_tups.append( new_rd_tup ) + else: + if new_rd_tup not in missing_rd_tups: + missing_rd_tups.append( new_rd_tup ) else: - missing_rd_tups.append( new_rd_tup ) - else: - new_rd_tup = [ tool_shed, name, owner, changeset_revision, None, 'Never installed' ] - missing_rd_tups.append( new_rd_tup ) + new_rd_tup = [ tool_shed, name, owner, changeset_revision, None, 'Never installed' ] + if new_rd_tup not in missing_rd_tups: + missing_rd_tups.append( new_rd_tup ) if installed_rd_tups: installed_repository_dependencies[ 'root_key' ] = root_key installed_repository_dependencies[ root_key ] = installed_rd_tups @@ -1415,16 +1415,11 @@ description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ suc.get_repo_info_tuple_contents( repo_info_tuple ) if tool_dependencies: - clone_dir = os.path.join( tool_path, generate_tool_path( repository_clone_url, changeset_revision ) ) # Add the install_dir attribute to the tool_dependencies. tool_dependencies = suc.add_installation_directories_to_tool_dependencies( trans=trans, tool_dependencies=tool_dependencies ) # The required_repository may have been installed with a different changeset revision. - required_repository, installed_changeset_revision = repository_was_previously_installed( trans, - tool_shed_url, - name, - repo_info_tuple, - clone_dir ) + required_repository, installed_changeset_revision = repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple ) if required_repository: required_repository_installed_tool_dependencies, required_repository_missing_tool_dependencies = \ get_installed_and_missing_tool_dependencies( trans, required_repository, tool_dependencies ) @@ -1610,7 +1605,7 @@ trans.sa_session.add( tool_dependency ) trans.sa_session.flush() return removed, error_message -def repository_was_previously_installed( trans, tool_shed_url, repository_name, repo_info_tuple, clone_dir ): +def repository_was_previously_installed( trans, tool_shed_url, repository_name, repo_info_tuple ): """ Handle the case where the repository was previously installed using an older changeset_revsion, but later the repository was updated in the tool shed and now we're trying to install the latest changeset revision of the same repository instead of updating the one Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: clements: Reindented license text to make it render better at bitbucket.
by Bitbucket 12 Jan '13

12 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/937966b77a10/ changeset: 937966b77a10 user: clements date: 2013-01-12 01:00:01 summary: Reindented license text to make it render better at bitbucket. Also dropped non-informative link from outside the license. affected #: 1 file diff -r 2e96c23c760b7d9259168e007bec52ffcdfa00a9 -r 937966b77a10fb229ee265f= 2a85eac6634fb7d08 LICENSE.txt --- a/LICENSE.txt +++ b/LICENSE.txt @@ -2,49 +2,178 @@ =20 Licensed under the Academic Free License version 3.0 =20 -1) Grant of Copyright License. Licensor grants You a worldwide, royalty-fr= ee, non-exclusive, sublicensable license, for the duration of the copyright= , to do the following: + 1) Grant of Copyright License. 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commit/galaxy-central: inithello: Tool shed functional tests for automated installation, reinstallation, and reactivation of repository dependencies. Enhancements to tool shed functional test framework.
by Bitbucket 11 Jan '13

11 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2e96c23c760b/ changeset: 2e96c23c760b user: inithello date: 2013-01-11 23:02:42 summary: Tool shed functional tests for automated installation, reinstallation, and reactivation of repository dependencies. Enhancements to tool shed functional test framework. affected #: 6 files diff -r 9bdc2c2e95aa05e9cc8cd01599b224e1a3c6b26e -r 2e96c23c760b7d9259168e007bec52ffcdfa00a9 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -103,10 +103,10 @@ url = '/repository/view_changelog?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) - def check_repository_dependency( self, repository, depends_on_repository, depends_on_changeset_revision, changeset_revision=None ): - if changeset_revision is None: - changeset_revision = self.get_repository_tip( repository ) - strings_displayed = [ depends_on_repository.name, depends_on_repository.user.username, depends_on_changeset_revision ] + def check_repository_dependency( self, repository, depends_on_repository, depends_on_changeset_revision=None, changeset_revision=None ): + strings_displayed = [ depends_on_repository.name, depends_on_repository.user.username ] + if depends_on_changeset_revision: + strings_displayed.append( depends_on_changeset_revision ) self.display_manage_repository_page( repository, changeset_revision=changeset_revision, strings_displayed=strings_displayed ) def check_repository_metadata( self, repository, tip_only=True ): if tip_only: @@ -178,6 +178,15 @@ return '%s=%s&%s=%s' % ( field_name, field_value, field_name, field_value ) else: return '%s=%s' % ( field_name, field_value ) + def create_repository_dependency( self, repository=None, depends_on=[], filepath=None ): + dependency_description = '%s depends on %s.' % ( repository.name, ', '.join( repo.name for repo in depends_on ) ) + self.generate_repository_dependency_xml( depends_on, + self.get_filename( 'repository_dependencies.xml', filepath=filepath ), + dependency_description=dependency_description ) + self.upload_file( repository, + 'repository_dependencies.xml', + filepath=filepath, + commit_message='Uploaded dependency on %s.' % ', '.join( repo.name for repo in depends_on ) ) def create_user_in_galaxy( self, cntrller='user', email='test(a)bx.psu.edu', password='testuser', username='admin-user', redirect='' ): self.visit_galaxy_url( "/user/create?cntrller=%s&use_panels=False" % cntrller ) tc.fv( '1', 'email', email ) @@ -247,11 +256,25 @@ self.check_for_strings( strings_displayed, strings_not_displayed ) def display_manage_repository_page( self, repository, changeset_revision=None, strings_displayed=[], strings_not_displayed=[] ): base_url = '/repository/manage_repository?id=%s' % self.security.encode_id( repository.id ) - if changeset_revision is not None: + if changeset_revision: url = '%s&changeset_revision=%s' % ( base_url, changeset_revision ) else: + changeset_revision = self.get_repository_tip( repository ) url = base_url self.visit_url( url ) + metadata = self.get_repository_metadata_by_changeset_revision( repository, changeset_revision ) + if metadata: + if 'tool_dependencies' in metadata.metadata: + strings_displayed.append( 'Tool dependencies' ) + for dependency in metadata.metadata[ 'tool_dependencies' ]: + if dependency == 'set_environment': + for environment_dependency in metadata.metadata[ 'tool_dependencies' ][ dependency ]: + strings_displayed.append( environment_dependency[ 'name' ] ) + strings_displayed.append( environment_dependency[ 'type' ] ) + else: + strings_displayed.append( metadata.metadata[ 'tool_dependencies' ][ dependency ][ 'name' ] ) + strings_displayed.append( metadata.metadata[ 'tool_dependencies' ][ dependency ][ 'version' ] ) + strings_displayed.append( metadata.metadata[ 'tool_dependencies' ][ dependency ][ 'type' ] ) self.check_for_strings( strings_displayed, strings_not_displayed ) def display_repository_clone_page( self, owner_name, repository_name, strings_displayed=[], strings_not_displayed=[] ): url = '/repos/%s/%s' % ( owner_name, repository_name ) @@ -384,6 +407,9 @@ return self.hgweb_config_manager.get_entry( lhs ) except: raise Exception( "Entry for repository %s missing in hgweb config file %s." % ( lhs, self.hgweb_config_manager.hgweb_config ) ) + def get_repository_changelog( self, repository ): + repo = hg.repository( ui.ui(), self.get_repo_path( repository ) ) + return [repo.changectx( changeset ) for changeset in repo.changelog ] def get_repository_datatypes_count( self, repository ): metadata = self.get_repository_metadata( repository )[0].metadata if 'datatypes' not in metadata: @@ -424,7 +450,7 @@ return [ metadata_revision for metadata_revision in repository.metadata_revisions ] def get_repository_metadata_by_changeset_revision( self, repository, changeset_revision ): found = None - for metadata_revision in self.get_repository_metadata( repository ): + for metadata_revision in repository.metadata_revisions: if metadata_revision.changeset_revision == changeset_revision: found = metadata_revision return found @@ -671,6 +697,30 @@ tc.formfile( "1", "file_data", self.get_filename( filename, filepath ) ) tc.submit( "upload_button" ) self.check_for_strings( strings_displayed, strings_not_displayed ) + # Uncomment this if it becomes necessary to wait for an asynchronous process to complete after submitting an upload. + #for i in range( 5 ): + # try: + # self.check_for_strings( strings_displayed, strings_not_displayed ) + # break + # except Exception, e: + # if i == 4: + # raise e + # else: + # time.sleep( 1 ) + # continue + def verify_installed_uninstalled_repositories( self, installed_repositories=[], uninstalled_repositories=[] ): + strings_displayed = [] + strings_not_displayed = [] + for repository_name, repository_owner in uninstalled_repositories: + repository = test_db_util.get_repository_by_name_and_owner( repository_name, repository_owner ) + strings_not_displayed.extend( [ repository_name, self.get_repository_tip( repository ) ] ) + for repository_name, repository_owner in installed_repositories: + repository = test_db_util.get_repository_by_name_and_owner( repository_name, repository_owner ) + galaxy_repository = test_db_util.get_installed_repository_by_name_owner( repository_name, repository_owner ) + if galaxy_repository: + assert galaxy_repository.status == 'Installed', 'Repository %s should be installed, but is %s' % ( repository_name, galaxy_repository.status ) + strings_displayed.extend( [ repository_name, self.get_repository_tip( repository ) ] ) + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) def verify_installed_repository_metadata_unchanged( self, name, owner ): installed_repository = test_db_util.get_installed_repository_by_name_owner( name, owner ) metadata = installed_repository.metadata diff -r 9bdc2c2e95aa05e9cc8cd01599b224e1a3c6b26e -r 2e96c23c760b7d9259168e007bec52ffcdfa00a9 test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py --- a/test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py +++ b/test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py @@ -17,8 +17,20 @@ freebayes_repository_description = "Galaxy's freebayes tool" freebayes_repository_long_description = "Long description of Galaxy's freebayes tool" -default_category = 'test_0050_repository_n_level_circular_dependencies' -default_category_description = 'Testing handling of circular repository dependencies to n levels.' +column_repository_name = 'column_maker_0050' +column_repository_description = "Add column" +column_repository_long_description = "Compute an expression on every row" + +convert_repository_name = 'convert_chars_0050' +convert_repository_description = "Convert delimiters" +convert_repository_long_description = "Convert delimiters to tab" + +bismark_repository_name = 'bismark_0050' +bismark_repository_description = "A flexible aligner." +bismark_repository_long_description = "A flexible aligner and methylation caller for Bisulfite-Seq applications." + +category_name = 'Test 0050 Circular Dependencies 5 Levels' +category_description = 'Test circular dependency features' class TestRepositoryCircularDependenciesToNLevels( ShedTwillTestCase ): '''Verify that the code correctly handles circular dependencies down to n levels.''' @@ -34,30 +46,57 @@ admin_user = test_db_util.get_user( common.admin_email ) assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = test_db_util.get_private_role( admin_user ) - def test_0005_create_category( self ): - """Create a category for this test suite""" - self.create_category( name=default_category, description=default_category_description ) - def test_0010_create_emboss_datatypes_repository( self ): + def test_0005_create_convert_repository( self ): + '''Create and populate convert_chars_0050.''' + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=convert_repository_name, + description=convert_repository_description, + long_description=convert_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + 'convert_chars/convert_chars.tar', + strings_displayed=[], + commit_message='Uploaded convert_chars.tar.' ) + def test_0010_create_column_repository( self ): + '''Create and populate convert_chars_0050.''' + category = self.create_category( name=category_name, description=category_description ) + repository = self.get_or_create_repository( name=column_repository_name, + description=column_repository_description, + long_description=column_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + 'column_maker/column_maker.tar', + strings_displayed=[], + commit_message='Uploaded column_maker.tar.' ) + def test_0015_create_emboss_datatypes_repository( self ): '''Create and populate emboss_datatypes_0050.''' + category = self.create_category( name=category_name, description=category_description ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = self.get_or_create_repository( name=emboss_datatypes_repository_name, description=emboss_datatypes_repository_description, long_description=emboss_datatypes_repository_long_description, owner=common.test_user_1_name, - categories=[ default_category ], + category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( repository, 'emboss/datatypes/datatypes_conf.xml', strings_displayed=[], commit_message='Uploaded datatypes_conf.xml.' ) - def test_0015_create_emboss_repository( self ): + def test_0020_create_emboss_repository( self ): '''Create and populate emboss_0050.''' + category = self.create_category( name=category_name, description=category_description ) repository = self.get_or_create_repository( name=emboss_repository_name, description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, - categories=[ default_category ], + category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( repository, 'emboss/emboss.tar', @@ -72,13 +111,14 @@ 'repository_dependencies.xml', filepath=repository_dependencies_path, commit_message='Uploaded dependency on emboss_datatypes.' ) - def test_0020_create_filtering_repository( self ): + def test_0025_create_filtering_repository( self ): '''Create and populate filtering_0050.''' + category = self.create_category( name=category_name, description=category_description ) filtering_repository = self.get_or_create_repository( name=filtering_repository_name, description=filtering_repository_description, long_description=filtering_repository_long_description, owner=common.test_user_1_name, - categories=[ default_category ], + category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( filtering_repository, 'filtering/filtering_1.1.0.tar', @@ -93,69 +133,95 @@ 'repository_dependencies.xml', filepath=repository_dependencies_path, commit_message='Uploaded dependency on emboss.' ) - def test_0025_create_freebayes_repository( self ): + def test_0030_create_freebayes_repository( self ): '''Create and populate freebayes_0050.''' + category = self.create_category( name=category_name, description=category_description ) repository = self.get_or_create_repository( name=freebayes_repository_name, description=freebayes_repository_description, long_description=freebayes_repository_long_description, owner=common.test_user_1_name, - categories=[ default_category ], + category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( repository, 'freebayes/freebayes.tar', strings_displayed=[], commit_message='Uploaded freebayes.tar.' ) + def test_0035_create_bismark_repository( self ): + '''Create and populate bismark_0050.''' + category = self.create_category( name=category_name, description=category_description ) + repository = self.get_or_create_repository( name=bismark_repository_name, + description=bismark_repository_description, + long_description=bismark_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + 'bismark/bismark.tar', + strings_displayed=[], + valid_tools_only=False, + commit_message='Uploaded bismark.tar.' ) + def test_0040_create_and_upload_dependency_definitions( self ): + column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) + convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) - repository_dependencies_path = self.generate_temp_path( 'test_0050', additional_paths=[ 'freebayes' ] ) - self.generate_repository_dependency_xml( [ filtering_repository ], - self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), - dependency_description='Emboss depends on the filtering repository.' ) - self.upload_file( emboss_repository, - 'repository_dependencies.xml', - filepath=repository_dependencies_path, - commit_message='Uploaded dependency on filtering.' ) - previous_tip = self.get_repository_tip( repository ) - self.generate_repository_dependency_xml( [ emboss_datatypes_repository, emboss_repository, filtering_repository, repository ], - self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), - dependency_description='Freebayes depends on the filtering repository.' ) - self.upload_file( repository, - 'repository_dependencies.xml', - filepath=repository_dependencies_path, - commit_message='Uploaded dependency on filtering.' ) - self.display_manage_repository_page( repository, strings_not_displayed=[ previous_tip ] ) - def test_0030_verify_repository_dependencies( self ): + freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + bismark_repository = test_db_util.get_repository_by_name_and_owner( bismark_repository_name, common.test_user_1_name ) + dependency_xml_path = self.generate_temp_path( 'test_0050', additional_paths=[ 'freebayes' ] ) + self.create_repository_dependency( convert_repository, depends_on=[ column_repository ], filepath=dependency_xml_path ) + self.create_repository_dependency( column_repository, depends_on=[ convert_repository ], filepath=dependency_xml_path ) + self.create_repository_dependency( emboss_datatypes_repository, depends_on=[ bismark_repository ], filepath=dependency_xml_path ) + self.create_repository_dependency( emboss_repository, depends_on=[ emboss_datatypes_repository ], filepath=dependency_xml_path ) + self.create_repository_dependency( freebayes_repository, + depends_on=[ freebayes_repository, emboss_datatypes_repository, emboss_repository, column_repository ], + filepath=dependency_xml_path ) + self.create_repository_dependency( filtering_repository, depends_on=[ emboss_repository ], filepath=dependency_xml_path ) + def test_0045_verify_repository_dependencies( self ): '''Verify that the generated dependency circle does not cause an infinite loop. - Expected structure: - id: 2 key: http://localhost:8634__ESEP__freebayes_0050__ESEP__user1__ESEP__2e73d8e1b59d - ['http://localhost:8634', 'emboss_datatypes_0050', 'user1', '596029c334b1'] - ['http://localhost:8634', 'emboss_0050', 'user1', '9f1503046640'] - id: 3 key: http://localhost:8634__ESEP__filtering_0050__ESEP__user1__ESEP__eefdd8bc0db9 - ['http://localhost:8634', 'emboss_0050', 'user1', '9f1503046640'] - id: 4 key: http://localhost:8634__ESEP__emboss_0050__ESEP__user1__ESEP__9f1503046640 - ['http://localhost:8634', 'emboss_datatypes_0050', 'user1', '596029c334b1'] + id: 2 key: http://toolshed.local:10001__ESEP__filtering__ESEP__test__ESEP__871602b4276b + ['http://toolshed.local:10001', 'emboss_5', 'test', '8de5fe0d7b04'] + id: 3 key: http://toolshed.local:10001__ESEP__emboss_datatypes__ESEP__test__ESEP__dbd4… + ['http://toolshed.local:10001', 'freebayes', 'test', 'f40028114098'] + id: 4 key: http://toolshed.local:10001__ESEP__freebayes__ESEP__test__ESEP__f40028114098 + ['http://toolshed.local:10001', 'emboss_datatypes', 'test', 'dbd4f68bf507'] + ['http://toolshed.local:10001', 'emboss_5', 'test', '8de5fe0d7b04'] + ['http://toolshed.local:10001', 'column_maker', 'test', '83e956bdbac0'] + id: 5 key: http://toolshed.local:10001__ESEP__column_maker__ESEP__test__ESEP__83e956bd… + ['http://toolshed.local:10001', 'convert_chars', 'test', 'b28134220c8a'] + id: 6 key: http://toolshed.local:10001__ESEP__convert_chars__ESEP__test__ESEP__b281342… + ['http://toolshed.local:10001', 'column_maker', 'test', '83e956bdbac0'] + id: 7 key: http://toolshed.local:10001__ESEP__emboss_5__ESEP__test__ESEP__8de5fe0d7b04 + ['http://toolshed.local:10001', 'emboss_datatypes', 'test', 'dbd4f68bf507'] ''' emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) - for repository in [ emboss_datatypes_repository, emboss_repository, filtering_repository ]: - self.check_repository_dependency( freebayes_repository, repository, self.get_repository_tip( repository ) ) - for changeset_revision in self.get_repository_metadata_revisions( emboss_repository ): - self.check_repository_dependency( freebayes_repository, emboss_repository, changeset_revision ) + column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) + convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) + bismark_repository = test_db_util.get_repository_by_name_and_owner( bismark_repository_name, common.test_user_1_name ) + self.check_repository_dependency( convert_repository, column_repository ) + self.check_repository_dependency( column_repository, convert_repository ) + self.check_repository_dependency( emboss_datatypes_repository, bismark_repository ) + self.check_repository_dependency( emboss_repository, emboss_datatypes_repository ) + self.check_repository_dependency( filtering_repository, emboss_repository ) + for repository in [ emboss_datatypes_repository, emboss_repository, column_repository ]: + self.check_repository_dependency( freebayes_repository, repository ) + freebayes_dependencies = [ freebayes_repository, emboss_datatypes_repository, emboss_repository, column_repository ] + strings_displayed = [ '%s depends on %s.' % ( freebayes_repository.name, ', '.join( repo.name for repo in freebayes_dependencies ) ) ] self.display_manage_repository_page( freebayes_repository, - strings_displayed=[ 'Freebayes depends on the filtering repository.' ] ) - def test_0035_verify_tool_dependencies( self ): + strings_displayed=strings_displayed ) + def test_0050_verify_tool_dependencies( self ): '''Check that freebayes and emboss display tool dependencies.''' freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) self.display_manage_repository_page( freebayes_repository, strings_displayed=[ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Tool dependencies' ] ) self.display_manage_repository_page( emboss_repository, strings_displayed=[ 'Tool dependencies', 'emboss', '5.0.0', 'package' ] ) - def test_0040_verify_repository_metadata( self ): + def test_0055_verify_repository_metadata( self ): '''Verify that resetting the metadata does not change it.''' emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) diff -r 9bdc2c2e95aa05e9cc8cd01599b224e1a3c6b26e -r 2e96c23c760b7d9259168e007bec52ffcdfa00a9 test/tool_shed/functional/test_0070_invalid_tool.py --- a/test/tool_shed/functional/test_0070_invalid_tool.py +++ b/test/tool_shed/functional/test_0070_invalid_tool.py @@ -45,5 +45,6 @@ remove_repo_files_not_in_tar='No', commit_message='Uploaded an updated tool xml.' ) valid_revision = self.get_repository_tip( repository ) + test_db_util.refresh( repository ) self.check_repository_tools_for_changeset_revision( repository, valid_revision ) self.check_repository_invalid_tools_for_changeset_revision( repository, invalid_revision ) diff -r 9bdc2c2e95aa05e9cc8cd01599b224e1a3c6b26e -r 2e96c23c760b7d9259168e007bec52ffcdfa00a9 test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py --- /dev/null +++ b/test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py @@ -0,0 +1,314 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +emboss_datatypes_repository_name = 'emboss_datatypes_0050' +emboss_datatypes_repository_description = "Datatypes for emboss" +emboss_datatypes_repository_long_description = "Long description of Emboss' datatypes" + +emboss_repository_name = 'emboss_0050' +emboss_repository_description = "Galaxy's emboss tool" +emboss_repository_long_description = "Long description of Galaxy's emboss tool" + +filtering_repository_name = 'filtering_0050' +filtering_repository_description = "Galaxy's filtering tool" +filtering_repository_long_description = "Long description of Galaxy's filtering tool" + +freebayes_repository_name = 'freebayes_0050' +freebayes_repository_description = "Galaxy's freebayes tool" +freebayes_repository_long_description = "Long description of Galaxy's freebayes tool" + +column_repository_name = 'column_maker_0050' +column_repository_description = "Add column" +column_repository_long_description = "Compute an expression on every row" + +convert_repository_name = 'convert_chars_0050' +convert_repository_description = "Convert delimiters" +convert_repository_long_description = "Convert delimiters to tab" + +bismark_repository_name = 'bismark_0050' +bismark_repository_description = "A flexible aligner." +bismark_repository_long_description = "A flexible aligner and methylation caller for Bisulfite-Seq applications." + +category_name = 'Test 0050 Circular Dependencies 5 Levels' +category_description = 'Test circular dependency features' + +running_standalone = False + +class TestInstallRepositoryCircularDependencies( ShedTwillTestCase ): + '''Verify that the code correctly handles circular dependencies down to n levels.''' + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_convert_repository( self ): + '''Create and populate convert_chars_0050.''' + category = self.create_category( name=category_name, description=category_description ) + global running_standalone + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=convert_repository_name, + description=convert_repository_description, + long_description=convert_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + running_standalone = True + self.upload_file( repository, + 'convert_chars/convert_chars.tar', + strings_displayed=[], + commit_message='Uploaded convert_chars.tar.' ) + def test_0010_create_column_repository( self ): + '''Create and populate convert_chars_0050.''' + category = self.create_category( name=category_name, description=category_description ) + repository = self.get_or_create_repository( name=column_repository_name, + description=column_repository_description, + long_description=column_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + self.upload_file( repository, + 'column_maker/column_maker.tar', + strings_displayed=[], + commit_message='Uploaded column_maker.tar.' ) + def test_0015_create_emboss_datatypes_repository( self ): + '''Create and populate emboss_datatypes_0050.''' + category = self.create_category( name=category_name, description=category_description ) + repository = self.get_or_create_repository( name=emboss_datatypes_repository_name, + description=emboss_datatypes_repository_description, + long_description=emboss_datatypes_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + self.upload_file( repository, + 'emboss/datatypes/datatypes_conf.xml', + strings_displayed=[], + commit_message='Uploaded datatypes_conf.xml.' ) + def test_0020_create_emboss_repository( self ): + '''Create and populate emboss_0050.''' + category = self.create_category( name=category_name, description=category_description ) + repository = self.get_or_create_repository( name=emboss_repository_name, + description=emboss_repository_description, + long_description=emboss_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + self.upload_file( repository, + 'emboss/emboss.tar', + strings_displayed=[], + commit_message='Uploaded tool tarball.' ) + def test_0025_create_filtering_repository( self ): + '''Create and populate filtering_0050.''' + category = self.create_category( name=category_name, description=category_description ) + repository = self.get_or_create_repository( name=filtering_repository_name, + description=filtering_repository_description, + long_description=filtering_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + self.upload_file( repository, + 'filtering/filtering_1.1.0.tar', + strings_displayed=[], + commit_message='Uploaded filtering.tar.' ) + def test_0030_create_freebayes_repository( self ): + '''Create and populate freebayes_0050.''' + category = self.create_category( name=category_name, description=category_description ) + repository = self.get_or_create_repository( name=freebayes_repository_name, + description=freebayes_repository_description, + long_description=freebayes_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + self.upload_file( repository, + 'freebayes/freebayes.tar', + strings_displayed=[], + commit_message='Uploaded freebayes.tar.' ) + def test_0035_create_bismark_repository( self ): + '''Create and populate bismark_0050.''' + category = self.create_category( name=category_name, description=category_description ) + repository = self.get_or_create_repository( name=bismark_repository_name, + description=bismark_repository_description, + long_description=bismark_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + self.upload_file( repository, + 'bismark/bismark.tar', + strings_displayed=[], + valid_tools_only=False, + commit_message='Uploaded bismark.tar.' ) + def test_0040_create_and_upload_dependency_definitions( self ): + '''Set up the dependency structure.''' + global running_standalone + if running_standalone: + column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) + convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) + emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + bismark_repository = test_db_util.get_repository_by_name_and_owner( bismark_repository_name, common.test_user_1_name ) + dependency_xml_path = self.generate_temp_path( 'test_1050', additional_paths=[ 'dependencies' ] ) + self.create_repository_dependency( convert_repository, depends_on=[ column_repository ], filepath=dependency_xml_path ) + self.create_repository_dependency( column_repository, depends_on=[ convert_repository ], filepath=dependency_xml_path ) + self.create_repository_dependency( emboss_datatypes_repository, depends_on=[ bismark_repository ], filepath=dependency_xml_path ) + self.create_repository_dependency( emboss_repository, depends_on=[ emboss_datatypes_repository ], filepath=dependency_xml_path ) + self.create_repository_dependency( freebayes_repository, + depends_on=[ freebayes_repository, emboss_datatypes_repository, emboss_repository, column_repository ], + filepath=dependency_xml_path ) + self.create_repository_dependency( filtering_repository, depends_on=[ emboss_repository ], filepath=dependency_xml_path ) + def test_0045_verify_repository_dependencies( self ): + '''Verify that the generated dependency circle does not cause an infinite loop. + Expected structure: + + id: 2 key: http://toolshed.local:10001__ESEP__filtering__ESEP__test__ESEP__871602b4276b + ['http://toolshed.local:10001', 'emboss_5', 'test', '8de5fe0d7b04'] + id: 3 key: http://toolshed.local:10001__ESEP__emboss_datatypes__ESEP__test__ESEP__dbd4… + ['http://toolshed.local:10001', 'freebayes', 'test', 'f40028114098'] + id: 4 key: http://toolshed.local:10001__ESEP__freebayes__ESEP__test__ESEP__f40028114098 + ['http://toolshed.local:10001', 'emboss_datatypes', 'test', 'dbd4f68bf507'] + ['http://toolshed.local:10001', 'emboss_5', 'test', '8de5fe0d7b04'] + ['http://toolshed.local:10001', 'column_maker', 'test', '83e956bdbac0'] + id: 5 key: http://toolshed.local:10001__ESEP__column_maker__ESEP__test__ESEP__83e956bd… + ['http://toolshed.local:10001', 'convert_chars', 'test', 'b28134220c8a'] + id: 6 key: http://toolshed.local:10001__ESEP__convert_chars__ESEP__test__ESEP__b281342… + ['http://toolshed.local:10001', 'column_maker', 'test', '83e956bdbac0'] + id: 7 key: http://toolshed.local:10001__ESEP__emboss_5__ESEP__test__ESEP__8de5fe0d7b04 + ['http://toolshed.local:10001', 'emboss_datatypes', 'test', 'dbd4f68bf507'] + ''' + emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) + convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) + bismark_repository = test_db_util.get_repository_by_name_and_owner( bismark_repository_name, common.test_user_1_name ) + self.check_repository_dependency( convert_repository, column_repository ) + self.check_repository_dependency( column_repository, convert_repository ) + self.check_repository_dependency( emboss_datatypes_repository, bismark_repository ) + self.check_repository_dependency( emboss_repository, emboss_datatypes_repository ) + self.check_repository_dependency( filtering_repository, emboss_repository ) + for repository in [ emboss_datatypes_repository, emboss_repository, column_repository ]: + self.check_repository_dependency( freebayes_repository, repository ) + freebayes_dependencies = [ freebayes_repository, emboss_datatypes_repository, emboss_repository, column_repository ] + strings_displayed = [ '%s depends on %s.' % ( freebayes_repository.name, ', '.join( repo.name for repo in freebayes_dependencies ) ) ] + self.display_manage_repository_page( freebayes_repository, strings_displayed=strings_displayed ) + def test_0050_verify_tool_dependencies( self ): + '''Check that freebayes and emboss display tool dependencies.''' + freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + self.display_manage_repository_page( freebayes_repository, + strings_displayed=[ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Tool dependencies' ] ) + self.display_manage_repository_page( emboss_repository, strings_displayed=[ 'Tool dependencies', 'emboss', '5.0.0', 'package' ] ) + def test_0055_install_column_repository( self ): + '''Install column_maker with repository dependencies.''' + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + self.install_repository( column_repository_name, + common.test_user_1_name, + category_name, + install_tool_dependencies=False, + install_repository_dependencies=True, + new_tool_panel_section='column_maker' ) + installed_repositories = [ ( column_repository_name, common.test_user_1_name ), + ( convert_repository_name, common.test_user_1_name ) ] + uninstalled_repositories = [ ( emboss_datatypes_repository_name, common.test_user_1_name ), + ( emboss_repository_name, common.test_user_1_name ), + ( filtering_repository_name, common.test_user_1_name ), + ( freebayes_repository_name, common.test_user_1_name ), + ( bismark_repository_name, common.test_user_1_name ) ] + self.verify_installed_uninstalled_repositories( installed_repositories=installed_repositories, uninstalled_repositories=uninstalled_repositories ) + def test_0060_install_emboss_repository( self ): + '''Install emboss_5 with repository dependencies.''' + global running_standalone + original_datatypes = self.get_datatypes_count() + self.install_repository( emboss_repository_name, + common.test_user_1_name, + category_name, + install_tool_dependencies=False, + install_repository_dependencies=True, + new_tool_panel_section='emboss_5_0050' ) + if running_standalone: + assert original_datatypes < self.get_datatypes_count(), 'Installing a repository that depends on emboss_datatypes did not add datatypes.' + installed_repositories = [ ( emboss_datatypes_repository_name, common.test_user_1_name ), + ( column_repository_name, common.test_user_1_name ), + ( emboss_repository_name, common.test_user_1_name ), + ( convert_repository_name, common.test_user_1_name ), + ( bismark_repository_name, common.test_user_1_name ) ] + uninstalled_repositories = [ ( filtering_repository_name, common.test_user_1_name ), + ( freebayes_repository_name, common.test_user_1_name ) ] + self.verify_installed_uninstalled_repositories( installed_repositories=installed_repositories, uninstalled_repositories=uninstalled_repositories ) + def test_0065_deactivate_datatypes_repository( self ): + '''Deactivate emboss_datatypes and verify that the datatypes count is reduced.''' + original_datatypes = self.get_datatypes_count() + repository = test_db_util.get_installed_repository_by_name_owner( emboss_datatypes_repository_name, common.test_user_1_name ) + self.uninstall_repository( repository, remove_from_disk=False ) + assert original_datatypes > self.get_datatypes_count(), 'Deactivating emboss_datatypes did not remove datatypes.' + installed_repositories = [ ( column_repository_name, common.test_user_1_name ), + ( emboss_repository_name, common.test_user_1_name ), + ( convert_repository_name, common.test_user_1_name ), + ( bismark_repository_name, common.test_user_1_name ) ] + uninstalled_repositories = [ ( emboss_datatypes_repository_name, common.test_user_1_name ), + ( filtering_repository_name, common.test_user_1_name ), + ( freebayes_repository_name, common.test_user_1_name ) ] + self.verify_installed_uninstalled_repositories( installed_repositories=installed_repositories, uninstalled_repositories=uninstalled_repositories ) + strings_not_displayed = [ repository.name, repository.installed_changeset_revision ] + self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) + def test_0070_uninstall_emboss_repository( self ): + '''Uninstall the emboss_5 repository.''' + repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) + self.uninstall_repository( repository, remove_from_disk=True ) + strings_not_displayed = [ repository.name, repository.installed_changeset_revision ] + self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) + test_db_util.ga_refresh( repository ) + self.check_galaxy_repository_tool_panel_section( repository, 'emboss_5_0050' ) + installed_repositories = [ ( column_repository_name, common.test_user_1_name ), + ( convert_repository_name, common.test_user_1_name ), + ( bismark_repository_name, common.test_user_1_name ) ] + uninstalled_repositories = [ ( emboss_datatypes_repository_name, common.test_user_1_name ), + ( emboss_repository_name, common.test_user_1_name ), + ( filtering_repository_name, common.test_user_1_name ), + ( freebayes_repository_name, common.test_user_1_name ) ] + self.verify_installed_uninstalled_repositories( installed_repositories=installed_repositories, uninstalled_repositories=uninstalled_repositories ) + def test_0075_install_freebayes_repository( self ): + '''Install freebayes with repository dependencies. This should also automatically reactivate emboss_datatypes and reinstall emboss_5.''' + original_datatypes = self.get_datatypes_count() + strings_displayed = [ 'Handle', 'tool dependencies', 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18' ] + self.install_repository( freebayes_repository_name, + common.test_user_1_name, + category_name, + strings_displayed=strings_displayed, + install_tool_dependencies=False, + install_repository_dependencies=True, + new_tool_panel_section='freebayes' ) + assert original_datatypes < self.get_datatypes_count(), 'Installing a repository that depends on emboss_datatypes did not add datatypes.' + emboss_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) + datatypes_repository = test_db_util.get_installed_repository_by_name_owner( emboss_datatypes_repository_name, common.test_user_1_name ) + strings_displayed = [ emboss_repository.name, + emboss_repository.installed_changeset_revision, + datatypes_repository.name, + datatypes_repository.installed_changeset_revision ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) + installed_repositories = [ ( column_repository_name, common.test_user_1_name ), + ( emboss_datatypes_repository_name, common.test_user_1_name ), + ( emboss_repository_name, common.test_user_1_name ), + ( freebayes_repository_name, common.test_user_1_name ), + ( convert_repository_name, common.test_user_1_name ), + ( bismark_repository_name, common.test_user_1_name ) ] + uninstalled_repositories = [ ( filtering_repository_name, common.test_user_1_name ) ] + self.verify_installed_uninstalled_repositories( installed_repositories=installed_repositories, uninstalled_repositories=uninstalled_repositories ) + diff -r 9bdc2c2e95aa05e9cc8cd01599b224e1a3c6b26e -r 2e96c23c760b7d9259168e007bec52ffcdfa00a9 test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py --- a/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py +++ b/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py @@ -210,10 +210,8 @@ common.test_user_1_name ) self.uninstall_repository( installed_convert_repository, remove_from_disk=False ) strings_not_displayed = [ installed_column_repository.name, - installed_column_repository.description, installed_column_repository.installed_changeset_revision, installed_convert_repository.name, - installed_convert_repository.description, installed_convert_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) def test_0050_reactivate_column_repository( self ): diff -r 9bdc2c2e95aa05e9cc8cd01599b224e1a3c6b26e -r 2e96c23c760b7d9259168e007bec52ffcdfa00a9 test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -139,6 +139,7 @@ galaxy_file_path = os.path.join( galaxy_db_path, 'files' ) hgweb_config_file_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) new_repos_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) + galaxy_tempfiles = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) galaxy_shed_tool_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) galaxy_tool_dependency_dir = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) os.environ[ 'GALAXY_TEST_TOOL_DEPENDENCY_DIR' ] = galaxy_tool_dependency_dir @@ -269,6 +270,7 @@ database_connection = galaxy_database_connection, database_engine_option_pool_size = '10', file_path = galaxy_file_path, + new_file_path = galaxy_tempfiles, tool_path = tool_path, tool_data_path = tool_data_path, shed_tool_path = galaxy_shed_tool_path, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for rendering tool dependencies defined for tools cotnained in tool shed repositories.
by Bitbucket 11 Jan '13

11 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9bdc2c2e95aa/ changeset: 9bdc2c2e95aa user: greg date: 2013-01-11 22:49:36 summary: Fix for rendering tool dependencies defined for tools cotnained in tool shed repositories. affected #: 2 files diff -r 6cd4058d7b32f788e3c7484f0c5709e89cfbed0f -r 9bdc2c2e95aa05e9cc8cd01599b224e1a3c6b26e lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1251,18 +1251,20 @@ old_container_tool_dependencies_root = old_container_dict[ 'tool_dependencies' ] if old_container_tool_dependencies_root: if tool_dependencies_root_folder is None: - tool_dependencies_root_folder = old_container_tool_dependencies_root - # Change the folder id so it won't confict with others being merged. - tool_dependencies_root_folder.id = folder_id + tool_dependencies_root_folder = container_util.Folder( id=folder_id, key='root', label='root', parent=None ) folder_id += 1 - tool_dependencies_folder = tool_dependencies_root_folder.folders[ 0 ] - tool_dependencies_folder.id = folder_id + tool_dependencies_folder = container_util.Folder( id=folder_id, + key='merged', + label='Tool dependencies', + parent=tool_dependencies_root_folder ) folder_id += 1 else: + td_list = [ td.listify for td in tool_dependencies_folder.tool_dependencies ] # The old_container_tool_dependencies_root will be a root folder containing a single sub_folder. old_container_tool_dependencies_folder = old_container_tool_dependencies_root.folders[ 0 ] for td in old_container_tool_dependencies_folder.tool_dependencies: - tool_dependencies_folder.tool_dependencies.append( td ) + if td.listify not in td_list: + tool_dependencies_folder.tool_dependencies.append( td ) if repository_dependencies_root_folder: repository_dependencies_root_folder.folders.append( repository_dependencies_folder ) new_containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder diff -r 6cd4058d7b32f788e3c7484f0c5709e89cfbed0f -r 9bdc2c2e95aa05e9cc8cd01599b224e1a3c6b26e lib/galaxy/webapps/community/util/container_util.py --- a/lib/galaxy/webapps/community/util/container_util.py +++ b/lib/galaxy/webapps/community/util/container_util.py @@ -112,6 +112,9 @@ self.installation_status = installation_status self.repository_id = repository_id self.tool_dependency_id = tool_dependency_id + @property + def listify( self ): + return [ self.name, self.version, self.type ] class Workflow( object ): """Workflow object.""" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for external display applications and permissions.
by Bitbucket 11 Jan '13

11 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6cd4058d7b32/ changeset: 6cd4058d7b32 user: dan date: 2013-01-11 21:41:29 summary: Fix for external display applications and permissions. affected #: 1 file diff -r 3674685eeb0d171b9f4c0b01e2c7f56cfba86ce7 -r 6cd4058d7b32f788e3c7484f0c5709e89cfbed0f lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -163,8 +163,11 @@ assert hda and self._can_access_dataset( trans, hda ) return hda.creating_job - def _can_access_dataset( self, trans, dataset_association, allow_admin=True ): - return ( allow_admin and trans.user_is_admin() ) or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), dataset_association.dataset ) + def _can_access_dataset( self, trans, dataset_association, allow_admin=True, additional_roles=None ): + roles = trans.get_current_user_roles() + if additional_roles: + roles = roles + additional_roles + return ( allow_admin and trans.user_is_admin() ) or trans.app.security_agent.can_access_dataset( roles, dataset_association.dataset ) @web.expose def errors( self, trans, id ): @@ -736,7 +739,7 @@ link_name = urllib.unquote_plus( link_name ) if None in [ app_name, link_name ]: return trans.show_error_message( "A display application name and link name must be provided." ) - if self._can_access_dataset( trans, data ): + if self._can_access_dataset( trans, data, additional_roles=user_roles ): msg = [] refresh = False display_app = trans.app.datatypes_registry.display_applications.get( app_name ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Restrice display of certain tool dependency columns when in the tool shed.
by Bitbucket 11 Jan '13

11 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3674685eeb0d/ changeset: 3674685eeb0d user: greg date: 2013-01-11 21:09:33 summary: Restrice display of certain tool dependency columns when in the tool shed. affected #: 1 file diff -r 1bd3e09417b16e31d2ecce606ac1db5f5564e887 -r 3674685eeb0d171b9f4c0b01e2c7f56cfba86ce7 templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -507,10 +507,12 @@ ${version_str | h} </${cell_type}><${cell_type}>${tool_dependency.type | h}</${cell_type}> - %if is_missing: - <${cell_type}>${tool_dependency.installation_status | h}</${cell_type}> - %elif tool_dependency.install_dir: - <${cell_type}>${tool_dependency.install_dir | h}</${cell_type}> + %if trans.webapp.name == 'galaxy': + %if is_missing: + <${cell_type}>${tool_dependency.installation_status | h}</${cell_type}> + %elif tool_dependency.install_dir: + <${cell_type}>${tool_dependency.install_dir | h}</${cell_type}> + %endif %endif </tr><% Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: When installing multiple repositories sumultaneously, merge all repository and tool dependenceis into a single container for display.
by Bitbucket 11 Jan '13

11 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1bd3e09417b1/ changeset: 1bd3e09417b1 user: greg date: 2013-01-11 21:06:35 summary: When installing multiple repositories sumultaneously, merge all repository and tool dependenceis into a single container for display. affected #: 3 files diff -r be7625f376d16cefa2fb4984fa6483f37b4b71d4 -r 1bd3e09417b16e31d2ecce606ac1db5f5564e887 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1,4 +1,4 @@ -import os, tempfile, shutil, logging, urllib2 +import os, tempfile, shutil, logging, urllib2, threading from galaxy.datatypes import checkers from galaxy.web import url_for from galaxy import util @@ -1202,6 +1202,78 @@ def load_installed_display_applications( app, installed_repository_dict, deactivate=False ): # Load or deactivate proprietary datatype display applications app.datatypes_registry.load_display_applications( installed_repository_dict=installed_repository_dict, deactivate=deactivate ) +def merge_containers_dicts_for_new_install( containers_dicts ): + """ + When installing one or more tool shed repositories for the first time, the received list of containers_dicts contains a containers_dict for + each repository being installed. Since the repositories are being installed for the first time, all entries are None except the repository + dependencies and tool dependencies. The entries for missing dependencies are all None since they have previously been merged into the installed + dependencies. This method will merge the dependencies entries into a single container and return it for display. + """ + new_containers_dict = dict( readme_files=None, + datatypes=None, + missing_repository_dependencies=None, + repository_dependencies=None, + missing_tool_dependencies=None, + tool_dependencies=None, + invalid_tools=None, + valid_tools=None, + workflows=None ) + if containers_dicts: + lock = threading.Lock() + lock.acquire( True ) + try: + repository_dependencies_root_folder = None + tool_dependencies_root_folder = None + # Use a unique folder id (hopefully the following is). + folder_id = 867 + for old_container_dict in containers_dicts: + # Merge repository_dependencies. + old_container_repository_dependencies_root = old_container_dict[ 'repository_dependencies' ] + if old_container_repository_dependencies_root: + if repository_dependencies_root_folder is None: + repository_dependencies_root_folder = container_util.Folder( id=folder_id, key='root', label='root', parent=None ) + folder_id += 1 + repository_dependencies_folder = container_util.Folder( id=folder_id, + key='merged', + label='Repository dependencies', + parent=repository_dependencies_root_folder ) + folder_id += 1 + # The old_container_repository_dependencies_root will be a root folder containing a single sub_folder. + old_container_repository_dependencies_folder = old_container_repository_dependencies_root.folders[ 0 ] + # Change the folder id so it won't confict with others being merged. + old_container_repository_dependencies_folder.id = folder_id + folder_id += 1 + # Generate the label by retrieving the repository name. + toolshed, name, owner, changeset_revision = container_util.get_components_from_key( old_container_repository_dependencies_folder.key ) + old_container_repository_dependencies_folder.label = str( name ) + repository_dependencies_folder.folders.append( old_container_repository_dependencies_folder ) + # Merge tool_dependencies. + old_container_tool_dependencies_root = old_container_dict[ 'tool_dependencies' ] + if old_container_tool_dependencies_root: + if tool_dependencies_root_folder is None: + tool_dependencies_root_folder = old_container_tool_dependencies_root + # Change the folder id so it won't confict with others being merged. + tool_dependencies_root_folder.id = folder_id + folder_id += 1 + tool_dependencies_folder = tool_dependencies_root_folder.folders[ 0 ] + tool_dependencies_folder.id = folder_id + folder_id += 1 + else: + # The old_container_tool_dependencies_root will be a root folder containing a single sub_folder. + old_container_tool_dependencies_folder = old_container_tool_dependencies_root.folders[ 0 ] + for td in old_container_tool_dependencies_folder.tool_dependencies: + tool_dependencies_folder.tool_dependencies.append( td ) + if repository_dependencies_root_folder: + repository_dependencies_root_folder.folders.append( repository_dependencies_folder ) + new_containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder + if tool_dependencies_root_folder: + tool_dependencies_root_folder.folders.append( tool_dependencies_folder ) + new_containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder + except Exception, e: + log.debug( "Exception in merge_containers_dicts_for_new_install: %s" % str( e ) ) + finally: + lock.release() + return new_containers_dict def panel_entry_per_tool( tool_section_dict ): # Return True if tool_section_dict looks like this. # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} diff -r be7625f376d16cefa2fb4984fa6483f37b4b71d4 -r 1bd3e09417b16e31d2ecce606ac1db5f5564e887 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1266,7 +1266,6 @@ shed_tool_conf_select_field = None tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ) tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) - containers_dicts = [] if len( repo_info_dicts ) == 1: # If we're installing a single repository, see if it contains a readme or dependencies that we can display. repo_info_dict = repo_info_dicts[ 0 ] @@ -1287,13 +1286,9 @@ missing_repository_dependencies=missing_repository_dependencies, installed_tool_dependencies=installed_tool_dependencies, missing_tool_dependencies=missing_tool_dependencies ) - containers_dicts.append( containers_dict ) else: # We're installing a list of repositories, each of which may have tool dependencies or repository dependencies. - all_installed_repository_dependencies = [] - all_missing_repository_dependencies = [] - all_installed_tool_dependencies = [] - all_missing_tool_dependencies = [] + containers_dicts = [] for repo_info_dict in repo_info_dicts: name, repository_owner, changeset_revision, includes_tool_dependencies, installed_repository_dependencies, \ missing_repository_dependencies, installed_tool_dependencies, missing_tool_dependencies = \ @@ -1302,11 +1297,13 @@ tool_shed_url=tool_shed_url, tool_path=tool_path, readme_files_dict=None, - repository_dependencies=installed_repository_dependencies, + installed_repository_dependencies=installed_repository_dependencies, missing_repository_dependencies=missing_repository_dependencies, - tool_dependencies=installed_tool_dependencies, + installed_tool_dependencies=installed_tool_dependencies, missing_tool_dependencies=missing_tool_dependencies ) containers_dicts.append( containers_dict ) + # Merge all containers into a single container. + containers_dict = shed_util.merge_containers_dicts_for_new_install( containers_dicts ) # Handle tool dependencies chack box. if trans.app.config.tool_dependency_dir is None: if includes_tool_dependencies: @@ -1327,7 +1324,7 @@ includes_repository_dependencies=includes_repository_dependencies, install_repository_dependencies_check_box=install_repository_dependencies_check_box, new_tool_panel_section=new_tool_panel_section, - containers_dicts=containers_dicts, + containers_dict=containers_dict, shed_tool_conf=shed_tool_conf, shed_tool_conf_select_field=shed_tool_conf_select_field, tool_panel_section_select_field=tool_panel_section_select_field, diff -r be7625f376d16cefa2fb4984fa6483f37b4b71d4 -r 1bd3e09417b16e31d2ecce606ac1db5f5564e887 templates/admin/tool_shed_repository/select_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -20,25 +20,24 @@ # this case, the repository metadata is an empty dictionary, but one or both of includes_repository_dependencies # and includes_tool_dependencies may be True. If either of these are True but we have no metadata, we cannot install # repository dependencies on this pass. - - # TODO: do we need this? - can_display_repository_dependencies = False - can_display_tool_dependencies = False - - if includes_repository_dependencies and not can_display_repository_dependencies: - for containers_dict in containers_dicts: - repository_dependencies = containers_dict[ 'repository_dependencies' ] - missing_repository_dependencies = containers_dict[ 'missing_repository_dependencies' ] - if repository_dependencies or missing_repository_dependencies: - can_display_repository_dependencies = True - break - if includes_tool_dependencies and not can_display_tool_dependencies: - for containers_dict in containers_dicts: - tool_dependencies = containers_dict[ 'tool_dependencies' ] - missing_tool_dependencies = containers_dict[ 'missing_tool_dependencies' ] - if tool_dependencies or missing_tool_dependencies: - can_display_tool_dependencies = True - break + if includes_repository_dependencies: + repository_dependencies = containers_dict[ 'repository_dependencies' ] + missing_repository_dependencies = containers_dict[ 'missing_repository_dependencies' ] + if repository_dependencies or missing_repository_dependencies: + can_display_repository_dependencies = True + else: + can_display_repository_dependencies = False + else: + can_display_repository_dependencies = False + if includes_tool_dependencies: + tool_dependencies = containers_dict[ 'tool_dependencies' ] + missing_tool_dependencies = containers_dict[ 'missing_tool_dependencies' ] + if tool_dependencies or missing_tool_dependencies: + can_display_tool_dependencies = True + else: + can_display_tool_dependencies = False + else: + can_display_tool_dependencies = False %> %if message: @@ -63,14 +62,7 @@ <div class="toolFormBody"><form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='prepare_for_install', tool_shed_url=tool_shed_url, encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, includes_tool_dependencies=includes_tool_dependencies )}" method="post" ><div style="clear: both"></div> - <% - if len( containers_dicts ) == 1: - containers_dict = containers_dicts[ 0 ] - readme_files_dict = containers_dict.get( 'readme_files', None ) - else: - containers_dict = None - readme_files_dict = None - %> + <% readme_files_dict = containers_dict.get( 'readme_files', None ) %> %if readme_files_dict: <div class="form-row"><table class="colored" width="100%"> @@ -86,15 +78,8 @@ <th bgcolor="#EBD9B2">Confirm dependency installation</th></table></div> - %for index, containers_dict in enumerate( containers_dicts ): - %if index == 0: - ${render_dependencies_section( install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict )} - <div style="clear: both"></div> - %else: - ${render_dependencies_section( None, None, containers_dict )} - <div style="clear: both"></div> - %endif - %endfor + ${render_dependencies_section( install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict )} + <div style="clear: both"></div> %endif <div class="form-row"><table class="colored" width="100%"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: james_taylor: ClusterJobRunner: make sure workers are daemon threads, shutdown now works again
by Bitbucket 11 Jan '13

11 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/be7625f376d1/ changeset: be7625f376d1 user: james_taylor date: 2013-01-11 20:49:24 summary: ClusterJobRunner: make sure workers are daemon threads, shutdown now works again affected #: 1 file diff -r 71a616ffce1c85aa31d3e5311d5babfc12c49381 -r be7625f376d16cefa2fb4984fa6483f37b4b71d4 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -152,6 +152,7 @@ nworkers = self.app.config.cluster_job_queue_workers for i in range( nworkers ): worker = threading.Thread( name="%s.work_thread-%d" % (self.runner_name, i), target=self.run_next ) + worker.setDaemon( True ) worker.start() self.work_threads.append( worker ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fixes for showing job parameters when tools have been updated.
by Bitbucket 11 Jan '13

11 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/71a616ffce1c/ changeset: 71a616ffce1c user: dan date: 2013-01-11 20:41:12 summary: Fixes for showing job parameters when tools have been updated. affected #: 3 files diff -r e9f81b5154bb71c6c12d4591c8f9519e52c93212 -r 71a616ffce1c85aa31d3e5311d5babfc12c49381 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1347,7 +1347,7 @@ rval = [] for val in value: rval.append( get_option_display( val, self.options ) or val ) - return "\n".join( rval ) + suffix + return "\n".join( map( str, rval ) ) + suffix def get_dependencies( self ): """ @@ -1611,9 +1611,11 @@ if value and not isinstance( value, list ): value = [ value ] if value: - return ", ".join( [ "%s: %s" % ( item.hid, item.name ) for item in value ] ) - else: - return "No dataset" + try: + return ", ".join( [ "%s: %s" % ( item.hid, item.name ) for item in value ] ) + except: + pass + return "No dataset" def validate( self, value, history=None ): for validator in self.validators: diff -r e9f81b5154bb71c6c12d4591c8f9519e52c93212 -r 71a616ffce1c85aa31d3e5311d5babfc12c49381 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -997,6 +997,8 @@ params_objects = None job = None tool = None + upgrade_messages = {} + has_parameter_errors = False inherit_chain = hda.source_dataset_chain if inherit_chain: job_dataset_association, dataset_association_container_name = inherit_chain[-1] @@ -1013,12 +1015,19 @@ toolbox = self.get_toolbox() tool = toolbox.get_tool( job.tool_id ) assert tool is not None, 'Requested tool has not been loaded.' - params_objects = job.get_param_values( trans.app ) + #Load parameter objects, if a parameter type has changed, its possible for the value to no longer be valid + try: + params_objects = job.get_param_values( trans.app, ignore_errors=False ) + except: + params_objects = job.get_param_values( trans.app, ignore_errors=True ) + upgrade_messages = tool.check_and_update_param_values( job.get_param_values( trans.app, ignore_errors=True ), trans, update_values=False ) #use different param_objects here, since we want to display original values as much as possible + has_parameter_errors = True except: pass if job is None: return trans.show_error_message( "Job information is not available for this dataset." ) - return trans.fill_template( "show_params.mako", inherit_chain=inherit_chain, history=trans.get_history(), hda=hda, job=job, tool=tool, params_objects=params_objects ) + #TODO: we should provide the basic values along with the objects, in order to better handle reporting of old values during upgrade + return trans.fill_template( "show_params.mako", inherit_chain=inherit_chain, history=trans.get_history(), hda=hda, job=job, tool=tool, params_objects=params_objects, upgrade_messages=upgrade_messages, has_parameter_errors=has_parameter_errors ) @web.expose def copy_datasets( self, trans, source_history=None, source_dataset_ids="", target_history_id=None, target_history_ids="", new_history_name="", do_copy=False, **kwd ): diff -r e9f81b5154bb71c6c12d4591c8f9519e52c93212 -r 71a616ffce1c85aa31d3e5311d5babfc12c49381 templates/show_params.mako --- a/templates/show_params.mako +++ b/templates/show_params.mako @@ -1,4 +1,5 @@ <%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /><% from galaxy.util import nice_size %><style> @@ -10,7 +11,11 @@ } </style> -<%def name="inputs_recursive( input_params, param_values, depth=1 )"> +<%def name="inputs_recursive( input_params, param_values, depth=1, upgrade_messages=None )"> + <% + if upgrade_messages is None: + upgrade_messages = {} + %> %for input_index, input in enumerate( input_params.itervalues() ): %if input.name in param_values: %if input.type == "repeat": @@ -18,17 +23,47 @@ ${ inputs_recursive(input.inputs, param_values[input.name][i], depth=depth+1) } %endfor %elif input.type == "conditional": - <% current_case = param_values[input.name]['__current_case__'] %> + <% + try: + current_case = param_values[input.name]['__current_case__'] + is_valid = True + except: + current_case = None + is_valid = False + %> + %if is_valid: + <tr> + ${ inputs_recursive_indent( text=input.test_param.label, depth=depth )} + ## + <td>${input.cases[current_case].value | h}</td> + <td></td> + </tr> + ${ inputs_recursive( input.cases[current_case].inputs, param_values[input.name], depth=depth+1, upgrade_messages=upgrade_messages.get( input.name ) ) } + %else: + <tr> + ${ inputs_recursive_indent( text=input.name, depth=depth )} + <td><em>The previously used value is no longer valid</em></td> + <td></td> + </tr> + %endif + %elif input.type == "upload_dataset": + <tr> + ${inputs_recursive_indent( text=input.group_title( param_values ), depth=depth )} + <td>${ len( param_values[input.name] ) } uploaded datasets</td> + <td></td> + </tr> + %elif input.visible: + <% + if hasattr( input, "label" ) and input.label: + label = input.label + else: + #value for label not required, fallback to input name (same as tool panel) + label = input.name + %><tr> - ${ inputs_recursive_indent( text=input.test_param.label, depth=depth )} -  - <td>${input.cases[current_case].value}</td> - </tr> - ${ inputs_recursive(input.cases[current_case].inputs, param_values[input.name], depth=depth+1) } - %elif getattr(input, "label", None): - <tr> - ${inputs_recursive_indent( text=input.label, depth=depth )} - <td>${input.value_to_display_text(param_values[input.name], trans.app)}</td> + ${inputs_recursive_indent( text=label, depth=depth )} + <td>${input.value_to_display_text( param_values[input.name], trans.app ) | h}</td> + <td>${ upgrade_messages.get( input.name, '' ) | h }</td></tr> %endif %else: @@ -38,11 +73,14 @@ # Get parameter label. if input.type == "conditional": label = input.test_param.label + elif input.type == "repeat": + label = input.label() else: - label = input.label + label = input.label or input.name %> ${inputs_recursive_indent( text=label, depth=depth )} <td><em>not used (parameter was added after this job was run)</em></td> + <td></td></tr> %endif @@ -52,7 +90,7 @@ ## function to add a indentation depending on the depth in a <tr><%def name="inputs_recursive_indent( text, depth )"><td style="padding-left: ${ ( depth - 1 ) * 10 }px"> - ${text} + ${text | h} </td></%def> @@ -60,50 +98,57 @@ <thead><tr><th colspan="2" style="font-size: 120%;"> % if tool: - Tool: ${tool.name} + Tool: ${tool.name | h} % else: Unknown Tool % endif </th></tr></thead><tbody> - <tr><td>Name:</td><td>${hda.name}</td></tr> + <tr><td>Name:</td><td>${hda.name | h}</td></tr><tr><td>Created:</td><td>${hda.create_time.strftime("%b %d, %Y")}</td></tr> ## <tr><td>Copied from another history?</td><td>${hda.source_library_dataset}</td></tr><tr><td>Filesize:</td><td>${nice_size(hda.dataset.file_size)}</td></tr> - <tr><td>Dbkey:</td><td>${hda.dbkey}</td></tr> - <tr><td>Format:</td><td>${hda.ext}</td></tr> - <tr><td>Tool Version:</td><td>${hda.tool_version}</td></tr> + <tr><td>Dbkey:</td><td>${hda.dbkey | h}</td></tr> + <tr><td>Format:</td><td>${hda.ext | h}</td></tr> + <tr><td>Tool Version:</td><td>${hda.tool_version | h}</td></tr><tr><td>Tool Standard Output:</td><td><a href="${h.url_for( controller='dataset', action='stdout')}">stdout</a></td></tr><tr><td>Tool Standard Error:</td><td><a href="${h.url_for( controller='dataset', action='stderr')}">stderr</a></td></tr> - <tr><td>Tool Exit Code:</td><td>${job.exit_code}</td></tr> + <tr><td>Tool Exit Code:</td><td>${job.exit_code | h}</td></tr> %if trans.user_is_admin() or trans.app.config.expose_dataset_path: - <tr><td>Full Path:</td><td>${hda.file_name}</td></tr> + <tr><td>Full Path:</td><td>${hda.file_name | h}</td></tr> %endif </table><br /> + <table class="tabletip"><thead><tr><th>Input Parameter</th><th>Value</th> + <th>Note for rerun</th></tr></thead><tbody> % if params_objects and tool: - ${ inputs_recursive(tool.inputs, params_objects, depth=1) } + ${ inputs_recursive( tool.inputs, params_objects, depth=1, upgrade_messages=upgrade_messages ) } + %elif params_objects is None: + <tr><td colspan="2">Unable to load parameters.</td></tr> % else: <tr><td colspan="2">No parameters.</td></tr> % endif </tbody></table> - +%if has_parameter_errors: + <br /> + ${ render_msg( 'One or more of your original parameters may no longer be valid or displayed properly.', status='warning' ) } +%endif <h3>Inheritance Chain</h3> - <div class="inherit" style="background-color: #fff; font-weight:bold;">${hda.name}</div> + <div class="inherit" style="background-color: #fff; font-weight:bold;">${hda.name | h}</div> % for dep in inherit_chain: <div style="font-size: 36px; text-align: center;">↑</div> - <div class="inherit">${dep[0].name}<br/>${dep[1]}</div> + <div class="inherit">${dep[0].name | h}<br/>${dep[1]}</div> % endfor Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Fix for installing a repository with set_environment tool dependencies.
by Bitbucket 11 Jan '13

11 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e9f81b5154bb/ changeset: e9f81b5154bb user: inithello date: 2013-01-11 19:31:02 summary: Fix for installing a repository with set_environment tool dependencies. affected #: 1 file diff -r e5ec6ed8f0337893cf4bc64e61089471b00b28b0 -r e9f81b5154bb71c6c12d4591c8f9519e52c93212 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -791,9 +791,17 @@ tool_dependencies = {} missing_tool_dependencies = {} for td_key, val in all_tool_dependencies.items(): - # Since we have a new install, missing tool dependencies have never been installed. - val[ 'status' ] = trans.model.ToolDependency.installation_status.NEVER_INSTALLED - missing_tool_dependencies[ td_key ] = val + # Set environment tool dependencies are a list, set each member to never installed. + if td_key == 'set_environment': + new_val = [] + for requirement_dict in val: + requirement_dict[ 'status' ] = trans.model.ToolDependency.installation_status.NEVER_INSTALLED + new_val.append( requirement_dict ) + missing_tool_dependencies[ td_key ] = new_val + else: + # Since we have a new install, missing tool dependencies have never been installed. + val[ 'status' ] = trans.model.ToolDependency.installation_status.NEVER_INSTALLED + missing_tool_dependencies[ td_key ] = val else: tool_dependencies = None missing_tool_dependencies = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 11 new changesets
by Bitbucket 11 Jan '13

11 Jan '13

11 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/611bc9467b22/ changeset: 611bc9467b22 user: jmchilton date: 2013-01-11 17:53:05 summary: Implement new job runner super class ClusterJobRunner intended to reduce amount of duplicated code between drmaa, pbs, and lwr job runners (also I guess cli and condor classes seem like they could benefit from this as well). This super class will manage the monitor and worker threads and queues. I am submitting only changes to the LWR that use this class, but I would encourage the Galaxy team to refactor the drmaa and pbs runners to use this class as well (or I would be happy to make these changes if given access or a promise the changes will be accepted quickly). A variant of the drmaa runner that has been refactored to use this class can be found here: https://bitbucket.org/jmchilton/galaxy-central-lwr-enhancement-1/src/tip/li… from the now defunct pull request 80. affected #: 1 file diff -r 3faa833c15b5162db69f061bdbd4e951ba2ffdc7 -r 611bc9467b222bb1cf0b1ef5d5b6120f210a471f lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -1,5 +1,10 @@ import os, logging, os.path +from galaxy import model +from Queue import Queue, Empty +import time +import threading + log = logging.getLogger( __name__ ) class BaseJobRunner( object ): @@ -90,3 +95,158 @@ set_extension = False, kwds = { 'overwrite' : False } ) return commands + +class ClusterJobState( object ): + """ + Encapsulate the state of a cluster job, this should be subclassed as + needed for various job runners to capture additional information needed + to communicate with cluster job manager. + """ + + def __init__( self ): + self.job_wrapper = None + self.job_id = None + self.old_state = None + self.running = False + self.runner_url = None + +STOP_SIGNAL = object() + +JOB_STATUS_QUEUED = 'queue' +JOB_STATUS_FAILED = 'fail' +JOB_STATUS_FINISHED = 'finish' + +class ClusterJobRunner( BaseJobRunner ): + """ + Not sure this is the best name for this class, but there is common code + shared between sge, pbs, drmaa, etc... + """ + + def __init__( self, app ): + self.app = app + self.sa_session = app.model.context + # 'watched' and 'queue' are both used to keep track of jobs to watch. + # 'queue' is used to add new watched jobs, and can be called from + # any thread (usually by the 'queue_job' method). 'watched' must only + # be modified by the monitor thread, which will move items from 'queue' + # to 'watched' and then manage the watched jobs. + self.watched = [] + self.monitor_queue = Queue() + + def _init_monitor_thread(self): + self.monitor_thread = threading.Thread( name="%s.monitor_thread" % self.runner_name, target=self.monitor ) + self.monitor_thread.setDaemon( True ) + self.monitor_thread.start() + + def _init_worker_threads(self): + self.work_queue = Queue() + self.work_threads = [] + nworkers = self.app.config.cluster_job_queue_workers + for i in range( nworkers ): + worker = threading.Thread( name="%s.work_thread-%d" % (self.runner_name, i), target=self.run_next ) + worker.start() + self.work_threads.append( worker ) + + def handle_stop(self): + # DRMAA and SGE runners should override this and disconnect. + pass + + def monitor( self ): + """ + Watches jobs currently in the cluster queue and deals with state changes + (queued to running) and job completion + """ + while 1: + # Take any new watched jobs and put them on the monitor list + try: + while 1: + cluster_job_state = self.monitor_queue.get_nowait() + if cluster_job_state is STOP_SIGNAL: + # TODO: This is where any cleanup would occur + self.handle_stop() + return + self.watched.append( cluster_job_state ) + except Empty: + pass + # Iterate over the list of watched jobs and check state + self.check_watched_items() + # Sleep a bit before the next state check + time.sleep( 1 ) + + def run_next( self ): + """ + Run the next item in the queue (a job waiting to run or finish ) + """ + while 1: + ( op, obj ) = self.work_queue.get() + if op is STOP_SIGNAL: + return + try: + if op == JOB_STATUS_QUEUED: + # If the next item is to be run, then only run it if the + # job state is "queued". Otherwise the next item was either + # cancelled or one of its siblings encountered an error. + job_state = obj.get_state() + if model.Job.states.QUEUED == job_state: + self.queue_job( obj ) + else: + log.debug( "Not executing job %d in state %s" % ( obj.get_id_tag(), job_state ) ) + elif op == JOB_STATUS_FINISHED: + self.finish_job( obj ) + elif op == JOB_STATUS_FAILED: + self.fail_job( obj ) + except: + log.exception( "Uncaught exception %sing job" % op ) + + def monitor_job(self, job_state): + self.monitor_queue.put( job_state ) + + def put( self, job_wrapper ): + """Add a job to the queue (by job identifier)""" + # Change to queued state before handing to worker thread so the runner won't pick it up again + job_wrapper.change_state( model.Job.states.QUEUED ) + self.mark_as_queued(job_wrapper) + + def shutdown( self ): + """Attempts to gracefully shut down the monitor thread""" + log.info( "sending stop signal to worker threads" ) + self.monitor_queue.put( STOP_SIGNAL ) + for i in range( len( self.work_threads ) ): + self.work_queue.put( ( STOP_SIGNAL, None ) ) + + def check_watched_items(self): + """ + This method is responsible for iterating over self.watched and handling + state changes and updating self.watched with a new list of watched job + states. Subclasses can opt to override this directly (as older job runners will + initially) or just override check_watched_item and allow the list processing to + reuse the logic here. + """ + new_watched = [] + for cluster_job_state in self.watched: + new_cluster_job_state = self.check_watched_item(cluster_job_state) + if new_cluster_job_state: + new_watched.append(new_cluster_job_state) + self.watched = new_watched + + # Subclasses should implement this unless they override check_watched_items all together. + def check_watched_item(self): + raise NotImplementedError() + + def queue_job(self, job_wrapper): + raise NotImplementedError() + + def finish_job(self, job_state): + raise NotImplementedError() + + def fail_job(self, job_state): + raise NotImplementedError() + + def mark_as_finished(self, job_state): + self.work_queue.put( ( JOB_STATUS_FINISHED, job_state ) ) + + def mark_as_failed(self, job_state): + self.work_queue.put( ( JOB_STATUS_FAILED, job_state ) ) + + def mark_as_queued(self, job_wrapper): + self.work_queue.put( ( JOB_STATUS_QUEUED, job_wrapper ) ) https://bitbucket.org/galaxy/galaxy-central/commits/57d33740aa70/ changeset: 57d33740aa70 user: jmchilton date: 2013-01-11 17:53:05 summary: Refactor the LWRJobRunner to be a ClusterJobRunner and implement a recover method for this runner, the upshot of this is that LWR jobs can now survive Galaxy restarts. Downside is that jobs are no longer queued on Galaxy server, so LWR server should be updated (to changeset 5213f6d or newer) to queue jobs on the remote server. This is not manidatory however, this will still work it is just more jobs may run simultaneously than is desired. affected #: 1 file diff -r 611bc9467b222bb1cf0b1ef5d5b6120f210a471f -r 57d33740aa70c18c0fa082c0e2ef40042edb62e4 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -7,7 +7,7 @@ from galaxy import model from galaxy.datatypes.data import nice_size -from galaxy.jobs.runners import BaseJobRunner +from galaxy.jobs.runners import ClusterJobState, ClusterJobRunner import os, errno from time import sleep @@ -199,12 +199,18 @@ def wait(self): """ """ while True: - check_complete_response = self.__raw_execute_and_parse("check_complete", {"job_id" : self.job_id }) - complete = check_complete_response["complete"] == "true" + complete = self.check_complete() if complete: return check_complete_response time.sleep(1) + def raw_check_complete(self): + check_complete_response = self.__raw_execute_and_parse("check_complete", {"job_id" : self.job_id }) + return check_complete_response + + def check_complete(self): + return self.raw_check_complete()["complete"] == "true" + def clean(self): self.__raw_execute("clean", { "job_id" : self.job_id }) @@ -213,51 +219,34 @@ -class LwrJobRunner( BaseJobRunner ): +class LwrJobRunner( ClusterJobRunner ): """ - Lwr Job Runner + LWR Job Runner """ - STOP_SIGNAL = object() + runner_name = "LWRRunner" + def __init__( self, app ): - """Start the job runner with 'nworkers' worker threads""" - self.app = app - self.sa_session = app.model.context + """Start the job runner """ + super( LwrJobRunner, self ).__init__( app ) + self._init_monitor_thread() + log.info( "starting LWR workers" ) + self._init_worker_threads() - # start workers - self.queue = Queue() - self.threads = [] - nworkers = app.config.local_job_queue_workers - log.info( "starting workers" ) - for i in range( nworkers ): - worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), target=self.run_next ) - worker.setDaemon( True ) - worker.start() - self.threads.append( worker ) - log.debug( "%d workers ready", nworkers ) + def check_watched_item(self, job_state): + try: + client = self.get_client_from_state(job_state) + complete = client.check_complete() + except Exception: + # An orphaned job was put into the queue at app startup, so remote server went down + # either way we are done I guess. + self.mark_as_finished(job_state) + return None + if complete: + self.mark_as_finished(job_state) + return None + return job_state - def run_next( self ): - """Run the next job, waiting until one is available if neccesary""" - while 1: - job_wrapper = self.queue.get() - if job_wrapper is self.STOP_SIGNAL: - return - try: - self.run_job( job_wrapper ) - except: - log.exception( "Uncaught exception running job" ) - - def determine_lwr_url(self, url): - lwr_url = url[ len( 'lwr://' ) : ] - return lwr_url - - def get_client_from_wrapper(self, job_wrapper): - return self.get_client( job_wrapper.get_job_runner_url(), job_wrapper.job_id ) - - def get_client(self, job_runner, job_id): - lwr_url = self.determine_lwr_url( job_runner ) - return Client(lwr_url, job_id) - - def run_job( self, job_wrapper ): + def queue_job(self, job_wrapper): stderr = stdout = command_line = '' runner_url = job_wrapper.get_job_runner_url() @@ -277,35 +266,76 @@ return # If we were able to get a command line, run the job - if command_line: - try: - #log.debug( 'executing: %s' % command_line ) - client = self.get_client_from_wrapper(job_wrapper) - output_fnames = job_wrapper.get_output_fnames() - output_files = [ str( o ) for o in output_fnames ] - input_files = job_wrapper.get_input_fnames() - file_stager = FileStager(client, command_line, job_wrapper.extra_filenames, input_files, output_files, job_wrapper.tool.tool_dir) - rebuilt_command_line = file_stager.get_rewritten_command_line() - client.launch( rebuilt_command_line ) + if not command_line: + job_wrapper.finish( '', '' ) + return - job_wrapper.set_runner( runner_url, job_wrapper.job_id ) - job_wrapper.change_state( model.Job.states.RUNNING ) + try: + #log.debug( 'executing: %s' % command_line ) + client = self.get_client_from_wrapper(job_wrapper) + output_files = self.get_output_files(job_wrapper) + input_files = job_wrapper.get_input_fnames() + file_stager = FileStager(client, command_line, job_wrapper.extra_filenames, input_files, output_files, job_wrapper.tool.tool_dir) + rebuilt_command_line = file_stager.get_rewritten_command_line() + client.launch( rebuilt_command_line ) + job_wrapper.set_runner( runner_url, job_wrapper.job_id ) + job_wrapper.change_state( model.Job.states.RUNNING ) - run_results = client.wait() - log.debug('run_results %s' % run_results ) - stdout = run_results['stdout'] - stderr = run_results['stderr'] + except Exception, exc: + job_wrapper.fail( "failure running job", exception=True ) + log.exception("failure running job %d" % job_wrapper.job_id) + return - - if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ]: - for output_file in output_files: - client.download_output(output_file) - client.clean() - log.debug('execution finished: %s' % command_line) - except Exception, exc: - job_wrapper.fail( "failure running job", exception=True ) - log.exception("failure running job %d" % job_wrapper.job_id) - return + lwr_job_state = ClusterJobState() + lwr_job_state.job_wrapper = job_wrapper + lwr_job_state.job_id = job_wrapper.job_id + lwr_job_state.old_state = True + lwr_job_state.running = True + lwr_job_state.runner_url = runner_url + self.monitor_job(lwr_job_state) + + def get_output_files(self, job_wrapper): + output_fnames = job_wrapper.get_output_fnames() + return [ str( o ) for o in output_fnames ] + + + def determine_lwr_url(self, url): + lwr_url = url[ len( 'lwr://' ) : ] + return lwr_url + + def get_client_from_wrapper(self, job_wrapper): + return self.get_client( job_wrapper.get_job_runner_url(), job_wrapper.job_id ) + + def get_client_from_state(self, job_state): + job_runner = job_state.runner_url + job_id = job_state.job_id + return self.get_client(job_runner, job_id) + + def get_client(self, job_runner, job_id): + lwr_url = self.determine_lwr_url( job_runner ) + return Client(lwr_url, job_id) + + def finish_job( self, job_state ): + stderr = stdout = command_line = '' + job_wrapper = job_state.job_wrapper + try: + client = self.get_client_from_state(job_state) + + run_results = client.raw_check_complete() + log.debug('run_results %s' % run_results ) + stdout = run_results['stdout'] + stderr = run_results['stderr'] + + if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ]: + output_files = self.get_output_files(job_wrapper) + for output_file in output_files: + client.download_output(output_file) + client.clean() + log.debug('execution finished: %s' % command_line) + except Exception, exc: + job_wrapper.fail( "failure running job", exception=True ) + log.exception("failure running job %d" % job_wrapper.job_id) + return #run the metadata setting script here #this is terminate-able when output dataset/job is deleted #so that long running set_meta()s can be canceled without having to reboot the server @@ -321,7 +351,7 @@ job_wrapper.external_output_metadata.set_job_runner_external_pid( external_metadata_proc.pid, self.sa_session ) external_metadata_proc.wait() log.debug( 'execution of external set_meta finished for job %d' % job_wrapper.job_id ) - + # Finish the job try: job_wrapper.finish( stdout, stderr ) @@ -329,12 +359,13 @@ log.exception("Job wrapper finish method failed") job_wrapper.fail("Unable to finish job", exception=True) - def put( self, job_wrapper ): - """Add a job to the queue (by job identifier)""" - # Change to queued state before handing to worker thread so the runner won't pick it up again - job_wrapper.change_state( model.Job.states.QUEUED ) - self.queue.put( job_wrapper ) - + def fail_job( self, job_state ): + """ + Seperated out so we can use the worker threads for it. + """ + self.stop_job( self.sa_session.query( self.app.model.Job ).get( job_state.job_wrapper.job_id ) ) + job_state.job_wrapper.fail( job_state.fail_message ) + def shutdown( self ): """Attempts to gracefully shut down the worker threads""" log.info( "sending stop signal to worker threads" ) @@ -383,7 +414,21 @@ log.debug("Attempt remote lwr kill of job with url %s and id %s" % (lwr_url, job_id)) client = self.get_client(lwr_url, job_id) client.kill() + + def recover( self, job, job_wrapper ): - # local jobs can't be recovered - job_wrapper.change_state( model.Job.states.ERROR, info = "This job was killed when Galaxy was restarted. Please retry the job." ) - + """Recovers jobs stuck in the queued/running state when Galaxy started""" + job_state = ClusterJobState() + job_state.job_id = str( job.get_job_runner_external_id() ) + job_state.runner_url = job_wrapper.get_job_runner_url() + job_wrapper.command_line = job.get_command_line() + job_state.job_wrapper = job_wrapper + if job.get_state() == model.Job.states.RUNNING: + log.debug( "(LWR/%s) is still in running state, adding to the LWR queue" % ( job.get_id()) ) + job_state.old_state = True + job_state.running = True + self.monitor_queue.put( job_state ) + elif job.get_state() == model.Job.states.QUEUED: + # LWR doesn't queue currently, so this indicates galaxy was shutoff while + # job was being staged. Not sure how to recover from that. + job_state.job_wrapper.fail( "This job was killed when Galaxy was restarted. Please retry the job." ) https://bitbucket.org/galaxy/galaxy-central/commits/0a2976ff3b73/ changeset: 0a2976ff3b73 user: jmchilton date: 2013-01-11 17:53:05 summary: Allow execution of jobs created by task splitting via the LWR job runner. affected #: 1 file diff -r 57d33740aa70c18c0fa082c0e2ef40042edb62e4 -r 0a2976ff3b73d5130674c1e1019e3425b16d1fc0 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -27,13 +27,14 @@ class FileStager(object): - def __init__(self, client, command_line, config_files, input_files, output_files, tool_dir): + def __init__(self, client, command_line, config_files, input_files, output_files, tool_dir, working_directory): self.client = client self.command_line = command_line self.config_files = config_files self.input_files = input_files self.output_files = output_files self.tool_dir = os.path.abspath(tool_dir) + self.working_directory = working_directory self.file_renames = {} @@ -46,7 +47,9 @@ self.__initialize_referenced_tool_files() self.__upload_tool_files() self.__upload_input_files() + self.__upload_working_directory_files() self.__initialize_output_file_renames() + self.__initialize_task_output_file_renames() self.__initialize_config_file_renames() self.__rewrite_and_upload_config_files() self.__rewrite_command_line() @@ -69,13 +72,27 @@ for input_file in self.input_files: input_upload_response = self.client.upload_input(input_file) self.file_renames[input_file] = input_upload_response['path'] - + + def __upload_working_directory_files(self): + # Task manager stages files into working directory, these need to be uploaded + for working_directory_file in os.listdir(self.working_directory): + path = os.path.join(self.working_directory, working_directory_file) + working_file_response = self.client.upload_working_directory_file(path) + self.file_renames[path] = working_file_response['path'] + def __initialize_output_file_renames(self): for output_file in self.output_files: self.file_renames[output_file] = r'%s%s%s' % (self.new_outputs_directory, self.remote_path_separator, os.path.basename(output_file)) + def __initialize_task_output_file_renames(self): + for output_file in self.output_files: + name = os.path.basename(output_file) + self.file_renames[os.path.join(self.working_directory, name)] = r'%s%s%s' % (self.new_working_directory, + self.remote_path_separator, + name) + def __initialize_config_file_renames(self): for config_file in self.config_files: self.file_renames[config_file] = r'%s%s%s' % (self.new_working_directory, @@ -172,13 +189,27 @@ def upload_config_file(self, path, contents): return self.__upload_contents("upload_config_file", path, contents) - - def download_output(self, path): + + def upload_working_directory_file(self, path): + return self.__upload_file("upload_working_directory_file", path) + + def _get_output_type(self, name): + return self.__raw_execute_and_parse('get_output_type', {'name': name, + 'job_id': self.job_id}) + + def download_output(self, path, working_directory): """ """ name = os.path.basename(path) - response = self.__raw_execute('download_output', {'name' : name, - "job_id" : self.job_id}) - output = open(path, 'wb') + output_type = self._get_output_type(name) + response = self.__raw_execute('download_output', {'name' : name, + "job_id" : self.job_id, + 'output_type': output_type}) + if output_type == 'direct': + output = open(path, 'wb') + elif output_type == 'task': + output = open(os.path.join(working_directory, name), 'wb') + else: + raise Exception("No remote output found for dataset with path %s" % path) try: while True: buffer = response.read(1024) @@ -254,7 +285,7 @@ try: job_wrapper.prepare() if hasattr(job_wrapper, 'prepare_input_files_cmds') and job_wrapper.prepare_input_files_cmds is not None: - for cmd in job_wrapper.prepare_input_file_cmds: # run the commands to stage the input files + for cmd in job_wrapper.prepare_input_files_cmds: # run the commands to stage the input files #log.debug( 'executing: %s' % cmd ) if 0 != os.system(cmd): raise Exception('Error running file staging command: %s' % cmd) @@ -275,7 +306,8 @@ client = self.get_client_from_wrapper(job_wrapper) output_files = self.get_output_files(job_wrapper) input_files = job_wrapper.get_input_fnames() - file_stager = FileStager(client, command_line, job_wrapper.extra_filenames, input_files, output_files, job_wrapper.tool.tool_dir) + working_directory = job_wrapper.working_directory + file_stager = FileStager(client, command_line, job_wrapper.extra_filenames, input_files, output_files, job_wrapper.tool.tool_dir, working_directory) rebuilt_command_line = file_stager.get_rewritten_command_line() client.launch( rebuilt_command_line ) job_wrapper.set_runner( runner_url, job_wrapper.job_id ) @@ -304,7 +336,10 @@ return lwr_url def get_client_from_wrapper(self, job_wrapper): - return self.get_client( job_wrapper.get_job_runner_url(), job_wrapper.job_id ) + job_id = job_wrapper.job_id + if hasattr(job_wrapper, 'task_id'): + job_id = "%s_%s" % (job_id, job_wrapper.task_id) + return self.get_client( job_wrapper.get_job_runner_url(), job_id ) def get_client_from_state(self, job_state): job_runner = job_state.runner_url @@ -329,7 +364,7 @@ if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ]: output_files = self.get_output_files(job_wrapper) for output_file in output_files: - client.download_output(output_file) + client.download_output(output_file, working_directory=job_wrapper.working_directory) client.clean() log.debug('execution finished: %s' % command_line) except Exception, exc: @@ -386,8 +421,9 @@ def stop_job( self, job ): #if our local job has JobExternalOutputMetadata associated, then our primary job has to have already finished - if job.external_output_metadata: - pid = job.external_output_metadata[0].job_runner_external_pid #every JobExternalOutputMetadata has a pid set, we just need to take from one of them + job_ext_output_metadata = job.get_external_output_metadata() + if job_ext_output_metadata: + pid = job_ext_output_metadata[0].job_runner_external_pid #every JobExternalOutputMetadata has a pid set, we just need to take from one of them if pid in [ None, '' ]: log.warning( "stop_job(): %s: no PID in database for job, unable to stop" % job.id ) return https://bitbucket.org/galaxy/galaxy-central/commits/ed3d477d056f/ changeset: ed3d477d056f user: jmchilton date: 2013-01-11 17:53:05 summary: Extend LWR job runner to stage an input's extra_files_path (if present). affected #: 1 file diff -r 0a2976ff3b73d5130674c1e1019e3425b16d1fc0 -r ed3d477d056fd77a207e61ae7ee7ed9cc2c1e9b2 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -72,6 +72,16 @@ for input_file in self.input_files: input_upload_response = self.client.upload_input(input_file) self.file_renames[input_file] = input_upload_response['path'] + # TODO: Determine if this is object store safe and what needs to be + # done if it is not. + files_path = "%s_files" % input_file[0:-len(".dat")] + if os.path.exists(files_path): + for extra_file in os.listdir(files_path): + extra_file_path = os.path.join(files_path, extra_file) + relative_path = os.path.basename(files_path) + extra_file_relative_path = os.path.join(relative_path, extra_file) + response = self.client.upload_extra_input(extra_file_path, extra_file_relative_path) + self.file_renames[extra_file_path] = response['path'] def __upload_working_directory_files(self): # Task manager stages files into working directory, these need to be uploaded @@ -167,17 +177,18 @@ response = self.__raw_execute(command, args, data) return simplejson.loads(response.read()) - def __upload_file(self, action, path, contents = None): + def __upload_file(self, action, path, name=None, contents = None): """ """ input = open(path, 'rb') try: mmapped_input = mmap.mmap(input.fileno(), 0, access = mmap.ACCESS_READ) - return self.__upload_contents(action, path, mmapped_input) + return self.__upload_contents(action, path, mmapped_input, name) finally: input.close() - def __upload_contents(self, action, path, contents): - name = os.path.basename(path) + def __upload_contents(self, action, path, contents, name=None): + if not name: + name = os.path.basename(path) args = {"job_id" : self.job_id, "name" : name} return self.__raw_execute_and_parse(action, args, contents) @@ -187,6 +198,9 @@ def upload_input(self, path): return self.__upload_file("upload_input", path) + def upload_extra_input(self, path, relative_name): + return self.__upload_file("upload_extra_input", path, name=relative_name) + def upload_config_file(self, path, contents): return self.__upload_contents("upload_config_file", path, contents) https://bitbucket.org/galaxy/galaxy-central/commits/6fa106f2678d/ changeset: 6fa106f2678d user: jmchilton date: 2013-01-11 17:53:05 summary: Refactor much of the lwr client code out into its own module. This will make it easier to keep content insync with client code from lwr source. affected #: 2 files diff -r ed3d477d056fd77a207e61ae7ee7ed9cc2c1e9b2 -r 6fa106f2678da0e0af8d8c25e90928817254c6f5 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -1,268 +1,18 @@ import logging import subprocess -from Queue import Queue -import threading - -import re from galaxy import model -from galaxy.datatypes.data import nice_size from galaxy.jobs.runners import ClusterJobState, ClusterJobRunner -import os, errno +import errno from time import sleep +from lwr_client import FileStager, Client + log = logging.getLogger( __name__ ) __all__ = [ 'LwrJobRunner' ] -import urllib -import urllib2 -import httplib -import mmap -import tempfile -import time - -import simplejson - -class FileStager(object): - - def __init__(self, client, command_line, config_files, input_files, output_files, tool_dir, working_directory): - self.client = client - self.command_line = command_line - self.config_files = config_files - self.input_files = input_files - self.output_files = output_files - self.tool_dir = os.path.abspath(tool_dir) - self.working_directory = working_directory - - self.file_renames = {} - - job_config = client.setup() - - self.new_working_directory = job_config['working_directory'] - self.new_outputs_directory = job_config['outputs_directory'] - self.remote_path_separator = job_config['path_separator'] - - self.__initialize_referenced_tool_files() - self.__upload_tool_files() - self.__upload_input_files() - self.__upload_working_directory_files() - self.__initialize_output_file_renames() - self.__initialize_task_output_file_renames() - self.__initialize_config_file_renames() - self.__rewrite_and_upload_config_files() - self.__rewrite_command_line() - - def __initialize_referenced_tool_files(self): - pattern = r"(%s%s\S+)" % (self.tool_dir, os.sep) - referenced_tool_files = [] - referenced_tool_files += re.findall(pattern, self.command_line) - if self.config_files != None: - for config_file in self.config_files: - referenced_tool_files += re.findall(pattern, self.__read(config_file)) - self.referenced_tool_files = referenced_tool_files - - def __upload_tool_files(self): - for referenced_tool_file in self.referenced_tool_files: - tool_upload_response = self.client.upload_tool_file(referenced_tool_file) - self.file_renames[referenced_tool_file] = tool_upload_response['path'] - - def __upload_input_files(self): - for input_file in self.input_files: - input_upload_response = self.client.upload_input(input_file) - self.file_renames[input_file] = input_upload_response['path'] - # TODO: Determine if this is object store safe and what needs to be - # done if it is not. - files_path = "%s_files" % input_file[0:-len(".dat")] - if os.path.exists(files_path): - for extra_file in os.listdir(files_path): - extra_file_path = os.path.join(files_path, extra_file) - relative_path = os.path.basename(files_path) - extra_file_relative_path = os.path.join(relative_path, extra_file) - response = self.client.upload_extra_input(extra_file_path, extra_file_relative_path) - self.file_renames[extra_file_path] = response['path'] - - def __upload_working_directory_files(self): - # Task manager stages files into working directory, these need to be uploaded - for working_directory_file in os.listdir(self.working_directory): - path = os.path.join(self.working_directory, working_directory_file) - working_file_response = self.client.upload_working_directory_file(path) - self.file_renames[path] = working_file_response['path'] - - def __initialize_output_file_renames(self): - for output_file in self.output_files: - self.file_renames[output_file] = r'%s%s%s' % (self.new_outputs_directory, - self.remote_path_separator, - os.path.basename(output_file)) - - def __initialize_task_output_file_renames(self): - for output_file in self.output_files: - name = os.path.basename(output_file) - self.file_renames[os.path.join(self.working_directory, name)] = r'%s%s%s' % (self.new_working_directory, - self.remote_path_separator, - name) - - def __initialize_config_file_renames(self): - for config_file in self.config_files: - self.file_renames[config_file] = r'%s%s%s' % (self.new_working_directory, - self.remote_path_separator, - os.path.basename(config_file)) - - def __rewrite_paths(self, contents): - new_contents = contents - for local_path, remote_path in self.file_renames.iteritems(): - new_contents = new_contents.replace(local_path, remote_path) - return new_contents - - def __rewrite_and_upload_config_files(self): - for config_file in self.config_files: - config_contents = self.__read(config_file) - new_config_contents = self.__rewrite_paths(config_contents) - self.client.upload_config_file(config_file, new_config_contents) - - def __rewrite_command_line(self): - self.rewritten_command_line = self.__rewrite_paths(self.command_line) - - def get_rewritten_command_line(self): - return self.rewritten_command_line - - def __read(self, path): - input = open(path, "r") - try: - return input.read() - finally: - input.close() - - - -class Client(object): - """ - """ - """ - """ - def __init__(self, remote_host, job_id, private_key=None): - if not remote_host.endswith("/"): - remote_host = remote_host + "/" - ## If we don't have an explicit private_key defined, check for - ## one embedded in the URL. A URL of the form - ## https://moo@cow:8913 will try to contact https://cow:8913 - ## with a private key of moo - private_key_format = "https?://(.*)@.*/?" - private_key_match= re.match(private_key_format, remote_host) - if not private_key and private_key_match: - private_key = private_key_match.group(1) - remote_host = remote_host.replace("%s@" % private_key, '', 1) - self.remote_host = remote_host - self.job_id = job_id - self.private_key = private_key - - def url_open(self, request, data): - return urllib2.urlopen(request, data) - - def __build_url(self, command, args): - if self.private_key: - args["private_key"] = self.private_key - data = urllib.urlencode(args) - url = self.remote_host + command + "?" + data - return url - - def __raw_execute(self, command, args = {}, data = None): - url = self.__build_url(command, args) - request = urllib2.Request(url=url, data=data) - response = self.url_open(request, data) - return response - - def __raw_execute_and_parse(self, command, args = {}, data = None): - response = self.__raw_execute(command, args, data) - return simplejson.loads(response.read()) - - def __upload_file(self, action, path, name=None, contents = None): - """ """ - input = open(path, 'rb') - try: - mmapped_input = mmap.mmap(input.fileno(), 0, access = mmap.ACCESS_READ) - return self.__upload_contents(action, path, mmapped_input, name) - finally: - input.close() - - def __upload_contents(self, action, path, contents, name=None): - if not name: - name = os.path.basename(path) - args = {"job_id" : self.job_id, "name" : name} - return self.__raw_execute_and_parse(action, args, contents) - - def upload_tool_file(self, path): - return self.__upload_file("upload_tool_file", path) - - def upload_input(self, path): - return self.__upload_file("upload_input", path) - - def upload_extra_input(self, path, relative_name): - return self.__upload_file("upload_extra_input", path, name=relative_name) - - def upload_config_file(self, path, contents): - return self.__upload_contents("upload_config_file", path, contents) - - def upload_working_directory_file(self, path): - return self.__upload_file("upload_working_directory_file", path) - - def _get_output_type(self, name): - return self.__raw_execute_and_parse('get_output_type', {'name': name, - 'job_id': self.job_id}) - - def download_output(self, path, working_directory): - """ """ - name = os.path.basename(path) - output_type = self._get_output_type(name) - response = self.__raw_execute('download_output', {'name' : name, - "job_id" : self.job_id, - 'output_type': output_type}) - if output_type == 'direct': - output = open(path, 'wb') - elif output_type == 'task': - output = open(os.path.join(working_directory, name), 'wb') - else: - raise Exception("No remote output found for dataset with path %s" % path) - try: - while True: - buffer = response.read(1024) - if buffer == "": - break - output.write(buffer) - finally: - output.close() - - def launch(self, command_line): - """ """ - return self.__raw_execute("launch", {"command_line" : command_line, - "job_id" : self.job_id}) - - def kill(self): - return self.__raw_execute("kill", {"job_id" : self.job_id}) - - def wait(self): - """ """ - while True: - complete = self.check_complete() - if complete: - return check_complete_response - time.sleep(1) - - def raw_check_complete(self): - check_complete_response = self.__raw_execute_and_parse("check_complete", {"job_id" : self.job_id }) - return check_complete_response - - def check_complete(self): - return self.raw_check_complete()["complete"] == "true" - - def clean(self): - self.__raw_execute("clean", { "job_id" : self.job_id }) - - def setup(self): - return self.__raw_execute_and_parse("setup", { "job_id" : self.job_id }) - - class LwrJobRunner( ClusterJobRunner ): """ diff -r ed3d477d056fd77a207e61ae7ee7ed9cc2c1e9b2 -r 6fa106f2678da0e0af8d8c25e90928817254c6f5 lib/galaxy/jobs/runners/lwr_client/__init__.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/__init__.py @@ -0,0 +1,246 @@ +import mmap +import os +import re +import time +import urllib +import urllib2 + +import simplejson + + +class FileStager(object): + + def __init__(self, client, command_line, config_files, input_files, output_files, tool_dir, working_directory): + self.client = client + self.command_line = command_line + self.config_files = config_files + self.input_files = input_files + self.output_files = output_files + self.tool_dir = os.path.abspath(tool_dir) + self.working_directory = working_directory + + self.file_renames = {} + + job_config = client.setup() + + self.new_working_directory = job_config['working_directory'] + self.new_outputs_directory = job_config['outputs_directory'] + self.remote_path_separator = job_config['path_separator'] + + self.__initialize_referenced_tool_files() + self.__upload_tool_files() + self.__upload_input_files() + self.__upload_working_directory_files() + self.__initialize_output_file_renames() + self.__initialize_task_output_file_renames() + self.__initialize_config_file_renames() + self.__rewrite_and_upload_config_files() + self.__rewrite_command_line() + + def __initialize_referenced_tool_files(self): + pattern = r"(%s%s\S+)" % (self.tool_dir, os.sep) + referenced_tool_files = [] + referenced_tool_files += re.findall(pattern, self.command_line) + if self.config_files != None: + for config_file in self.config_files: + referenced_tool_files += re.findall(pattern, self.__read(config_file)) + self.referenced_tool_files = referenced_tool_files + + def __upload_tool_files(self): + for referenced_tool_file in self.referenced_tool_files: + tool_upload_response = self.client.upload_tool_file(referenced_tool_file) + self.file_renames[referenced_tool_file] = tool_upload_response['path'] + + def __upload_input_files(self): + for input_file in self.input_files: + input_upload_response = self.client.upload_input(input_file) + self.file_renames[input_file] = input_upload_response['path'] + # TODO: Determine if this is object store safe and what needs to be + # done if it is not. + files_path = "%s_files" % input_file[0:-len(".dat")] + if os.path.exists(files_path): + for extra_file in os.listdir(files_path): + extra_file_path = os.path.join(files_path, extra_file) + relative_path = os.path.basename(files_path) + extra_file_relative_path = os.path.join(relative_path, extra_file) + response = self.client.upload_extra_input(extra_file_path, extra_file_relative_path) + self.file_renames[extra_file_path] = response['path'] + + def __upload_working_directory_files(self): + # Task manager stages files into working directory, these need to be uploaded + for working_directory_file in os.listdir(self.working_directory): + path = os.path.join(self.working_directory, working_directory_file) + working_file_response = self.client.upload_working_directory_file(path) + self.file_renames[path] = working_file_response['path'] + + def __initialize_output_file_renames(self): + for output_file in self.output_files: + self.file_renames[output_file] = r'%s%s%s' % (self.new_outputs_directory, + self.remote_path_separator, + os.path.basename(output_file)) + + def __initialize_task_output_file_renames(self): + for output_file in self.output_files: + name = os.path.basename(output_file) + self.file_renames[os.path.join(self.working_directory, name)] = r'%s%s%s' % (self.new_working_directory, + self.remote_path_separator, + name) + + def __initialize_config_file_renames(self): + for config_file in self.config_files: + self.file_renames[config_file] = r'%s%s%s' % (self.new_working_directory, + self.remote_path_separator, + os.path.basename(config_file)) + + def __rewrite_paths(self, contents): + new_contents = contents + for local_path, remote_path in self.file_renames.iteritems(): + new_contents = new_contents.replace(local_path, remote_path) + return new_contents + + def __rewrite_and_upload_config_files(self): + for config_file in self.config_files: + config_contents = self.__read(config_file) + new_config_contents = self.__rewrite_paths(config_contents) + self.client.upload_config_file(config_file, new_config_contents) + + def __rewrite_command_line(self): + self.rewritten_command_line = self.__rewrite_paths(self.command_line) + + def get_rewritten_command_line(self): + return self.rewritten_command_line + + def __read(self, path): + input = open(path, "r") + try: + return input.read() + finally: + input.close() + + + +class Client(object): + """ + """ + """ + """ + def __init__(self, remote_host, job_id, private_key=None): + if not remote_host.endswith("/"): + remote_host = remote_host + "/" + ## If we don't have an explicit private_key defined, check for + ## one embedded in the URL. A URL of the form + ## https://moo@cow:8913 will try to contact https://cow:8913 + ## with a private key of moo + private_key_format = "https?://(.*)@.*/?" + private_key_match= re.match(private_key_format, remote_host) + if not private_key and private_key_match: + private_key = private_key_match.group(1) + remote_host = remote_host.replace("%s@" % private_key, '', 1) + self.remote_host = remote_host + self.job_id = job_id + self.private_key = private_key + + def url_open(self, request, data): + return urllib2.urlopen(request, data) + + def __build_url(self, command, args): + if self.private_key: + args["private_key"] = self.private_key + data = urllib.urlencode(args) + url = self.remote_host + command + "?" + data + return url + + def __raw_execute(self, command, args = {}, data = None): + url = self.__build_url(command, args) + request = urllib2.Request(url=url, data=data) + response = self.url_open(request, data) + return response + + def __raw_execute_and_parse(self, command, args = {}, data = None): + response = self.__raw_execute(command, args, data) + return simplejson.loads(response.read()) + + def __upload_file(self, action, path, name=None, contents = None): + """ """ + input = open(path, 'rb') + try: + mmapped_input = mmap.mmap(input.fileno(), 0, access = mmap.ACCESS_READ) + return self.__upload_contents(action, path, mmapped_input, name) + finally: + input.close() + + def __upload_contents(self, action, path, contents, name=None): + if not name: + name = os.path.basename(path) + args = {"job_id" : self.job_id, "name" : name} + return self.__raw_execute_and_parse(action, args, contents) + + def upload_tool_file(self, path): + return self.__upload_file("upload_tool_file", path) + + def upload_input(self, path): + return self.__upload_file("upload_input", path) + + def upload_extra_input(self, path, relative_name): + return self.__upload_file("upload_extra_input", path, name=relative_name) + + def upload_config_file(self, path, contents): + return self.__upload_contents("upload_config_file", path, contents) + + def upload_working_directory_file(self, path): + return self.__upload_file("upload_working_directory_file", path) + + def _get_output_type(self, name): + return self.__raw_execute_and_parse('get_output_type', {'name': name, + 'job_id': self.job_id}) + + def download_output(self, path, working_directory): + """ """ + name = os.path.basename(path) + output_type = self._get_output_type(name) + response = self.__raw_execute('download_output', {'name' : name, + "job_id" : self.job_id, + 'output_type': output_type}) + if output_type == 'direct': + output = open(path, 'wb') + elif output_type == 'task': + output = open(os.path.join(working_directory, name), 'wb') + else: + raise Exception("No remote output found for dataset with path %s" % path) + try: + while True: + buffer = response.read(1024) + if buffer == "": + break + output.write(buffer) + finally: + output.close() + + def launch(self, command_line): + """ """ + return self.__raw_execute("launch", {"command_line" : command_line, + "job_id" : self.job_id}) + + def kill(self): + return self.__raw_execute("kill", {"job_id" : self.job_id}) + + def wait(self): + """ """ + while True: + complete = self.check_complete() + if complete: + return check_complete_response + time.sleep(1) + + def raw_check_complete(self): + check_complete_response = self.__raw_execute_and_parse("check_complete", {"job_id" : self.job_id }) + return check_complete_response + + def check_complete(self): + return self.raw_check_complete()["complete"] == "true" + + def clean(self): + self.__raw_execute("clean", { "job_id" : self.job_id }) + + def setup(self): + return self.__raw_execute_and_parse("setup", { "job_id" : self.job_id }) https://bitbucket.org/galaxy/galaxy-central/commits/b109c7db9347/ changeset: b109c7db9347 user: jmchilton date: 2013-01-11 17:53:05 summary: Documentation and PEP8 fixes for lwr client code. affected #: 1 file diff -r 6fa106f2678da0e0af8d8c25e90928817254c6f5 -r b109c7db9347271b35d426d3148120ce359977e6 lib/galaxy/jobs/runners/lwr_client/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/__init__.py @@ -1,3 +1,10 @@ +""" +lwr_client +========== + +This module contains logic for interfacing with an external LWR server. + +""" import mmap import os import re @@ -9,8 +16,32 @@ class FileStager(object): - + """ + Objects of the FileStager class interact with an LWR client object to + stage the files required to run jobs on a remote LWR server. + + **Parameters** + + client : Client + LWR client object. + command_line : str + The local command line to execute, this will be rewritten for the remote server. + config_files : list + List of Galaxy 'configfile's produced for this job. These will be rewritten and sent to remote server. + input_files : list + List of input files used by job. These will be transferred and references rewritten. + output_files : list + List of output_files produced by job. + tool_dir : str + Directory containing tool to execute (if a wrapper is used, it will be transferred to remote server). + working_directory : str + Local path created by Galaxy for running this job. + + """ + def __init__(self, client, command_line, config_files, input_files, output_files, tool_dir, working_directory): + """ + """ self.client = client self.command_line = command_line self.config_files = config_files @@ -67,7 +98,8 @@ self.file_renames[extra_file_path] = response['path'] def __upload_working_directory_files(self): - # Task manager stages files into working directory, these need to be uploaded + # Task manager stages files into working directory, these need to be + # uploaded if present. for working_directory_file in os.listdir(self.working_directory): path = os.path.join(self.working_directory, working_directory_file) working_file_response = self.client.upload_working_directory_file(path) @@ -75,8 +107,8 @@ def __initialize_output_file_renames(self): for output_file in self.output_files: - self.file_renames[output_file] = r'%s%s%s' % (self.new_outputs_directory, - self.remote_path_separator, + self.file_renames[output_file] = r'%s%s%s' % (self.new_outputs_directory, + self.remote_path_separator, os.path.basename(output_file)) def __initialize_task_output_file_renames(self): @@ -108,6 +140,10 @@ self.rewritten_command_line = self.__rewrite_paths(self.command_line) def get_rewritten_command_line(self): + """ + Returns the rewritten version of the command line to execute suitable + for remote host. + """ return self.rewritten_command_line def __read(self, path): @@ -117,13 +153,21 @@ finally: input.close() - - + class Client(object): - """ """ - """ + Objects of this client class perform low-level communication with a remote LWR server. + + **Parameters** + + remote_host : str + Remote URL of the LWR server. + job_id : str + Galaxy job/task id. + private_key : str (optional) + Secret key the remote LWR server is configured with. """ + def __init__(self, remote_host, job_id, private_key=None): if not remote_host.endswith("/"): remote_host = remote_host + "/" @@ -132,7 +176,7 @@ ## https://moo@cow:8913 will try to contact https://cow:8913 ## with a private key of moo private_key_format = "https?://(.*)@.*/?" - private_key_match= re.match(private_key_format, remote_host) + private_key_match = re.match(private_key_format, remote_host) if not private_key and private_key_match: private_key = private_key_match.group(1) remote_host = remote_host.replace("%s@" % private_key, '', 1) @@ -140,9 +184,9 @@ self.job_id = job_id self.private_key = private_key - def url_open(self, request, data): + def _url_open(self, request, data): return urllib2.urlopen(request, data) - + def __build_url(self, command, args): if self.private_key: args["private_key"] = self.private_key @@ -150,21 +194,20 @@ url = self.remote_host + command + "?" + data return url - def __raw_execute(self, command, args = {}, data = None): + def __raw_execute(self, command, args={}, data=None): url = self.__build_url(command, args) request = urllib2.Request(url=url, data=data) - response = self.url_open(request, data) + response = self._url_open(request, data) return response - def __raw_execute_and_parse(self, command, args = {}, data = None): + def __raw_execute_and_parse(self, command, args={}, data=None): response = self.__raw_execute(command, args, data) return simplejson.loads(response.read()) - def __upload_file(self, action, path, name=None, contents = None): - """ """ + def __upload_file(self, action, path, name=None, contents=None): input = open(path, 'rb') try: - mmapped_input = mmap.mmap(input.fileno(), 0, access = mmap.ACCESS_READ) + mmapped_input = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ) return self.__upload_contents(action, path, mmapped_input, name) finally: input.close() @@ -172,39 +215,93 @@ def __upload_contents(self, action, path, contents, name=None): if not name: name = os.path.basename(path) - args = {"job_id" : self.job_id, "name" : name} + args = {"job_id": self.job_id, "name": name} return self.__raw_execute_and_parse(action, args, contents) - + def upload_tool_file(self, path): + """ + Upload a tool related file (e.g. wrapper) required to run job. + + **Parameters** + + path : str + Local path tool. + """ return self.__upload_file("upload_tool_file", path) def upload_input(self, path): + """ + Upload input dataset to remote server. + + **Parameters** + + path : str + Local path of input dataset. + """ return self.__upload_file("upload_input", path) def upload_extra_input(self, path, relative_name): + """ + Upload extra input file to remote server. + + **Parameters** + + path : str + Extra files path of input dataset corresponding to this input. + relative_name : str + Relative path of extra file to upload relative to inputs extra files path. + """ return self.__upload_file("upload_extra_input", path, name=relative_name) def upload_config_file(self, path, contents): + """ + Upload a job's config file to the remote server. + + **Parameters** + + path : str + Local path to the original config file. + contents : str + Rewritten contents of the config file to upload. + """ return self.__upload_contents("upload_config_file", path, contents) def upload_working_directory_file(self, path): + """ + Upload the supplied file (path) from a job's working directory + to remote server. + + **Parameters** + + path : str + Path to file to upload. + """ return self.__upload_file("upload_working_directory_file", path) def _get_output_type(self, name): - return self.__raw_execute_and_parse('get_output_type', {'name': name, - 'job_id': self.job_id}) + return self.__raw_execute_and_parse("get_output_type", {"name": name, + "job_id": self.job_id}) def download_output(self, path, working_directory): - """ """ + """ + Download an output dataset from the remote server. + + **Parameters** + + path : str + Local path of the dataset. + working_directory : str + Local working_directory for the job. + """ name = os.path.basename(path) output_type = self._get_output_type(name) - response = self.__raw_execute('download_output', {'name' : name, - "job_id" : self.job_id, - 'output_type': output_type}) - if output_type == 'direct': - output = open(path, 'wb') - elif output_type == 'task': - output = open(os.path.join(working_directory, name), 'wb') + response = self.__raw_execute("download_output", {"name": name, + "job_id": self.job_id, + "output_type": output_type}) + if output_type == "direct": + output = open(path, "wb") + elif output_type == "task": + output = open(os.path.join(working_directory, name), "wb") else: raise Exception("No remote output found for dataset with path %s" % path) try: @@ -215,32 +312,57 @@ output.write(buffer) finally: output.close() - + def launch(self, command_line): - """ """ - return self.__raw_execute("launch", {"command_line" : command_line, - "job_id" : self.job_id}) + """ + Run or queue up the execution of the supplied + `command_line` on the remote server. + + **Parameters** + + command_line : str + Command to execute. + """ + return self.__raw_execute("launch", {"command_line": command_line, + "job_id": self.job_id}) def kill(self): - return self.__raw_execute("kill", {"job_id" : self.job_id}) - + """ + Cancel remote job, either removing from the queue or killing it. + """ + return self.__raw_execute("kill", {"job_id": self.job_id}) + def wait(self): - """ """ + """ + Wait for job to finish. + """ while True: - complete = self.check_complete() - if complete: - return check_complete_response + complete_response = self.raw_check_complete() + if complete_response["complete"] == "true": + return complete_response time.sleep(1) def raw_check_complete(self): - check_complete_response = self.__raw_execute_and_parse("check_complete", {"job_id" : self.job_id }) + """ + Get check_complete response from the remote server. + """ + check_complete_response = self.__raw_execute_and_parse("check_complete", {"job_id": self.job_id}) return check_complete_response def check_complete(self): + """ + Return boolean indicating whether the job is complete. + """ return self.raw_check_complete()["complete"] == "true" def clean(self): - self.__raw_execute("clean", { "job_id" : self.job_id }) + """ + Cleanup the remote job. + """ + self.__raw_execute("clean", {"job_id": self.job_id}) def setup(self): - return self.__raw_execute_and_parse("setup", { "job_id" : self.job_id }) + """ + Setup remote LWR server to run this job. + """ + return self.__raw_execute_and_parse("setup", {"job_id": self.job_id}) https://bitbucket.org/galaxy/galaxy-central/commits/856d9508b97f/ changeset: 856d9508b97f user: jmchilton date: 2013-01-11 17:53:05 summary: Extend lwr to allow execution of jobs with outputs specified using 'from_work_dir'. affected #: 3 files diff -r b109c7db9347271b35d426d3148120ce359977e6 -r 856d9508b97fe655e9652750b59fbb787c8f632a lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -8,7 +8,7 @@ log = logging.getLogger( __name__ ) class BaseJobRunner( object ): - def build_command_line( self, job_wrapper, include_metadata=False ): + def build_command_line( self, job_wrapper, include_metadata=False, include_work_dir_outputs=True ): """ Compose the sequence of commands necessary to execute a job. This will currently include: @@ -19,18 +19,6 @@ - commands to set metadata (if include_metadata is True) """ - def in_directory( file, directory ): - """ - Return true, if the common prefix of both is equal to directory - e.g. /a/b/c/d.rst and directory is /a/b, the common prefix is /a/b - """ - - # Make both absolute. - directory = os.path.abspath( directory ) - file = os.path.abspath( file ) - - return os.path.commonprefix( [ file, directory ] ) == directory - commands = job_wrapper.get_command_line() # All job runners currently handle this case which should never # occur @@ -47,6 +35,41 @@ commands = "; ".join( job_wrapper.dependency_shell_commands + [ commands ] ) # -- Append commands to copy job outputs based on from_work_dir attribute. -- + if include_work_dir_outputs: + work_dir_outputs = self.get_work_dir_outputs( job_wrapper ) + if work_dir_outputs: + commands += "; " + "; ".join( [ "cp %s %s" % ( source_file, destination ) for ( source_file, destination ) in work_dir_outputs ] ) + + # Append metadata setting commands, we don't want to overwrite metadata + # that was copied over in init_meta(), as per established behavior + if include_metadata and self.app.config.set_metadata_externally: + commands += "; cd %s; " % os.path.abspath( os.getcwd() ) + commands += job_wrapper.setup_external_metadata( + exec_dir = os.path.abspath( os.getcwd() ), + tmp_dir = job_wrapper.working_directory, + dataset_files_path = self.app.model.Dataset.file_path, + output_fnames = job_wrapper.get_output_fnames(), + set_extension = False, + kwds = { 'overwrite' : False } ) + return commands + + def get_work_dir_outputs( self, job_wrapper ): + """ + Returns list of pairs (source_file, destination) describing path + to work_dir output file and ultimate destination. + """ + + def in_directory( file, directory ): + """ + Return true, if the common prefix of both is equal to directory + e.g. /a/b/c/d.rst and directory is /a/b, the common prefix is /a/b + """ + + # Make both absolute. + directory = os.path.abspath( directory ) + file = os.path.abspath( file ) + + return os.path.commonprefix( [ file, directory ] ) == directory # Set up dict of dataset id --> output path; output path can be real or # false depending on outputs_to_working_directory @@ -57,6 +80,7 @@ path = dataset_path.false_path output_paths[ dataset_path.dataset_id ] = path + output_pairs = [] # Walk job's output associations to find and use from_work_dir attributes. job = job_wrapper.get_job() job_tool = self.app.toolbox.tools_by_id.get( job.tool_id, None ) @@ -72,30 +96,14 @@ source_file = os.path.join( os.path.abspath( job_wrapper.working_directory ), hda_tool_output.from_work_dir ) destination = output_paths[ dataset.dataset_id ] if in_directory( source_file, job_wrapper.working_directory ): - try: - commands += "; cp %s %s" % ( source_file, destination ) - log.debug( "Copying %s to %s as directed by from_work_dir" % ( source_file, destination ) ) - except ( IOError, OSError ): - log.debug( "Could not copy %s to %s as directed by from_work_dir" % ( source_file, destination ) ) + output_pairs.append( ( source_file, destination ) ) + log.debug( "Copying %s to %s as directed by from_work_dir" % ( source_file, destination ) ) else: # Security violation. log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) ) + return output_pairs - - # Append metadata setting commands, we don't want to overwrite metadata - # that was copied over in init_meta(), as per established behavior - if include_metadata and self.app.config.set_metadata_externally: - commands += "; cd %s; " % os.path.abspath( os.getcwd() ) - commands += job_wrapper.setup_external_metadata( - exec_dir = os.path.abspath( os.getcwd() ), - tmp_dir = job_wrapper.working_directory, - dataset_files_path = self.app.model.Dataset.file_path, - output_fnames = job_wrapper.get_output_fnames(), - set_extension = False, - kwds = { 'overwrite' : False } ) - return commands - class ClusterJobState( object ): """ Encapsulate the state of a cluster job, this should be subclassed as diff -r b109c7db9347271b35d426d3148120ce359977e6 -r 856d9508b97fe655e9652750b59fbb787c8f632a lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -54,7 +54,7 @@ if 0 != os.system(cmd): raise Exception('Error running file staging command: %s' % cmd) job_wrapper.prepare_input_files_cmds = None # prevent them from being used in-line - command_line = self.build_command_line( job_wrapper, include_metadata=False ) + command_line = self.build_command_line( job_wrapper, include_metadata=False, include_work_dir_outputs=False ) except: job_wrapper.fail( "failure preparing job", exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) @@ -126,7 +126,12 @@ stderr = run_results['stderr'] if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ]: + work_dir_outputs = self.get_work_dir_outputs(job_wrapper) output_files = self.get_output_files(job_wrapper) + for source_file, output_file in work_dir_outputs: + client.download_work_dir_output(source_file, job_wrapper.working_directory, output_file) + # Remove from full output_files list so don't try to download directly. + output_files.remove(output_file) for output_file in output_files: client.download_output(output_file, working_directory=job_wrapper.working_directory) client.clean() diff -r b109c7db9347271b35d426d3148120ce359977e6 -r 856d9508b97fe655e9652750b59fbb787c8f632a lib/galaxy/jobs/runners/lwr_client/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/__init__.py @@ -282,6 +282,24 @@ return self.__raw_execute_and_parse("get_output_type", {"name": name, "job_id": self.job_id}) + def download_work_dir_output(self, source, working_directory, output_path): + """ + Download an output dataset specified with from_work_dir from the + remote server. + + **Parameters** + + source : str + Path in job's working_directory to find output in. + working_directory : str + Local working_directory for the job. + output_path : str + Full path to output dataset. + """ + output = open(output_path, "wb") + name = os.path.basename(source) + self.__raw_download_output(name, self.job_id, "work_dir", output) + def download_output(self, path, working_directory): """ Download an output dataset from the remote server. @@ -295,23 +313,26 @@ """ name = os.path.basename(path) output_type = self._get_output_type(name) - response = self.__raw_execute("download_output", {"name": name, - "job_id": self.job_id, - "output_type": output_type}) if output_type == "direct": output = open(path, "wb") elif output_type == "task": output = open(os.path.join(working_directory, name), "wb") else: raise Exception("No remote output found for dataset with path %s" % path) + self.__raw_download_output(name, self.job_id, output_type, output) + + def __raw_download_output(self, name, job_id, output_type, output_file): + response = self.__raw_execute("download_output", {"name": name, + "job_id": self.job_id, + "output_type": output_type}) try: while True: buffer = response.read(1024) if buffer == "": break - output.write(buffer) + output_file.write(buffer) finally: - output.close() + output_file.close() def launch(self, command_line): """ https://bitbucket.org/galaxy/galaxy-central/commits/b749bb68c1f7/ changeset: b749bb68c1f7 user: jmchilton date: 2013-01-11 17:53:05 summary: Implement optimization attempting to not transfer unneeded inputs to remote LWR server. More general refactoring and testing of lwr client code. affected #: 1 file diff -r 856d9508b97fe655e9652750b59fbb787c8f632a -r b749bb68c1f7a71c775e7486152dcfe93813c668 lib/galaxy/jobs/runners/lwr_client/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/__init__.py @@ -15,6 +15,99 @@ import simplejson +class JobInputs(object): + """ + Abstractions over dynamic inputs created for a given job (namely the command to + execute and created configfiles). + + **Parameters** + + command_line : str + Local command to execute for this job. (To be rewritten.) + config_files : str + Config files created for this job. (To be rewritten.) + + + >>> import tempfile + >>> tf = tempfile.NamedTemporaryFile() + >>> def setup_inputs(tf): + ... open(tf.name, "w").write("world /path/to/input the rest") + ... inputs = JobInputs("hello /path/to/input", [tf.name]) + ... return inputs + >>> inputs = setup_inputs(tf) + >>> inputs.rewrite_paths("/path/to/input", 'C:\\input') + >>> inputs.rewritten_command_line + 'hello C:\\\\input' + >>> inputs.rewritten_config_files[tf.name] + 'world C:\\\\input the rest' + >>> tf.close() + >>> tf = tempfile.NamedTemporaryFile() + >>> inputs = setup_inputs(tf) + >>> inputs.find_referenced_subfiles('/path/to') + ['/path/to/input'] + >>> inputs.path_referenced('/path/to') + True + >>> inputs.path_referenced('/path/to/input') + True + >>> inputs.path_referenced('/path/to/notinput') + False + >>> tf.close() + """ + + def __init__(self, command_line, config_files): + self.rewritten_command_line = command_line + self.rewritten_config_files = {} + for config_file in config_files or []: + config_contents = _read(config_file) + self.rewritten_config_files[config_file] = config_contents + + def find_referenced_subfiles(self, directory): + """ + Return list of files below specified `directory` in job inputs. Could + use more sophisticated logic (match quotes to handle spaces, handle + subdirectories, etc...). + + **Parameters** + + directory : str + Full path to directory to search. + + """ + pattern = r"(%s%s\S+)" % (directory, os.sep) + referenced_files = set() + for input_contents in self.__items(): + referenced_files.update(re.findall(pattern, input_contents)) + return list(referenced_files) + + def path_referenced(self, path): + pattern = r"%s" % path + found = False + for input_contents in self.__items(): + if re.findall(pattern, input_contents): + found = True + break + return found + + def rewrite_paths(self, local_path, remote_path): + """ + Rewrite references to `local_path` with `remote_path` in job inputs. + """ + self.__rewrite_command_line(local_path, remote_path) + self.__rewrite_config_files(local_path, remote_path) + + def __rewrite_command_line(self, local_path, remote_path): + self.rewritten_command_line = self.rewritten_command_line.replace(local_path, remote_path) + + def __rewrite_config_files(self, local_path, remote_path): + for config_file, rewritten_contents in self.rewritten_config_files.iteritems(): + self.rewritten_config_files[config_file] = rewritten_contents.replace(local_path, remote_path) + + def __items(self): + items = [self.rewritten_command_line] + items.extend(self.rewritten_config_files.values()) + return items + + class FileStager(object): """ Objects of the FileStager class interact with an LWR client object to @@ -50,6 +143,10 @@ self.tool_dir = os.path.abspath(tool_dir) self.working_directory = working_directory + # Setup job inputs, these will need to be rewritten before + # shipping off to remote LWR server. + self.job_inputs = JobInputs(self.command_line, self.config_files) + self.file_renames = {} job_config = client.setup() @@ -65,17 +162,11 @@ self.__initialize_output_file_renames() self.__initialize_task_output_file_renames() self.__initialize_config_file_renames() - self.__rewrite_and_upload_config_files() - self.__rewrite_command_line() + self.__handle_rewrites() + self.__upload_rewritten_config_files() def __initialize_referenced_tool_files(self): - pattern = r"(%s%s\S+)" % (self.tool_dir, os.sep) - referenced_tool_files = [] - referenced_tool_files += re.findall(pattern, self.command_line) - if self.config_files != None: - for config_file in self.config_files: - referenced_tool_files += re.findall(pattern, self.__read(config_file)) - self.referenced_tool_files = referenced_tool_files + self.referenced_tool_files = self.job_inputs.find_referenced_subfiles(self.tool_dir) def __upload_tool_files(self): for referenced_tool_file in self.referenced_tool_files: @@ -84,18 +175,25 @@ def __upload_input_files(self): for input_file in self.input_files: + self.__upload_input_file(input_file) + self.__upload_input_extra_files(input_file) + + def __upload_input_file(self, input_file): + if self.job_inputs.path_referenced(input_file): input_upload_response = self.client.upload_input(input_file) self.file_renames[input_file] = input_upload_response['path'] - # TODO: Determine if this is object store safe and what needs to be - # done if it is not. - files_path = "%s_files" % input_file[0:-len(".dat")] - if os.path.exists(files_path): - for extra_file in os.listdir(files_path): - extra_file_path = os.path.join(files_path, extra_file) - relative_path = os.path.basename(files_path) - extra_file_relative_path = os.path.join(relative_path, extra_file) - response = self.client.upload_extra_input(extra_file_path, extra_file_relative_path) - self.file_renames[extra_file_path] = response['path'] + + def __upload_input_extra_files(self, input_file): + # TODO: Determine if this is object store safe and what needs to be + # done if it is not. + files_path = "%s_files" % input_file[0:-len(".dat")] + if os.path.exists(files_path) and self.job_inputs.path_referenced(files_path): + for extra_file in os.listdir(files_path): + extra_file_path = os.path.join(files_path, extra_file) + relative_path = os.path.basename(files_path) + extra_file_relative_path = os.path.join(relative_path, extra_file) + response = self.client.upload_extra_input(extra_file_path, extra_file_relative_path) + self.file_renames[extra_file_path] = response['path'] def __upload_working_directory_files(self): # Task manager stages files into working directory, these need to be @@ -130,28 +228,20 @@ new_contents = new_contents.replace(local_path, remote_path) return new_contents - def __rewrite_and_upload_config_files(self): - for config_file in self.config_files: - config_contents = self.__read(config_file) - new_config_contents = self.__rewrite_paths(config_contents) + def __handle_rewrites(self): + for local_path, remote_path in self.file_renames.iteritems(): + self.job_inputs.rewrite_paths(local_path, remote_path) + + def __upload_rewritten_config_files(self): + for config_file, new_config_contents in self.job_inputs.rewritten_config_files.iteritems(): self.client.upload_config_file(config_file, new_config_contents) - def __rewrite_command_line(self): - self.rewritten_command_line = self.__rewrite_paths(self.command_line) - def get_rewritten_command_line(self): """ Returns the rewritten version of the command line to execute suitable for remote host. """ - return self.rewritten_command_line - - def __read(self, path): - input = open(path, "r") - try: - return input.read() - finally: - input.close() + return self.job_inputs.rewritten_command_line class Client(object): @@ -387,3 +477,15 @@ Setup remote LWR server to run this job. """ return self.__raw_execute_and_parse("setup", {"job_id": self.job_id}) + + +def _read(path): + """ + Utility method to quickly read small files (config files and tool + wrappers) into memory as strings. + """ + input = open(path, "r") + try: + return input.read() + finally: + input.close() https://bitbucket.org/galaxy/galaxy-central/commits/2631faf42a8f/ changeset: 2631faf42a8f user: jmchilton date: 2013-01-11 17:53:05 summary: Rework job_id handling in LWR runner allowing remote LWR server to assign a job_id during setup, save this will serve as the job's external id. This change allows multiple Galaxy instances to submit jobs to the same LWR backend server and will prove useful when implementing additional backends (pbs/drmaa/etc...) for the LWR server. affected #: 2 files diff -r b749bb68c1f7a71c775e7486152dcfe93813c668 -r 2631faf42a8fe4f3b3f9b556809da07b69ee845a lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -73,8 +73,9 @@ working_directory = job_wrapper.working_directory file_stager = FileStager(client, command_line, job_wrapper.extra_filenames, input_files, output_files, job_wrapper.tool.tool_dir, working_directory) rebuilt_command_line = file_stager.get_rewritten_command_line() + job_id = file_stager.job_id client.launch( rebuilt_command_line ) - job_wrapper.set_runner( runner_url, job_wrapper.job_id ) + job_wrapper.set_runner( runner_url, job_id ) job_wrapper.change_state( model.Job.states.RUNNING ) except Exception, exc: @@ -84,7 +85,7 @@ lwr_job_state = ClusterJobState() lwr_job_state.job_wrapper = job_wrapper - lwr_job_state.job_id = job_wrapper.job_id + lwr_job_state.job_id = job_id lwr_job_state.old_state = True lwr_job_state.running = True lwr_job_state.runner_url = runner_url diff -r b749bb68c1f7a71c775e7486152dcfe93813c668 -r 2631faf42a8fe4f3b3f9b556809da07b69ee845a lib/galaxy/jobs/runners/lwr_client/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/__init__.py @@ -149,12 +149,7 @@ self.file_renames = {} - job_config = client.setup() - - self.new_working_directory = job_config['working_directory'] - self.new_outputs_directory = job_config['outputs_directory'] - self.remote_path_separator = job_config['path_separator'] - + self.__handle_setup() self.__initialize_referenced_tool_files() self.__upload_tool_files() self.__upload_input_files() @@ -165,6 +160,21 @@ self.__handle_rewrites() self.__upload_rewritten_config_files() + def __handle_setup(self): + job_config = self.client.setup() + + self.new_working_directory = job_config['working_directory'] + self.new_outputs_directory = job_config['outputs_directory'] + self.remote_path_separator = job_config['path_separator'] + # If remote LWR server assigned job id, use that otherwise + # just use local job_id assigned. + galaxy_job_id = self.client.job_id + self.job_id = job_config.get('job_id', galaxy_job_id) + if self.job_id != galaxy_job_id: + # Remote LWR server assigned an id different than the + # Galaxy job id, update client to reflect this. + self.client.job_id = self.job_id + def __initialize_referenced_tool_files(self): self.referenced_tool_files = self.job_inputs.find_referenced_subfiles(self.tool_dir) https://bitbucket.org/galaxy/galaxy-central/commits/21a91117bcc8/ changeset: 21a91117bcc8 user: jmchilton date: 2013-01-11 18:02:43 summary: Re-introduce LWR shutdown fixes from Dave B.. affected #: 1 file diff -r 2631faf42a8fe4f3b3f9b556809da07b69ee845a -r 21a91117bcc80e55aa5a196caa8b801180ed9480 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -2,7 +2,7 @@ import subprocess from galaxy import model -from galaxy.jobs.runners import ClusterJobState, ClusterJobRunner +from galaxy.jobs.runners import ClusterJobState, ClusterJobRunner, STOP_SIGNAL import errno from time import sleep @@ -174,8 +174,9 @@ def shutdown( self ): """Attempts to gracefully shut down the worker threads""" log.info( "sending stop signal to worker threads" ) - for i in range( len( self.threads ) ): - self.queue.put( self.STOP_SIGNAL ) + self.monitor_queue.put( STOP_SIGNAL ) + for i in range( len( self.work_threads ) ): + self.work_queue.put( ( STOP_SIGNAL, None ) ) log.info( "local job runner stopped" ) def check_pid( self, pid ): https://bitbucket.org/galaxy/galaxy-central/commits/e5ec6ed8f033/ changeset: e5ec6ed8f033 user: natefoo date: 2013-01-11 18:25:58 summary: Merged in jmchilton/galaxy-central-lwr (pull request #106: Ongoing LWR Enhancements) affected #: 3 files diff -r c2199c181f09fd5b94a9f5ea13fc39b28e803f2c -r e5ec6ed8f0337893cf4bc64e61089471b00b28b0 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -1,9 +1,14 @@ import os, logging, os.path +from galaxy import model +from Queue import Queue, Empty +import time +import threading + log = logging.getLogger( __name__ ) class BaseJobRunner( object ): - def build_command_line( self, job_wrapper, include_metadata=False ): + def build_command_line( self, job_wrapper, include_metadata=False, include_work_dir_outputs=True ): """ Compose the sequence of commands necessary to execute a job. This will currently include: @@ -14,18 +19,6 @@ - commands to set metadata (if include_metadata is True) """ - def in_directory( file, directory ): - """ - Return true, if the common prefix of both is equal to directory - e.g. /a/b/c/d.rst and directory is /a/b, the common prefix is /a/b - """ - - # Make both absolute. - directory = os.path.abspath( directory ) - file = os.path.abspath( file ) - - return os.path.commonprefix( [ file, directory ] ) == directory - commands = job_wrapper.get_command_line() # All job runners currently handle this case which should never # occur @@ -42,6 +35,41 @@ commands = "; ".join( job_wrapper.dependency_shell_commands + [ commands ] ) # -- Append commands to copy job outputs based on from_work_dir attribute. -- + if include_work_dir_outputs: + work_dir_outputs = self.get_work_dir_outputs( job_wrapper ) + if work_dir_outputs: + commands += "; " + "; ".join( [ "cp %s %s" % ( source_file, destination ) for ( source_file, destination ) in work_dir_outputs ] ) + + # Append metadata setting commands, we don't want to overwrite metadata + # that was copied over in init_meta(), as per established behavior + if include_metadata and self.app.config.set_metadata_externally: + commands += "; cd %s; " % os.path.abspath( os.getcwd() ) + commands += job_wrapper.setup_external_metadata( + exec_dir = os.path.abspath( os.getcwd() ), + tmp_dir = job_wrapper.working_directory, + dataset_files_path = self.app.model.Dataset.file_path, + output_fnames = job_wrapper.get_output_fnames(), + set_extension = False, + kwds = { 'overwrite' : False } ) + return commands + + def get_work_dir_outputs( self, job_wrapper ): + """ + Returns list of pairs (source_file, destination) describing path + to work_dir output file and ultimate destination. + """ + + def in_directory( file, directory ): + """ + Return true, if the common prefix of both is equal to directory + e.g. /a/b/c/d.rst and directory is /a/b, the common prefix is /a/b + """ + + # Make both absolute. + directory = os.path.abspath( directory ) + file = os.path.abspath( file ) + + return os.path.commonprefix( [ file, directory ] ) == directory # Set up dict of dataset id --> output path; output path can be real or # false depending on outputs_to_working_directory @@ -52,6 +80,7 @@ path = dataset_path.false_path output_paths[ dataset_path.dataset_id ] = path + output_pairs = [] # Walk job's output associations to find and use from_work_dir attributes. job = job_wrapper.get_job() job_tool = self.app.toolbox.tools_by_id.get( job.tool_id, None ) @@ -67,26 +96,165 @@ source_file = os.path.join( os.path.abspath( job_wrapper.working_directory ), hda_tool_output.from_work_dir ) destination = output_paths[ dataset.dataset_id ] if in_directory( source_file, job_wrapper.working_directory ): - try: - commands += "; cp %s %s" % ( source_file, destination ) - log.debug( "Copying %s to %s as directed by from_work_dir" % ( source_file, destination ) ) - except ( IOError, OSError ): - log.debug( "Could not copy %s to %s as directed by from_work_dir" % ( source_file, destination ) ) + output_pairs.append( ( source_file, destination ) ) + log.debug( "Copying %s to %s as directed by from_work_dir" % ( source_file, destination ) ) else: # Security violation. log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) ) + return output_pairs +class ClusterJobState( object ): + """ + Encapsulate the state of a cluster job, this should be subclassed as + needed for various job runners to capture additional information needed + to communicate with cluster job manager. + """ - # Append metadata setting commands, we don't want to overwrite metadata - # that was copied over in init_meta(), as per established behavior - if include_metadata and self.app.config.set_metadata_externally: - commands += "; cd %s; " % os.path.abspath( os.getcwd() ) - commands += job_wrapper.setup_external_metadata( - exec_dir = os.path.abspath( os.getcwd() ), - tmp_dir = job_wrapper.working_directory, - dataset_files_path = self.app.model.Dataset.file_path, - output_fnames = job_wrapper.get_output_fnames(), - set_extension = False, - kwds = { 'overwrite' : False } ) - return commands + def __init__( self ): + self.job_wrapper = None + self.job_id = None + self.old_state = None + self.running = False + self.runner_url = None + +STOP_SIGNAL = object() + +JOB_STATUS_QUEUED = 'queue' +JOB_STATUS_FAILED = 'fail' +JOB_STATUS_FINISHED = 'finish' + +class ClusterJobRunner( BaseJobRunner ): + """ + Not sure this is the best name for this class, but there is common code + shared between sge, pbs, drmaa, etc... + """ + + def __init__( self, app ): + self.app = app + self.sa_session = app.model.context + # 'watched' and 'queue' are both used to keep track of jobs to watch. + # 'queue' is used to add new watched jobs, and can be called from + # any thread (usually by the 'queue_job' method). 'watched' must only + # be modified by the monitor thread, which will move items from 'queue' + # to 'watched' and then manage the watched jobs. + self.watched = [] + self.monitor_queue = Queue() + + def _init_monitor_thread(self): + self.monitor_thread = threading.Thread( name="%s.monitor_thread" % self.runner_name, target=self.monitor ) + self.monitor_thread.setDaemon( True ) + self.monitor_thread.start() + + def _init_worker_threads(self): + self.work_queue = Queue() + self.work_threads = [] + nworkers = self.app.config.cluster_job_queue_workers + for i in range( nworkers ): + worker = threading.Thread( name="%s.work_thread-%d" % (self.runner_name, i), target=self.run_next ) + worker.start() + self.work_threads.append( worker ) + + def handle_stop(self): + # DRMAA and SGE runners should override this and disconnect. + pass + + def monitor( self ): + """ + Watches jobs currently in the cluster queue and deals with state changes + (queued to running) and job completion + """ + while 1: + # Take any new watched jobs and put them on the monitor list + try: + while 1: + cluster_job_state = self.monitor_queue.get_nowait() + if cluster_job_state is STOP_SIGNAL: + # TODO: This is where any cleanup would occur + self.handle_stop() + return + self.watched.append( cluster_job_state ) + except Empty: + pass + # Iterate over the list of watched jobs and check state + self.check_watched_items() + # Sleep a bit before the next state check + time.sleep( 1 ) + + def run_next( self ): + """ + Run the next item in the queue (a job waiting to run or finish ) + """ + while 1: + ( op, obj ) = self.work_queue.get() + if op is STOP_SIGNAL: + return + try: + if op == JOB_STATUS_QUEUED: + # If the next item is to be run, then only run it if the + # job state is "queued". Otherwise the next item was either + # cancelled or one of its siblings encountered an error. + job_state = obj.get_state() + if model.Job.states.QUEUED == job_state: + self.queue_job( obj ) + else: + log.debug( "Not executing job %d in state %s" % ( obj.get_id_tag(), job_state ) ) + elif op == JOB_STATUS_FINISHED: + self.finish_job( obj ) + elif op == JOB_STATUS_FAILED: + self.fail_job( obj ) + except: + log.exception( "Uncaught exception %sing job" % op ) + + def monitor_job(self, job_state): + self.monitor_queue.put( job_state ) + + def put( self, job_wrapper ): + """Add a job to the queue (by job identifier)""" + # Change to queued state before handing to worker thread so the runner won't pick it up again + job_wrapper.change_state( model.Job.states.QUEUED ) + self.mark_as_queued(job_wrapper) + + def shutdown( self ): + """Attempts to gracefully shut down the monitor thread""" + log.info( "sending stop signal to worker threads" ) + self.monitor_queue.put( STOP_SIGNAL ) + for i in range( len( self.work_threads ) ): + self.work_queue.put( ( STOP_SIGNAL, None ) ) + + def check_watched_items(self): + """ + This method is responsible for iterating over self.watched and handling + state changes and updating self.watched with a new list of watched job + states. Subclasses can opt to override this directly (as older job runners will + initially) or just override check_watched_item and allow the list processing to + reuse the logic here. + """ + new_watched = [] + for cluster_job_state in self.watched: + new_cluster_job_state = self.check_watched_item(cluster_job_state) + if new_cluster_job_state: + new_watched.append(new_cluster_job_state) + self.watched = new_watched + + # Subclasses should implement this unless they override check_watched_items all together. + def check_watched_item(self): + raise NotImplementedError() + + def queue_job(self, job_wrapper): + raise NotImplementedError() + + def finish_job(self, job_state): + raise NotImplementedError() + + def fail_job(self, job_state): + raise NotImplementedError() + + def mark_as_finished(self, job_state): + self.work_queue.put( ( JOB_STATUS_FINISHED, job_state ) ) + + def mark_as_failed(self, job_state): + self.work_queue.put( ( JOB_STATUS_FAILED, job_state ) ) + + def mark_as_queued(self, job_wrapper): + self.work_queue.put( ( JOB_STATUS_QUEUED, job_wrapper ) ) diff -r c2199c181f09fd5b94a9f5ea13fc39b28e803f2c -r e5ec6ed8f0337893cf4bc64e61089471b00b28b0 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -1,263 +1,47 @@ import logging import subprocess -from Queue import Queue -import threading - -import re from galaxy import model -from galaxy.datatypes.data import nice_size -from galaxy.jobs.runners import BaseJobRunner +from galaxy.jobs.runners import ClusterJobState, ClusterJobRunner, STOP_SIGNAL -import os, errno +import errno from time import sleep +from lwr_client import FileStager, Client + log = logging.getLogger( __name__ ) __all__ = [ 'LwrJobRunner' ] -import urllib -import urllib2 -import httplib -import mmap -import tempfile -import time -import simplejson +class LwrJobRunner( ClusterJobRunner ): + """ + LWR Job Runner + """ + runner_name = "LWRRunner" -class FileStager(object): - - def __init__(self, client, command_line, config_files, input_files, output_files, tool_dir): - self.client = client - self.command_line = command_line - self.config_files = config_files - self.input_files = input_files - self.output_files = output_files - self.tool_dir = os.path.abspath(tool_dir) + def __init__( self, app ): + """Start the job runner """ + super( LwrJobRunner, self ).__init__( app ) + self._init_monitor_thread() + log.info( "starting LWR workers" ) + self._init_worker_threads() - self.file_renames = {} + def check_watched_item(self, job_state): + try: + client = self.get_client_from_state(job_state) + complete = client.check_complete() + except Exception: + # An orphaned job was put into the queue at app startup, so remote server went down + # either way we are done I guess. + self.mark_as_finished(job_state) + return None + if complete: + self.mark_as_finished(job_state) + return None + return job_state - job_config = client.setup() - - self.new_working_directory = job_config['working_directory'] - self.new_outputs_directory = job_config['outputs_directory'] - self.remote_path_separator = job_config['path_separator'] - - self.__initialize_referenced_tool_files() - self.__upload_tool_files() - self.__upload_input_files() - self.__initialize_output_file_renames() - self.__initialize_config_file_renames() - self.__rewrite_and_upload_config_files() - self.__rewrite_command_line() - - def __initialize_referenced_tool_files(self): - pattern = r"(%s%s\S+)" % (self.tool_dir, os.sep) - referenced_tool_files = [] - referenced_tool_files += re.findall(pattern, self.command_line) - if self.config_files != None: - for config_file in self.config_files: - referenced_tool_files += re.findall(pattern, self.__read(config_file)) - self.referenced_tool_files = referenced_tool_files - - def __upload_tool_files(self): - for referenced_tool_file in self.referenced_tool_files: - tool_upload_response = self.client.upload_tool_file(referenced_tool_file) - self.file_renames[referenced_tool_file] = tool_upload_response['path'] - - def __upload_input_files(self): - for input_file in self.input_files: - input_upload_response = self.client.upload_input(input_file) - self.file_renames[input_file] = input_upload_response['path'] - - def __initialize_output_file_renames(self): - for output_file in self.output_files: - self.file_renames[output_file] = r'%s%s%s' % (self.new_outputs_directory, - self.remote_path_separator, - os.path.basename(output_file)) - - def __initialize_config_file_renames(self): - for config_file in self.config_files: - self.file_renames[config_file] = r'%s%s%s' % (self.new_working_directory, - self.remote_path_separator, - os.path.basename(config_file)) - - def __rewrite_paths(self, contents): - new_contents = contents - for local_path, remote_path in self.file_renames.iteritems(): - new_contents = new_contents.replace(local_path, remote_path) - return new_contents - - def __rewrite_and_upload_config_files(self): - for config_file in self.config_files: - config_contents = self.__read(config_file) - new_config_contents = self.__rewrite_paths(config_contents) - self.client.upload_config_file(config_file, new_config_contents) - - def __rewrite_command_line(self): - self.rewritten_command_line = self.__rewrite_paths(self.command_line) - - def get_rewritten_command_line(self): - return self.rewritten_command_line - - def __read(self, path): - input = open(path, "r") - try: - return input.read() - finally: - input.close() - - - -class Client(object): - """ - """ - """ - """ - def __init__(self, remote_host, job_id, private_key=None): - if not remote_host.endswith("/"): - remote_host = remote_host + "/" - ## If we don't have an explicit private_key defined, check for - ## one embedded in the URL. A URL of the form - ## https://moo@cow:8913 will try to contact https://cow:8913 - ## with a private key of moo - private_key_format = "https?://(.*)@.*/?" - private_key_match= re.match(private_key_format, remote_host) - if not private_key and private_key_match: - private_key = private_key_match.group(1) - remote_host = remote_host.replace("%s@" % private_key, '', 1) - self.remote_host = remote_host - self.job_id = job_id - self.private_key = private_key - - def url_open(self, request, data): - return urllib2.urlopen(request, data) - - def __build_url(self, command, args): - if self.private_key: - args["private_key"] = self.private_key - data = urllib.urlencode(args) - url = self.remote_host + command + "?" + data - return url - - def __raw_execute(self, command, args = {}, data = None): - url = self.__build_url(command, args) - request = urllib2.Request(url=url, data=data) - response = self.url_open(request, data) - return response - - def __raw_execute_and_parse(self, command, args = {}, data = None): - response = self.__raw_execute(command, args, data) - return simplejson.loads(response.read()) - - def __upload_file(self, action, path, contents = None): - """ """ - input = open(path, 'rb') - try: - mmapped_input = mmap.mmap(input.fileno(), 0, access = mmap.ACCESS_READ) - return self.__upload_contents(action, path, mmapped_input) - finally: - input.close() - - def __upload_contents(self, action, path, contents): - name = os.path.basename(path) - args = {"job_id" : self.job_id, "name" : name} - return self.__raw_execute_and_parse(action, args, contents) - - def upload_tool_file(self, path): - return self.__upload_file("upload_tool_file", path) - - def upload_input(self, path): - return self.__upload_file("upload_input", path) - - def upload_config_file(self, path, contents): - return self.__upload_contents("upload_config_file", path, contents) - - def download_output(self, path): - """ """ - name = os.path.basename(path) - response = self.__raw_execute('download_output', {'name' : name, - "job_id" : self.job_id}) - output = open(path, 'wb') - try: - while True: - buffer = response.read(1024) - if buffer == "": - break - output.write(buffer) - finally: - output.close() - - def launch(self, command_line): - """ """ - return self.__raw_execute("launch", {"command_line" : command_line, - "job_id" : self.job_id}) - - def kill(self): - return self.__raw_execute("kill", {"job_id" : self.job_id}) - - def wait(self): - """ """ - while True: - check_complete_response = self.__raw_execute_and_parse("check_complete", {"job_id" : self.job_id }) - complete = check_complete_response["complete"] == "true" - if complete: - return check_complete_response - time.sleep(1) - - def clean(self): - self.__raw_execute("clean", { "job_id" : self.job_id }) - - def setup(self): - return self.__raw_execute_and_parse("setup", { "job_id" : self.job_id }) - - - -class LwrJobRunner( BaseJobRunner ): - """ - Lwr Job Runner - """ - STOP_SIGNAL = object() - def __init__( self, app ): - """Start the job runner with 'nworkers' worker threads""" - self.app = app - self.sa_session = app.model.context - - # start workers - self.queue = Queue() - self.threads = [] - nworkers = app.config.local_job_queue_workers - log.info( "starting workers" ) - for i in range( nworkers ): - worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), target=self.run_next ) - worker.setDaemon( True ) - worker.start() - self.threads.append( worker ) - log.debug( "%d workers ready", nworkers ) - - def run_next( self ): - """Run the next job, waiting until one is available if neccesary""" - while 1: - job_wrapper = self.queue.get() - if job_wrapper is self.STOP_SIGNAL: - return - try: - self.run_job( job_wrapper ) - except: - log.exception( "Uncaught exception running job" ) - - def determine_lwr_url(self, url): - lwr_url = url[ len( 'lwr://' ) : ] - return lwr_url - - def get_client_from_wrapper(self, job_wrapper): - return self.get_client( job_wrapper.get_job_runner_url(), job_wrapper.job_id ) - - def get_client(self, job_runner, job_id): - lwr_url = self.determine_lwr_url( job_runner ) - return Client(lwr_url, job_id) - - def run_job( self, job_wrapper ): + def queue_job(self, job_wrapper): stderr = stdout = command_line = '' runner_url = job_wrapper.get_job_runner_url() @@ -265,47 +49,98 @@ try: job_wrapper.prepare() if hasattr(job_wrapper, 'prepare_input_files_cmds') and job_wrapper.prepare_input_files_cmds is not None: - for cmd in job_wrapper.prepare_input_file_cmds: # run the commands to stage the input files + for cmd in job_wrapper.prepare_input_files_cmds: # run the commands to stage the input files #log.debug( 'executing: %s' % cmd ) if 0 != os.system(cmd): raise Exception('Error running file staging command: %s' % cmd) job_wrapper.prepare_input_files_cmds = None # prevent them from being used in-line - command_line = self.build_command_line( job_wrapper, include_metadata=False ) + command_line = self.build_command_line( job_wrapper, include_metadata=False, include_work_dir_outputs=False ) except: job_wrapper.fail( "failure preparing job", exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) return # If we were able to get a command line, run the job - if command_line: - try: - #log.debug( 'executing: %s' % command_line ) - client = self.get_client_from_wrapper(job_wrapper) - output_fnames = job_wrapper.get_output_fnames() - output_files = [ str( o ) for o in output_fnames ] - input_files = job_wrapper.get_input_fnames() - file_stager = FileStager(client, command_line, job_wrapper.extra_filenames, input_files, output_files, job_wrapper.tool.tool_dir) - rebuilt_command_line = file_stager.get_rewritten_command_line() - client.launch( rebuilt_command_line ) + if not command_line: + job_wrapper.finish( '', '' ) + return - job_wrapper.set_runner( runner_url, job_wrapper.job_id ) - job_wrapper.change_state( model.Job.states.RUNNING ) + try: + #log.debug( 'executing: %s' % command_line ) + client = self.get_client_from_wrapper(job_wrapper) + output_files = self.get_output_files(job_wrapper) + input_files = job_wrapper.get_input_fnames() + working_directory = job_wrapper.working_directory + file_stager = FileStager(client, command_line, job_wrapper.extra_filenames, input_files, output_files, job_wrapper.tool.tool_dir, working_directory) + rebuilt_command_line = file_stager.get_rewritten_command_line() + job_id = file_stager.job_id + client.launch( rebuilt_command_line ) + job_wrapper.set_runner( runner_url, job_id ) + job_wrapper.change_state( model.Job.states.RUNNING ) - run_results = client.wait() - log.debug('run_results %s' % run_results ) - stdout = run_results['stdout'] - stderr = run_results['stderr'] + except Exception, exc: + job_wrapper.fail( "failure running job", exception=True ) + log.exception("failure running job %d" % job_wrapper.job_id) + return - - if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ]: - for output_file in output_files: - client.download_output(output_file) - client.clean() - log.debug('execution finished: %s' % command_line) - except Exception, exc: - job_wrapper.fail( "failure running job", exception=True ) - log.exception("failure running job %d" % job_wrapper.job_id) - return + lwr_job_state = ClusterJobState() + lwr_job_state.job_wrapper = job_wrapper + lwr_job_state.job_id = job_id + lwr_job_state.old_state = True + lwr_job_state.running = True + lwr_job_state.runner_url = runner_url + self.monitor_job(lwr_job_state) + + def get_output_files(self, job_wrapper): + output_fnames = job_wrapper.get_output_fnames() + return [ str( o ) for o in output_fnames ] + + + def determine_lwr_url(self, url): + lwr_url = url[ len( 'lwr://' ) : ] + return lwr_url + + def get_client_from_wrapper(self, job_wrapper): + job_id = job_wrapper.job_id + if hasattr(job_wrapper, 'task_id'): + job_id = "%s_%s" % (job_id, job_wrapper.task_id) + return self.get_client( job_wrapper.get_job_runner_url(), job_id ) + + def get_client_from_state(self, job_state): + job_runner = job_state.runner_url + job_id = job_state.job_id + return self.get_client(job_runner, job_id) + + def get_client(self, job_runner, job_id): + lwr_url = self.determine_lwr_url( job_runner ) + return Client(lwr_url, job_id) + + def finish_job( self, job_state ): + stderr = stdout = command_line = '' + job_wrapper = job_state.job_wrapper + try: + client = self.get_client_from_state(job_state) + + run_results = client.raw_check_complete() + log.debug('run_results %s' % run_results ) + stdout = run_results['stdout'] + stderr = run_results['stderr'] + + if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ]: + work_dir_outputs = self.get_work_dir_outputs(job_wrapper) + output_files = self.get_output_files(job_wrapper) + for source_file, output_file in work_dir_outputs: + client.download_work_dir_output(source_file, job_wrapper.working_directory, output_file) + # Remove from full output_files list so don't try to download directly. + output_files.remove(output_file) + for output_file in output_files: + client.download_output(output_file, working_directory=job_wrapper.working_directory) + client.clean() + log.debug('execution finished: %s' % command_line) + except Exception, exc: + job_wrapper.fail( "failure running job", exception=True ) + log.exception("failure running job %d" % job_wrapper.job_id) + return #run the metadata setting script here #this is terminate-able when output dataset/job is deleted #so that long running set_meta()s can be canceled without having to reboot the server @@ -321,7 +156,7 @@ job_wrapper.external_output_metadata.set_job_runner_external_pid( external_metadata_proc.pid, self.sa_session ) external_metadata_proc.wait() log.debug( 'execution of external set_meta finished for job %d' % job_wrapper.job_id ) - + # Finish the job try: job_wrapper.finish( stdout, stderr ) @@ -329,17 +164,19 @@ log.exception("Job wrapper finish method failed") job_wrapper.fail("Unable to finish job", exception=True) - def put( self, job_wrapper ): - """Add a job to the queue (by job identifier)""" - # Change to queued state before handing to worker thread so the runner won't pick it up again - job_wrapper.change_state( model.Job.states.QUEUED ) - self.queue.put( job_wrapper ) - + def fail_job( self, job_state ): + """ + Seperated out so we can use the worker threads for it. + """ + self.stop_job( self.sa_session.query( self.app.model.Job ).get( job_state.job_wrapper.job_id ) ) + job_state.job_wrapper.fail( job_state.fail_message ) + def shutdown( self ): """Attempts to gracefully shut down the worker threads""" log.info( "sending stop signal to worker threads" ) - for i in range( len( self.threads ) ): - self.queue.put( self.STOP_SIGNAL ) + self.monitor_queue.put( STOP_SIGNAL ) + for i in range( len( self.work_threads ) ): + self.work_queue.put( ( STOP_SIGNAL, None ) ) log.info( "local job runner stopped" ) def check_pid( self, pid ): @@ -355,8 +192,9 @@ def stop_job( self, job ): #if our local job has JobExternalOutputMetadata associated, then our primary job has to have already finished - if job.external_output_metadata: - pid = job.external_output_metadata[0].job_runner_external_pid #every JobExternalOutputMetadata has a pid set, we just need to take from one of them + job_ext_output_metadata = job.get_external_output_metadata() + if job_ext_output_metadata: + pid = job_ext_output_metadata[0].job_runner_external_pid #every JobExternalOutputMetadata has a pid set, we just need to take from one of them if pid in [ None, '' ]: log.warning( "stop_job(): %s: no PID in database for job, unable to stop" % job.id ) return @@ -383,7 +221,21 @@ log.debug("Attempt remote lwr kill of job with url %s and id %s" % (lwr_url, job_id)) client = self.get_client(lwr_url, job_id) client.kill() + + def recover( self, job, job_wrapper ): - # local jobs can't be recovered - job_wrapper.change_state( model.Job.states.ERROR, info = "This job was killed when Galaxy was restarted. Please retry the job." ) - + """Recovers jobs stuck in the queued/running state when Galaxy started""" + job_state = ClusterJobState() + job_state.job_id = str( job.get_job_runner_external_id() ) + job_state.runner_url = job_wrapper.get_job_runner_url() + job_wrapper.command_line = job.get_command_line() + job_state.job_wrapper = job_wrapper + if job.get_state() == model.Job.states.RUNNING: + log.debug( "(LWR/%s) is still in running state, adding to the LWR queue" % ( job.get_id()) ) + job_state.old_state = True + job_state.running = True + self.monitor_queue.put( job_state ) + elif job.get_state() == model.Job.states.QUEUED: + # LWR doesn't queue currently, so this indicates galaxy was shutoff while + # job was being staged. Not sure how to recover from that. + job_state.job_wrapper.fail( "This job was killed when Galaxy was restarted. Please retry the job." ) diff -r c2199c181f09fd5b94a9f5ea13fc39b28e803f2c -r e5ec6ed8f0337893cf4bc64e61089471b00b28b0 lib/galaxy/jobs/runners/lwr_client/__init__.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/__init__.py @@ -0,0 +1,501 @@ +""" +lwr_client +========== + +This module contains logic for interfacing with an external LWR server. + +""" +import mmap +import os +import re +import time +import urllib +import urllib2 + +import simplejson + + +class JobInputs(object): + """ + Abstractions over dynamic inputs created for a given job (namely the command to + execute and created configfiles). + + **Parameters** + + command_line : str + Local command to execute for this job. (To be rewritten.) + config_files : str + Config files created for this job. (To be rewritten.) + + + >>> import tempfile + >>> tf = tempfile.NamedTemporaryFile() + >>> def setup_inputs(tf): + ... open(tf.name, "w").write("world /path/to/input the rest") + ... inputs = JobInputs("hello /path/to/input", [tf.name]) + ... return inputs + >>> inputs = setup_inputs(tf) + >>> inputs.rewrite_paths("/path/to/input", 'C:\\input') + >>> inputs.rewritten_command_line + 'hello C:\\\\input' + >>> inputs.rewritten_config_files[tf.name] + 'world C:\\\\input the rest' + >>> tf.close() + >>> tf = tempfile.NamedTemporaryFile() + >>> inputs = setup_inputs(tf) + >>> inputs.find_referenced_subfiles('/path/to') + ['/path/to/input'] + >>> inputs.path_referenced('/path/to') + True + >>> inputs.path_referenced('/path/to/input') + True + >>> inputs.path_referenced('/path/to/notinput') + False + >>> tf.close() + """ + + def __init__(self, command_line, config_files): + self.rewritten_command_line = command_line + self.rewritten_config_files = {} + for config_file in config_files or []: + config_contents = _read(config_file) + self.rewritten_config_files[config_file] = config_contents + + def find_referenced_subfiles(self, directory): + """ + Return list of files below specified `directory` in job inputs. Could + use more sophisticated logic (match quotes to handle spaces, handle + subdirectories, etc...). + + **Parameters** + + directory : str + Full path to directory to search. + + """ + pattern = r"(%s%s\S+)" % (directory, os.sep) + referenced_files = set() + for input_contents in self.__items(): + referenced_files.update(re.findall(pattern, input_contents)) + return list(referenced_files) + + def path_referenced(self, path): + pattern = r"%s" % path + found = False + for input_contents in self.__items(): + if re.findall(pattern, input_contents): + found = True + break + return found + + def rewrite_paths(self, local_path, remote_path): + """ + Rewrite references to `local_path` with `remote_path` in job inputs. + """ + self.__rewrite_command_line(local_path, remote_path) + self.__rewrite_config_files(local_path, remote_path) + + def __rewrite_command_line(self, local_path, remote_path): + self.rewritten_command_line = self.rewritten_command_line.replace(local_path, remote_path) + + def __rewrite_config_files(self, local_path, remote_path): + for config_file, rewritten_contents in self.rewritten_config_files.iteritems(): + self.rewritten_config_files[config_file] = rewritten_contents.replace(local_path, remote_path) + + def __items(self): + items = [self.rewritten_command_line] + items.extend(self.rewritten_config_files.values()) + return items + + +class FileStager(object): + """ + Objects of the FileStager class interact with an LWR client object to + stage the files required to run jobs on a remote LWR server. + + **Parameters** + + client : Client + LWR client object. + command_line : str + The local command line to execute, this will be rewritten for the remote server. + config_files : list + List of Galaxy 'configfile's produced for this job. These will be rewritten and sent to remote server. + input_files : list + List of input files used by job. These will be transferred and references rewritten. + output_files : list + List of output_files produced by job. + tool_dir : str + Directory containing tool to execute (if a wrapper is used, it will be transferred to remote server). + working_directory : str + Local path created by Galaxy for running this job. + + """ + + def __init__(self, client, command_line, config_files, input_files, output_files, tool_dir, working_directory): + """ + """ + self.client = client + self.command_line = command_line + self.config_files = config_files + self.input_files = input_files + self.output_files = output_files + self.tool_dir = os.path.abspath(tool_dir) + self.working_directory = working_directory + + # Setup job inputs, these will need to be rewritten before + # shipping off to remote LWR server. + self.job_inputs = JobInputs(self.command_line, self.config_files) + + self.file_renames = {} + + self.__handle_setup() + self.__initialize_referenced_tool_files() + self.__upload_tool_files() + self.__upload_input_files() + self.__upload_working_directory_files() + self.__initialize_output_file_renames() + self.__initialize_task_output_file_renames() + self.__initialize_config_file_renames() + self.__handle_rewrites() + self.__upload_rewritten_config_files() + + def __handle_setup(self): + job_config = self.client.setup() + + self.new_working_directory = job_config['working_directory'] + self.new_outputs_directory = job_config['outputs_directory'] + self.remote_path_separator = job_config['path_separator'] + # If remote LWR server assigned job id, use that otherwise + # just use local job_id assigned. + galaxy_job_id = self.client.job_id + self.job_id = job_config.get('job_id', galaxy_job_id) + if self.job_id != galaxy_job_id: + # Remote LWR server assigned an id different than the + # Galaxy job id, update client to reflect this. + self.client.job_id = self.job_id + + def __initialize_referenced_tool_files(self): + self.referenced_tool_files = self.job_inputs.find_referenced_subfiles(self.tool_dir) + + def __upload_tool_files(self): + for referenced_tool_file in self.referenced_tool_files: + tool_upload_response = self.client.upload_tool_file(referenced_tool_file) + self.file_renames[referenced_tool_file] = tool_upload_response['path'] + + def __upload_input_files(self): + for input_file in self.input_files: + self.__upload_input_file(input_file) + self.__upload_input_extra_files(input_file) + + def __upload_input_file(self, input_file): + if self.job_inputs.path_referenced(input_file): + input_upload_response = self.client.upload_input(input_file) + self.file_renames[input_file] = input_upload_response['path'] + + def __upload_input_extra_files(self, input_file): + # TODO: Determine if this is object store safe and what needs to be + # done if it is not. + files_path = "%s_files" % input_file[0:-len(".dat")] + if os.path.exists(files_path) and self.job_inputs.path_referenced(files_path): + for extra_file in os.listdir(files_path): + extra_file_path = os.path.join(files_path, extra_file) + relative_path = os.path.basename(files_path) + extra_file_relative_path = os.path.join(relative_path, extra_file) + response = self.client.upload_extra_input(extra_file_path, extra_file_relative_path) + self.file_renames[extra_file_path] = response['path'] + + def __upload_working_directory_files(self): + # Task manager stages files into working directory, these need to be + # uploaded if present. + for working_directory_file in os.listdir(self.working_directory): + path = os.path.join(self.working_directory, working_directory_file) + working_file_response = self.client.upload_working_directory_file(path) + self.file_renames[path] = working_file_response['path'] + + def __initialize_output_file_renames(self): + for output_file in self.output_files: + self.file_renames[output_file] = r'%s%s%s' % (self.new_outputs_directory, + self.remote_path_separator, + os.path.basename(output_file)) + + def __initialize_task_output_file_renames(self): + for output_file in self.output_files: + name = os.path.basename(output_file) + self.file_renames[os.path.join(self.working_directory, name)] = r'%s%s%s' % (self.new_working_directory, + self.remote_path_separator, + name) + + def __initialize_config_file_renames(self): + for config_file in self.config_files: + self.file_renames[config_file] = r'%s%s%s' % (self.new_working_directory, + self.remote_path_separator, + os.path.basename(config_file)) + + def __rewrite_paths(self, contents): + new_contents = contents + for local_path, remote_path in self.file_renames.iteritems(): + new_contents = new_contents.replace(local_path, remote_path) + return new_contents + + def __handle_rewrites(self): + for local_path, remote_path in self.file_renames.iteritems(): + self.job_inputs.rewrite_paths(local_path, remote_path) + + def __upload_rewritten_config_files(self): + for config_file, new_config_contents in self.job_inputs.rewritten_config_files.iteritems(): + self.client.upload_config_file(config_file, new_config_contents) + + def get_rewritten_command_line(self): + """ + Returns the rewritten version of the command line to execute suitable + for remote host. + """ + return self.job_inputs.rewritten_command_line + + +class Client(object): + """ + Objects of this client class perform low-level communication with a remote LWR server. + + **Parameters** + + remote_host : str + Remote URL of the LWR server. + job_id : str + Galaxy job/task id. + private_key : str (optional) + Secret key the remote LWR server is configured with. + """ + + def __init__(self, remote_host, job_id, private_key=None): + if not remote_host.endswith("/"): + remote_host = remote_host + "/" + ## If we don't have an explicit private_key defined, check for + ## one embedded in the URL. A URL of the form + ## https://moo@cow:8913 will try to contact https://cow:8913 + ## with a private key of moo + private_key_format = "https?://(.*)@.*/?" + private_key_match = re.match(private_key_format, remote_host) + if not private_key and private_key_match: + private_key = private_key_match.group(1) + remote_host = remote_host.replace("%s@" % private_key, '', 1) + self.remote_host = remote_host + self.job_id = job_id + self.private_key = private_key + + def _url_open(self, request, data): + return urllib2.urlopen(request, data) + + def __build_url(self, command, args): + if self.private_key: + args["private_key"] = self.private_key + data = urllib.urlencode(args) + url = self.remote_host + command + "?" + data + return url + + def __raw_execute(self, command, args={}, data=None): + url = self.__build_url(command, args) + request = urllib2.Request(url=url, data=data) + response = self._url_open(request, data) + return response + + def __raw_execute_and_parse(self, command, args={}, data=None): + response = self.__raw_execute(command, args, data) + return simplejson.loads(response.read()) + + def __upload_file(self, action, path, name=None, contents=None): + input = open(path, 'rb') + try: + mmapped_input = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ) + return self.__upload_contents(action, path, mmapped_input, name) + finally: + input.close() + + def __upload_contents(self, action, path, contents, name=None): + if not name: + name = os.path.basename(path) + args = {"job_id": self.job_id, "name": name} + return self.__raw_execute_and_parse(action, args, contents) + + def upload_tool_file(self, path): + """ + Upload a tool related file (e.g. wrapper) required to run job. + + **Parameters** + + path : str + Local path tool. + """ + return self.__upload_file("upload_tool_file", path) + + def upload_input(self, path): + """ + Upload input dataset to remote server. + + **Parameters** + + path : str + Local path of input dataset. + """ + return self.__upload_file("upload_input", path) + + def upload_extra_input(self, path, relative_name): + """ + Upload extra input file to remote server. + + **Parameters** + + path : str + Extra files path of input dataset corresponding to this input. + relative_name : str + Relative path of extra file to upload relative to inputs extra files path. + """ + return self.__upload_file("upload_extra_input", path, name=relative_name) + + def upload_config_file(self, path, contents): + """ + Upload a job's config file to the remote server. + + **Parameters** + + path : str + Local path to the original config file. + contents : str + Rewritten contents of the config file to upload. + """ + return self.__upload_contents("upload_config_file", path, contents) + + def upload_working_directory_file(self, path): + """ + Upload the supplied file (path) from a job's working directory + to remote server. + + **Parameters** + + path : str + Path to file to upload. + """ + return self.__upload_file("upload_working_directory_file", path) + + def _get_output_type(self, name): + return self.__raw_execute_and_parse("get_output_type", {"name": name, + "job_id": self.job_id}) + + def download_work_dir_output(self, source, working_directory, output_path): + """ + Download an output dataset specified with from_work_dir from the + remote server. + + **Parameters** + + source : str + Path in job's working_directory to find output in. + working_directory : str + Local working_directory for the job. + output_path : str + Full path to output dataset. + """ + output = open(output_path, "wb") + name = os.path.basename(source) + self.__raw_download_output(name, self.job_id, "work_dir", output) + + def download_output(self, path, working_directory): + """ + Download an output dataset from the remote server. + + **Parameters** + + path : str + Local path of the dataset. + working_directory : str + Local working_directory for the job. + """ + name = os.path.basename(path) + output_type = self._get_output_type(name) + if output_type == "direct": + output = open(path, "wb") + elif output_type == "task": + output = open(os.path.join(working_directory, name), "wb") + else: + raise Exception("No remote output found for dataset with path %s" % path) + self.__raw_download_output(name, self.job_id, output_type, output) + + def __raw_download_output(self, name, job_id, output_type, output_file): + response = self.__raw_execute("download_output", {"name": name, + "job_id": self.job_id, + "output_type": output_type}) + try: + while True: + buffer = response.read(1024) + if buffer == "": + break + output_file.write(buffer) + finally: + output_file.close() + + def launch(self, command_line): + """ + Run or queue up the execution of the supplied + `command_line` on the remote server. + + **Parameters** + + command_line : str + Command to execute. + """ + return self.__raw_execute("launch", {"command_line": command_line, + "job_id": self.job_id}) + + def kill(self): + """ + Cancel remote job, either removing from the queue or killing it. + """ + return self.__raw_execute("kill", {"job_id": self.job_id}) + + def wait(self): + """ + Wait for job to finish. + """ + while True: + complete_response = self.raw_check_complete() + if complete_response["complete"] == "true": + return complete_response + time.sleep(1) + + def raw_check_complete(self): + """ + Get check_complete response from the remote server. + """ + check_complete_response = self.__raw_execute_and_parse("check_complete", {"job_id": self.job_id}) + return check_complete_response + + def check_complete(self): + """ + Return boolean indicating whether the job is complete. + """ + return self.raw_check_complete()["complete"] == "true" + + def clean(self): + """ + Cleanup the remote job. + """ + self.__raw_execute("clean", {"job_id": self.job_id}) + + def setup(self): + """ + Setup remote LWR server to run this job. + """ + return self.__raw_execute_and_parse("setup", {"job_id": self.job_id}) + + +def _read(path): + """ + Utility method to quickly read small files (config files and tool + wrappers) into memory as strings. + """ + input = open(path, "r") + try: + return input.read() + finally: + input.close() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Change variable names to avoid conflict with built-in functions.
by Bitbucket 11 Jan '13

11 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c2199c181f09/ changeset: c2199c181f09 user: jgoecks date: 2013-01-11 18:16:44 summary: Change variable names to avoid conflict with built-in functions. affected #: 1 file diff -r 3faa833c15b5162db69f061bdbd4e951ba2ffdc7 -r c2199c181f09fd5b94a9f5ea13fc39b28e803f2c lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -1062,8 +1062,8 @@ summary = _summarize_bbi( bbi, chrom, start, end, 1 ) f.close() - min = 0 - max = 0 + min_val = 0 + max_val = 0 mean = 0 sd = 0 if summary is not None: @@ -1077,10 +1077,10 @@ if valid_count > 1: var /= valid_count - 1 sd = numpy.sqrt( var ) - min = summary.min_val[0] - max = summary.max_val[0] + min_val = summary.min_val[0] + max_val = summary.max_val[0] - return dict( data=dict( min=min, max=max, mean=mean, sd=sd ) ) + return dict( data=dict( min=min_val, max=max_val, mean=mean, sd=sd ) ) def summarize_region( bbi, chrom, start, end, num_points ): ''' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Begin to reintroduce the ability to install multiple tool shed repositories into Galaxy simultaneously.
by Bitbucket 11 Jan '13

11 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3faa833c15b5/ changeset: 3faa833c15b5 user: greg date: 2013-01-11 17:47:59 summary: Begin to reintroduce the ability to install multiple tool shed repositories into Galaxy simultaneously. affected #: 16 files diff -r 753130def2f89698bb95a554ce76c7ea8c5102d7 -r 3faa833c15b5162db69f061bdbd4e951ba2ffdc7 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -584,6 +584,68 @@ if converter_path and display_path: break return converter_path, display_path +def get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ): + """ + Return dictionaries containing the sets of installed and missing tool dependencies and repository dependencies associated with the repository defined + by the received repo_info_dict. + """ + name = repo_info_dict.keys()[ 0 ] + repo_info_tuple = repo_info_dict[ name ] + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td = \ + suc.get_repo_info_tuple_contents( repo_info_tuple ) + if repository_dependencies: + missing_td = {} + # Handle the scenario where a repository was installed, then uninstalled and an error occurred during the reinstallation process. + # In this case, a record for the repository will exist in the database with the status of 'New'. + repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed_url, name, repository_owner, changeset_revision ) + if repository and repository.metadata: + installed_rd, missing_rd = \ + get_installed_and_missing_repository_dependencies( trans, repository ) + else: + installed_rd, missing_rd = \ + get_installed_and_missing_repository_dependencies_for_new_install( trans, repository_dependencies ) + # Discover all repository dependencies and retrieve information for installing them. + required_repo_info_dicts = get_required_repo_info_dicts( tool_shed_url, util.listify( repo_info_dict ) ) + # Display tool dependencies defined for each of the repository dependencies. + if required_repo_info_dicts: + all_tool_dependencies = {} + for rid in required_repo_info_dicts: + for name, repo_info_tuple in rid.items(): + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, rid_installed_td = \ + suc.get_repo_info_tuple_contents( repo_info_tuple ) + if rid_installed_td: + for td_key, td_dict in rid_installed_td.items(): + if td_key not in all_tool_dependencies: + all_tool_dependencies[ td_key ] = td_dict + if all_tool_dependencies: + if installed_td is None: + installed_td = {} + else: + # Move all tool dependencies to the missing_tool_dependencies container. + for td_key, td_dict in installed_td.items(): + if td_key not in missing_td: + missing_td[ td_key ] = td_dict + installed_td = {} + # Discover and categorize all tool dependencies defined for this repository's repository dependencies. + required_tool_dependencies, required_missing_tool_dependencies = \ + get_installed_and_missing_tool_dependencies_for_new_install( trans, all_tool_dependencies ) + if required_tool_dependencies: + if not includes_tool_dependencies: + includes_tool_dependencies = True + for td_key, td_dict in required_tool_dependencies.items(): + if td_key not in installed_td: + installed_td[ td_key ] = td_dict + if required_missing_tool_dependencies: + if not includes_tool_dependencies: + includes_tool_dependencies = True + for td_key, td_dict in required_missing_tool_dependencies.items(): + if td_key not in missing_td: + missing_td[ td_key ] = td_dict + else: + installed_rd = None + missing_rd = None + missing_td = None + return name, repository_owner, changeset_revision, includes_tool_dependencies, installed_rd, missing_rd, installed_td, missing_td def get_headers( fname, sep, count=60, is_multi_byte=False ): """Returns a list with the first 'count' lines split by 'sep'.""" headers = [] @@ -689,7 +751,11 @@ if tool_dependency: td_info_dict[ 'repository_id' ] = repository.id td_info_dict[ 'tool_dependency_id' ] = tool_dependency.id - td_info_dict[ 'status' ] = str( tool_dependency.status ) + if tool_dependency.status: + tool_dependency_status = str( tool_dependency.status ) + else: + tool_dependency_status = 'Never installed' + td_info_dict[ 'status' ] = tool_dependency_status val[ index ] = td_info_dict if tool_dependency.status == trans.model.ToolDependency.installation_status.INSTALLED: tool_dependencies[ td_key ] = val @@ -703,7 +769,11 @@ if tool_dependency: val[ 'repository_id' ] = repository.id val[ 'tool_dependency_id' ] = tool_dependency.id - val[ 'status' ] = str( tool_dependency.status ) + if tool_dependency.status: + tool_dependency_status = str( tool_dependency.status ) + else: + tool_dependency_status = 'Never installed' + val[ 'status' ] = tool_dependency_status if tool_dependency.status == trans.model.ToolDependency.installation_status.INSTALLED: tool_dependencies[ td_key ] = val else: @@ -728,18 +798,8 @@ tool_dependencies = None missing_tool_dependencies = None return tool_dependencies, missing_tool_dependencies -def get_repository_owner( cleaned_repository_url ): - items = cleaned_repository_url.split( 'repos' ) - repo_path = items[ 1 ] - if repo_path.startswith( '/' ): - repo_path = repo_path.replace( '/', '', 1 ) - return repo_path.lstrip( '/' ).split( '/' )[ 0 ] -def get_repository_owner_from_clone_url( repository_clone_url ): - tmp_url = suc.clean_repository_clone_url( repository_clone_url ) - tool_shed = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' ) - return get_repository_owner( tmp_url ) -def get_repository_readme_and_dependencies_for_display( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ): - # If we're installing a single repository, see if it contains a readme or dependencies that we can display. +def get_readme_files_dict_for_display( trans, tool_shed_url, repo_info_dict ): + """Return a dictionary of README files contained in the single repository being installed so they can be displayed on the tool panel section selection page.""" name = repo_info_dict.keys()[ 0 ] repo_info_tuple = repo_info_dict[ name ] description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td = \ @@ -752,59 +812,17 @@ raw_text = response.read() response.close() readme_files_dict = json.from_json_string( raw_text ) - if repository_dependencies: - missing_td = {} - # Handle the scenario where a repository was installed, then uninstalled and an error occurred during the reinstallation process. - # In this case, a record for the repository will exist in the database with the status of 'New'. - repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed_url, name, repository_owner, changeset_revision ) - if repository and repository.metadata: - installed_rd, missing_rd = \ - get_installed_and_missing_repository_dependencies( trans, repository ) - else: - installed_rd, missing_rd = \ - get_installed_and_missing_repository_dependencies_for_new_install( trans, repository_dependencies ) - # Discover all repository dependencies and retrieve information for installing them. - required_repo_info_dicts = get_required_repo_info_dicts( tool_shed_url, util.listify( repo_info_dict ) ) - # Display tool dependencies defined for each of the repository dependencies. - if required_repo_info_dicts: - all_tool_dependencies = {} - for rid in required_repo_info_dicts: - for name, repo_info_tuple in rid.items(): - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, rid_installed_td = \ - suc.get_repo_info_tuple_contents( repo_info_tuple ) - if rid_installed_td: - for td_key, td_dict in rid_installed_td.items(): - if td_key not in all_tool_dependencies: - all_tool_dependencies[ td_key ] = td_dict - if all_tool_dependencies: - if installed_td is None: - installed_td = {} - else: - # Move all tool dependencies to the missing_tool_dependencies container. - for td_key, td_dict in installed_td.items(): - if td_key not in missing_td: - missing_td[ td_key ] = td_dict - installed_td = {} - # Discover and categorize all tool dependencies defined for this repository's repository dependencies. - required_tool_dependencies, required_missing_tool_dependencies = \ - get_installed_and_missing_tool_dependencies_for_new_install( trans, all_tool_dependencies ) - if required_tool_dependencies: - if not includes_tool_dependencies: - includes_tool_dependencies = True - for td_key, td_dict in required_tool_dependencies.items(): - if td_key not in installed_td: - installed_td[ td_key ] = td_dict - if required_missing_tool_dependencies: - if not includes_tool_dependencies: - includes_tool_dependencies = True - for td_key, td_dict in required_missing_tool_dependencies.items(): - if td_key not in missing_td: - missing_td[ td_key ] = td_dict - else: - installed_rd = None - missing_rd = None - missing_td = None - return name, repository_owner, changeset_revision, readme_files_dict, includes_tool_dependencies, installed_rd, missing_rd, installed_td, missing_td + return readme_files_dict +def get_repository_owner( cleaned_repository_url ): + items = cleaned_repository_url.split( 'repos' ) + repo_path = items[ 1 ] + if repo_path.startswith( '/' ): + repo_path = repo_path.replace( '/', '', 1 ) + return repo_path.lstrip( '/' ).split( '/' )[ 0 ] +def get_repository_owner_from_clone_url( repository_clone_url ): + tmp_url = suc.clean_repository_clone_url( repository_clone_url ) + tool_shed = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' ) + return get_repository_owner( tmp_url ) def get_required_repo_info_dicts( tool_shed_url, repo_info_dicts ): """ Inspect the list of repo_info_dicts for repository dependencies and append a repo_info_dict for each of them to the list. All @@ -1220,46 +1238,17 @@ installed_repository_dependencies, missing_repository_dependencies = get_installed_and_missing_repository_dependencies( trans, repository ) # Handle the current repository's tool dependencies. repository_tool_dependencies = metadata.get( 'tool_dependencies', None ) - repository_installed_tool_dependencies, repository_missing_tool_dependencies = \ - get_installed_and_missing_tool_dependencies( trans, repository, repository_tool_dependencies ) + repository_installed_tool_dependencies, repository_missing_tool_dependencies = get_installed_and_missing_tool_dependencies( trans, + repository, + repository_tool_dependencies ) if reinstalling: - installed_tool_dependencies = None - missing_tool_dependencies = None - if repository_installed_tool_dependencies is None: - repository_installed_tool_dependencies = {} - if repository_missing_tool_dependencies is None: - repository_missing_tool_dependencies = {} - if required_repo_info_dicts: - # Handle the tool dependencies defined for each of the repository's repository dependencies. - for rid in required_repo_info_dicts: - for name, repo_info_tuple in rid.items(): - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ - suc.get_repo_info_tuple_contents( repo_info_tuple ) - if tool_dependencies: - tool_shed = suc.get_tool_shed_from_clone_url( repository_clone_url ) - required_repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed, name, repository_owner, changeset_revision ) - if not required_repository: - # The required_repository may have been installed with a different changeset revision. - required_repository, installed_changeset_revision = repository_was_previously_installed( trans, - tool_shed_url, - name, - repo_info_tuple, - clone_dir ) - if required_repository: - required_repository_installed_tool_dependencies, required_repository_missing_tool_dependencies = \ - get_installed_and_missing_tool_dependencies( trans, required_repository, tool_dependencies ) - if required_repository_installed_tool_dependencies: - for td_key, td_dict in required_repository_installed_tool_dependencies.items(): - if td_key not in repository_installed_tool_dependencies: - repository_installed_tool_dependencies[ td_key ] = td_dict - if required_repository_missing_tool_dependencies: - for td_key, td_dict in required_repository_missing_tool_dependencies.items(): - if td_key not in repository_missing_tool_dependencies: - repository_missing_tool_dependencies[ td_key ] = td_dict - if repository_installed_tool_dependencies: - installed_tool_dependencies = repository_installed_tool_dependencies - if repository_missing_tool_dependencies: - missing_tool_dependencies = repository_missing_tool_dependencies + installed_tool_dependencies, missing_tool_dependencies = \ + populate_tool_dependencies_dicts( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + repository_installed_tool_dependencies=repository_installed_tool_dependencies, + repository_missing_tool_dependencies=repository_missing_tool_dependencies, + required_repo_info_dicts=required_repo_info_dicts ) else: installed_tool_dependencies = repository_installed_tool_dependencies missing_tool_dependencies = repository_missing_tool_dependencies @@ -1268,10 +1257,6 @@ # Handle workflows. workflows = metadata.get( 'workflows', None ) containers_dict = suc.build_repository_containers_for_galaxy( trans=trans, - toolshed_base_url=tool_shed_url, - repository_name=repository.name, - repository_owner=repository.owner, - changeset_revision=repository.installed_changeset_revision, repository=repository, datatypes=datatypes, invalid_tools=invalid_tools, @@ -1293,6 +1278,95 @@ valid_tools=None, workflows=None ) return containers_dict +def populate_containers_dict_for_new_install( trans, tool_shed_url, tool_path, readme_files_dict, installed_repository_dependencies, missing_repository_dependencies, + installed_tool_dependencies, missing_tool_dependencies ): + """Return the populated containers for a repository being installed for the first time.""" + installed_tool_dependencies, missing_tool_dependencies = populate_tool_dependencies_dicts( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + repository_installed_tool_dependencies=installed_tool_dependencies, + repository_missing_tool_dependencies=missing_tool_dependencies, + required_repo_info_dicts=None ) + # Since we are installing a new repository, most of the repository contents are set to None since we don't yet know what they are. + containers_dict = suc.build_repository_containers_for_galaxy( trans=trans, + repository=None, + datatypes=None, + invalid_tools=None, + missing_repository_dependencies=missing_repository_dependencies, + missing_tool_dependencies=missing_tool_dependencies, + readme_files_dict=readme_files_dict, + repository_dependencies=installed_repository_dependencies, + tool_dependencies=installed_tool_dependencies, + valid_tools=None, + workflows=None, + new_install=True, + reinstalling=False ) + # Merge the missing_repository_dependencies container contents to the installed_repository_dependencies container. + containers_dict = suc.merge_missing_repository_dependencies_to_installed_container( containers_dict ) + # Merge the missing_tool_dependencies container contents to the installed_tool_dependencies container. + containers_dict = suc.merge_missing_tool_dependencies_to_installed_container( containers_dict ) + return containers_dict +def populate_tool_dependencies_dicts( trans, tool_shed_url, tool_path, repository_installed_tool_dependencies, repository_missing_tool_dependencies, + required_repo_info_dicts ): + """ + Return the populated installed_tool_dependencies and missing_tool_dependencies dictionaries for all repositories defined by entries in the received + required_repo_info_dicts. + """ + installed_tool_dependencies = None + missing_tool_dependencies = None + if repository_installed_tool_dependencies is None: + repository_installed_tool_dependencies = {} + else: + # Add the install_dir attribute to the tool_dependencies. + repository_installed_tool_dependencies = suc.add_installation_directories_to_tool_dependencies( trans=trans, + tool_dependencies=repository_installed_tool_dependencies ) + if repository_missing_tool_dependencies is None: + repository_missing_tool_dependencies = {} + else: + # Add the install_dir attribute to the tool_dependencies. + repository_missing_tool_dependencies = suc.add_installation_directories_to_tool_dependencies( trans=trans, + tool_dependencies=repository_missing_tool_dependencies ) + if required_repo_info_dicts: + # Handle the tool dependencies defined for each of the repository's repository dependencies. + for rid in required_repo_info_dicts: + for name, repo_info_tuple in rid.items(): + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tuple ) + if tool_dependencies: + clone_dir = os.path.join( tool_path, generate_tool_path( repository_clone_url, changeset_revision ) ) + # Add the install_dir attribute to the tool_dependencies. + tool_dependencies = suc.add_installation_directories_to_tool_dependencies( trans=trans, + tool_dependencies=tool_dependencies ) + # The required_repository may have been installed with a different changeset revision. + required_repository, installed_changeset_revision = repository_was_previously_installed( trans, + tool_shed_url, + name, + repo_info_tuple, + clone_dir ) + if required_repository: + required_repository_installed_tool_dependencies, required_repository_missing_tool_dependencies = \ + get_installed_and_missing_tool_dependencies( trans, required_repository, tool_dependencies ) + if required_repository_installed_tool_dependencies: + # Add the install_dir attribute to the tool_dependencies. + required_repository_installed_tool_dependencies = \ + suc.add_installation_directories_to_tool_dependencies( trans=trans, + tool_dependencies=required_repository_installed_tool_dependencies ) + for td_key, td_dict in required_repository_installed_tool_dependencies.items(): + if td_key not in repository_installed_tool_dependencies: + repository_installed_tool_dependencies[ td_key ] = td_dict + if required_repository_missing_tool_dependencies: + # Add the install_dir attribute to the tool_dependencies. + required_repository_missing_tool_dependencies = \ + suc.add_installation_directories_to_tool_dependencies( trans=trans, + tool_dependencies=required_repository_missing_tool_dependencies ) + for td_key, td_dict in required_repository_missing_tool_dependencies.items(): + if td_key not in repository_missing_tool_dependencies: + repository_missing_tool_dependencies[ td_key ] = td_dict + if repository_installed_tool_dependencies: + installed_tool_dependencies = repository_installed_tool_dependencies + if repository_missing_tool_dependencies: + missing_tool_dependencies = repository_missing_tool_dependencies + return installed_tool_dependencies, missing_tool_dependencies def pull_repository( repo, repository_clone_url, ctx_rev ): """Pull changes from a remote repository to a local one.""" commands.pull( suc.get_configured_ui(), repo, source=repository_clone_url, rev=[ ctx_rev ] ) diff -r 753130def2f89698bb95a554ce76c7ea8c5102d7 -r 3faa833c15b5162db69f061bdbd4e951ba2ffdc7 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -38,9 +38,17 @@ TOOL_SHED_ADMIN_CONTROLLER = 'TOOL_SHED_ADMIN_CONTROLLER' VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" ) -def add_installation_directories_to_tool_dependencies( trans, repository_name, repository_owner, changeset_revision, tool_dependencies ): +def add_installation_directories_to_tool_dependencies( trans, tool_dependencies ): + """ + Determine the path to the installation directory for each of the received tool dependencies. This path will be displayed within the tool dependencies + container on the select_tool_panel_section or reselect_tool_panel_section pages when installing or reinstalling repositories that contain tools with the + defined tool dependencies. The list of tool dependencies may be associated with more than a single repository. + """ for dependency_key, requirements_dict in tool_dependencies.items(): if dependency_key not in [ 'set_environment' ]: + repository_name = requirements_dict[ 'repository_name' ] + repository_owner = requirements_dict[ 'repository_owner' ] + changeset_revision = requirements_dict[ 'changeset_revision' ] dependency_name = requirements_dict[ 'name' ] version = requirements_dict[ 'version' ] type = requirements_dict[ 'type' ] @@ -76,9 +84,9 @@ except Exception, e: log.debug( "Error reading README file '%s' defined in metadata: %s" % ( str( relative_path_to_readme_file ), str( e ) ) ) return readme_files_dict -def build_repository_containers_for_galaxy( trans, toolshed_base_url, repository_name, repository_owner, changeset_revision, repository, datatypes, - invalid_tools, missing_repository_dependencies, missing_tool_dependencies, readme_files_dict, - repository_dependencies, tool_dependencies, valid_tools, workflows, new_install=False, reinstalling=False ): +def build_repository_containers_for_galaxy( trans, repository, datatypes, invalid_tools, missing_repository_dependencies, missing_tool_dependencies, + readme_files_dict, repository_dependencies, tool_dependencies, valid_tools, workflows, new_install=False, + reinstalling=False ): """Return a dictionary of containers for the received repository's dependencies and readme files for display during installation to Galaxy.""" containers_dict = dict( datatypes=None, invalid_tools=None, @@ -93,17 +101,12 @@ # id. However we need to be careful because sometimes the repository object is None. if repository: repository_id = repository.id + changeset_revision = repository.changeset_revision else: repository_id = None + changeset_revision = None lock = threading.Lock() lock.acquire( True ) - if tool_dependencies: - # Add the install_dir attribute to the tool_dependencies. - tool_dependencies = add_installation_directories_to_tool_dependencies( trans, - repository_name, - repository_owner, - changeset_revision, - tool_dependencies ) try: folder_id = 0 # Datatypes container. @@ -126,10 +129,6 @@ # Installed repository dependencies container. if repository_dependencies: folder_id, repository_dependencies_root_folder = container_util.build_repository_dependencies_folder( trans=trans, - toolshed_base_url=toolshed_base_url, - repository_name=repository_name, - repository_owner=repository_owner, - changeset_revision=changeset_revision, folder_id=folder_id, repository_dependencies=repository_dependencies, label='Installed repository dependencies', @@ -139,10 +138,6 @@ if missing_repository_dependencies: folder_id, missing_repository_dependencies_root_folder = \ container_util.build_repository_dependencies_folder( trans=trans, - toolshed_base_url=toolshed_base_url, - repository_name=repository_name, - repository_owner=repository_owner, - changeset_revision=changeset_revision, folder_id=folder_id, repository_dependencies=missing_repository_dependencies, label='Missing repository dependencies', @@ -236,12 +231,7 @@ folder_id, readme_files_root_folder = container_util.build_readme_files_folder( trans, folder_id, readme_files_dict ) containers_dict[ 'readme_files' ] = readme_files_root_folder # Repository dependencies container. - toolshed_base_url = str( url_for( '/', qualified=True ) ).rstrip( '/' ) folder_id, repository_dependencies_root_folder = container_util.build_repository_dependencies_folder( trans=trans, - toolshed_base_url=toolshed_base_url, - repository_name=repository.name, - repository_owner=repository.user.username, - changeset_revision=changeset_revision, folder_id=folder_id, repository_dependencies=repository_dependencies, label='Repository dependencies', @@ -816,6 +806,27 @@ all_repository_dependencies=None, handled_key_rd_dicts=None, circular_repository_dependencies=None ) + if metadata: + tool_dependencies = metadata.get( 'tool_dependencies', None ) + if tool_dependencies: + new_tool_dependencies = {} + for dependency_key, requirements_dict in tool_dependencies.items(): + if dependency_key in [ 'set_environment' ]: + new_set_environment_dict_list = [] + for set_environment_dict in requirements_dict: + set_environment_dict[ 'repository_name' ] = repository_name + set_environment_dict[ 'repository_owner' ] = repository_owner + set_environment_dict[ 'changeset_revision' ] = changeset_revision + new_set_environment_dict_list.append( set_environment_dict ) + new_tool_dependencies[ dependency_key ] = new_set_environment_dict_list + else: + requirements_dict[ 'repository_name' ] = repository_name + requirements_dict[ 'repository_owner' ] = repository_owner + requirements_dict[ 'changeset_revision' ] = changeset_revision + new_tool_dependencies[ dependency_key ] = requirements_dict + tool_dependencies = new_tool_dependencies + else: + tool_dependencies = None # Cast unicode to string. repo_info_dict[ str( repository.name ) ] = ( str( repository.description ), str( repository_clone_url ), @@ -823,7 +834,7 @@ str( ctx_rev ), str( repository_owner ), repository_dependencies, - metadata.get( 'tool_dependencies', None ) ) + tool_dependencies ) return repo_info_dict def ensure_required_repositories_exist_for_reinstall( trans, repository_dependencies ): """ @@ -1900,14 +1911,12 @@ for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs: config_filename = shed_tool_conf_dict[ 'config_filename' ] if config_filename == shed_tool_conf: - tool_path = shed_tool_conf_dict[ 'tool_path' ] - break + return shed_tool_conf_dict[ 'tool_path' ] else: file_name = strip_path( config_filename ) if file_name == shed_tool_conf: - tool_path = shed_tool_conf_dict[ 'tool_path' ] - break - return tool_path + return shed_tool_conf_dict[ 'tool_path' ] + return None def get_tool_shed_repository_by_id( trans, repository_id ): return trans.sa_session.query( trans.model.ToolShedRepository ) \ .filter( trans.model.ToolShedRepository.table.c.id == trans.security.decode_id( repository_id ) ) \ @@ -2308,6 +2317,33 @@ containers_dict[ 'repository_dependencies' ] = root_container containers_dict[ 'missing_repository_dependencies' ] = None return containers_dict +def merge_missing_tool_dependencies_to_installed_container( containers_dict ): + """ Merge the list of missing tool dependencies into the list of installed tool dependencies.""" + missing_td_container_root = containers_dict.get( 'missing_tool_dependencies', None ) + if missing_td_container_root: + # The missing_td_container_root will be a root folder containing a single sub_folder. + missing_td_container = missing_td_container_root.folders[ 0 ] + installed_td_container_root = containers_dict.get( 'tool_dependencies', None ) + # The installed_td_container_root will be a root folder containing a single sub_folder. + if installed_td_container_root: + installed_td_container = installed_td_container_root.folders[ 0 ] + installed_td_container.label = 'Tool dependencies' + for index, td in enumerate( missing_td_container.tool_dependencies ): + # Skip the header row. + if index == 0: + continue + installed_td_container.tool_dependencies.append( td ) + installed_td_container_root.folders = [ installed_td_container ] + containers_dict[ 'tool_dependencies' ] = installed_td_container_root + else: + # Change the folder label from 'Missing tool dependencies' to be 'Tool dependencies' for display. + root_container = containers_dict[ 'missing_tool_dependencies' ] + for sub_container in root_container.folders: + # There should only be 1 subfolder. + sub_container.label = 'Tool dependencies' + containers_dict[ 'tool_dependencies' ] = root_container + containers_dict[ 'missing_tool_dependencies' ] = None + return containers_dict def open_repository_files_folder( trans, folder_path ): try: files_list = get_repository_files( trans, folder_path ) @@ -2417,15 +2453,6 @@ error_message = '' return removed, error_message def repository_dependencies_have_tool_dependencies( trans, repository_dependencies ): - """ - repository_dependencies': - {'http://localhost:9009__ESEP__emboss_6__ESEP__test__ESEP__92bedb60b0c9': - [['http://localhost:9009', 'emboss_datatypes', 'test', '27df73fe48a6']], - 'root_key': 'http://localhost:9009__ESEP__emboss__ESEP__test__ESEP__06d729cb3f34', - 'description': 'required to enable emboss 6 tools', - 'http://localhost:9009__ESEP__emboss__ESEP__test__ESEP__06d729cb3f34': - [['http://localhost:9009', 'emboss_6', 'test', '92bedb60b0c9']]}} - """ rd_tups_processed = [] for key, rd_tups in repository_dependencies.items(): if key in [ 'root_key', 'description' ]: diff -r 753130def2f89698bb95a554ce76c7ea8c5102d7 -r 3faa833c15b5162db69f061bdbd4e951ba2ffdc7 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -480,7 +480,9 @@ model_class=model.User, attach_popup=False ) ] - operations = [] + operations = [ + grids.GridOperation( "Install to Galaxy", allow_multiple=True ) + ] standard_filters = [] default_filter = {} num_rows_per_page = 50 @@ -1101,7 +1103,7 @@ return trans.response.send_redirect( web.url_for( controller='repository', action=a, **kwd ) ) - if operation == "install": + if operation == "install to galaxy": # We've received a list of RepositoryMetadata ids, so we need to build a list of associated Repository ids. encoded_repository_ids = [] changeset_revisions = [] @@ -1109,6 +1111,7 @@ repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) encoded_repository_ids.append( trans.security.encode_id( repository_metadata.repository.id ) ) changeset_revisions.append( repository_metadata.changeset_revision ) + new_kwd = {} new_kwd[ 'repository_ids' ] = encoded_repository_ids new_kwd[ 'changeset_revisions' ] = changeset_revisions return trans.response.send_redirect( web.url_for( controller='repository', @@ -1186,7 +1189,7 @@ return trans.response.send_redirect( web.url_for( controller='repository', action=a, **kwd ) ) - if operation == "install": + if operation == "install to galaxy": # We've received a list of RepositoryMetadata ids, so we need to build a list of associated Repository ids. encoded_repository_ids = [] changeset_revisions = [] @@ -1372,8 +1375,8 @@ @web.json def get_repository_information( self, trans, repository_ids, changeset_revisions, **kwd ): """ - Generate a list of dictionaries, each of which contains the information about a repository that will be necessary for installing - it into a local Galaxy instance. + Generate a list of dictionaries, each of which contains the information about a repository that will be necessary for installing it into + a local Galaxy instance. """ includes_tools = False includes_repository_dependencies = False diff -r 753130def2f89698bb95a554ce76c7ea8c5102d7 -r 3faa833c15b5162db69f061bdbd4e951ba2ffdc7 lib/galaxy/webapps/community/util/container_util.py --- a/lib/galaxy/webapps/community/util/container_util.py +++ b/lib/galaxy/webapps/community/util/container_util.py @@ -211,8 +211,7 @@ else: readme_files_root_folder = None return folder_id, readme_files_root_folder -def build_repository_dependencies_folder( trans, toolshed_base_url, repository_name, repository_owner, changeset_revision, folder_id, repository_dependencies, - label='Repository dependencies', installed=False ): +def build_repository_dependencies_folder( trans, folder_id, repository_dependencies, label='Repository dependencies', installed=False ): """Return a folder hierarchy containing repository dependencies.""" if repository_dependencies: repository_dependency_id = 0 @@ -293,10 +292,10 @@ return folder_id, tools_root_folder def build_tool_dependencies_folder( trans, folder_id, tool_dependencies, label='Tool dependencies', missing=False, new_install=False, reinstalling=False ): """Return a folder hierarchy containing tool dependencies.""" - # The status will be displayed only if the received value for missing is True. When this is the case, we're in Galaxy (not the tool shed) - # and the tool dependencies are not installed or are in an error state, so they are considered missing. The tool dependency status will be - # displayed only if a record exists for the tool dependency in the database, but the tool dependency is not installed. The value for new_install - # will be True only if the associated repository in being installed for the first time. This value is used in setting the container description. + # When we're in Galaxy (not the tool shed) and the tool dependencies are not installed or are in an error state, they are considered missing. The tool + # dependency status will be displayed only if a record exists for the tool dependency in the Galaxy database, but the tool dependency is not installed. + # The value for new_install will be True only if the associated repository in being installed for the first time. This value is used in setting the + # container description. if tool_dependencies: tool_dependency_id = 0 folder_id += 1 @@ -304,15 +303,12 @@ folder_id += 1 folder = Folder( id=folder_id, key='tool_dependencies', label=label, parent=tool_dependencies_root_folder ) if trans.webapp.name == 'galaxy': - if reinstalling: - folder.description = "this repository's tools require handling of these dependencies" - elif missing and not reinstalling: + if new_install or reinstalling: + folder.description = "repository tools require handling of these dependencies" + elif missing and not new_install and not reinstalling: folder.description = 'click the name to install the missing dependency' else: - if new_install: - folder.description = "this repository's tools require handling of these dependencies" - else: - folder.description = 'click the name to browse the dependency installation directory' + folder.description = 'click the name to browse the dependency installation directory' tool_dependencies_root_folder.folders.append( folder ) # Insert a header row. tool_dependency_id += 1 @@ -321,11 +317,9 @@ tool_dependency = ToolDependency( id=tool_dependency_id, name='Name', version='Version', - type='Type' ) - if missing: - tool_dependency.installation_status = 'Status' - else: - tool_dependency.install_dir = 'Install directory' + type='Type', + install_dir='Install directory', + installation_status='Installation status' ) else: tool_dependency = ToolDependency( id=tool_dependency_id, name='Name', @@ -341,7 +335,7 @@ repository_id = set_environment_dict.get( 'repository_id', None ) td_id = set_environment_dict.get( 'tool_dependency_id', None ) if trans.webapp.name == 'galaxy': - installation_status = set_environment_dict.get( 'status', None ) + installation_status = set_environment_dict.get( 'status', 'Never installed' ) else: installation_status = None tool_dependency = ToolDependency( id=tool_dependency_id, @@ -359,7 +353,7 @@ repository_id = requirements_dict.get( 'repository_id', None ) td_id = requirements_dict.get( 'tool_dependency_id', None ) if trans.webapp.name == 'galaxy': - installation_status = requirements_dict.get( 'status', None ) + installation_status = requirements_dict.get( 'status', 'Never installed' ) else: installation_status = None tool_dependency = ToolDependency( id=tool_dependency_id, diff -r 753130def2f89698bb95a554ce76c7ea8c5102d7 -r 3faa833c15b5162db69f061bdbd4e951ba2ffdc7 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -946,7 +946,12 @@ trans.sa_session.add( repository ) trans.sa_session.flush() message = "The repository information has been updated." - containers_dict = shed_util.populate_containers_dict_from_repository_metadata( trans, tool_shed_url, tool_path, repository, reinstalling=False ) + containers_dict = shed_util.populate_containers_dict_from_repository_metadata( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + repository=repository, + reinstalling=False, + required_repo_info_dicts=None ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako', repository=repository, description=description, @@ -1259,46 +1264,49 @@ shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] shed_tool_conf = shed_tool_conf.replace( './', '', 1 ) shed_tool_conf_select_field = None + tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ) tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) + containers_dicts = [] if len( repo_info_dicts ) == 1: # If we're installing a single repository, see if it contains a readme or dependencies that we can display. repo_info_dict = repo_info_dicts[ 0 ] - name, repository_owner, changeset_revision, readme_files_dict, includes_tool_dependencies, \ - installed_repository_dependencies, missing_repository_dependencies, tool_dependencies, missing_tool_dependencies = \ - shed_util.get_repository_readme_and_dependencies_for_display( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) - # Since we are installing a new repository, most of the repository contents are set to None since we don't yet know what they are. - containers_dict = suc.build_repository_containers_for_galaxy( trans=trans, - toolshed_base_url=tool_shed_url, - repository_name=name, - repository_owner=repository_owner, - changeset_revision=changeset_revision, - repository=None, - datatypes=None, - invalid_tools=None, - missing_repository_dependencies=missing_repository_dependencies, - missing_tool_dependencies=missing_tool_dependencies, - readme_files_dict=readme_files_dict, - repository_dependencies=installed_repository_dependencies, - tool_dependencies=tool_dependencies, - valid_tools=None, - workflows=None, - new_install=True, - reinstalling=False ) + name, repository_owner, changeset_revision, includes_tool_dependencies, installed_repository_dependencies, \ + missing_repository_dependencies, installed_tool_dependencies, missing_tool_dependencies = \ + shed_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) + readme_files_dict = shed_util.get_readme_files_dict_for_display( trans, tool_shed_url, repo_info_dict ) # We're handling 1 of 2 scenarios here: (1) we're installing a tool shed repository for the first time, so we've retrieved the list of installed # and missing repository dependencies from the database (2) we're handling the scenario where an error occurred during the installation process, # so we have a tool_shed_repository record in the database with associated repository dependency records. Since we have the repository # dependencies in either case, we'll merge the list of missing repository dependencies into the list of installed repository dependencies since # each displayed repository dependency will display a status, whether installed or missing. - containers_dict = suc.merge_missing_repository_dependencies_to_installed_container( containers_dict ) + containers_dict = shed_util.populate_containers_dict_for_new_install( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + readme_files_dict=readme_files_dict, + installed_repository_dependencies=installed_repository_dependencies, + missing_repository_dependencies=missing_repository_dependencies, + installed_tool_dependencies=installed_tool_dependencies, + missing_tool_dependencies=missing_tool_dependencies ) + containers_dicts.append( containers_dict ) else: - # FIXME: support the intallation of repository dependencies and tool dependencies for a list of tool shed repositories being installed. - containers_dict = dict( datatypes=None, - invalid_tools=None, - readme_files_dict=None, - repository_dependencies=None, - tool_dependencies=None, - valid_tools=None, - workflows=None ) + # We're installing a list of repositories, each of which may have tool dependencies or repository dependencies. + all_installed_repository_dependencies = [] + all_missing_repository_dependencies = [] + all_installed_tool_dependencies = [] + all_missing_tool_dependencies = [] + for repo_info_dict in repo_info_dicts: + name, repository_owner, changeset_revision, includes_tool_dependencies, installed_repository_dependencies, \ + missing_repository_dependencies, installed_tool_dependencies, missing_tool_dependencies = \ + shed_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) + containers_dict = shed_util.populate_containers_dict_for_new_install( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + readme_files_dict=None, + repository_dependencies=installed_repository_dependencies, + missing_repository_dependencies=missing_repository_dependencies, + tool_dependencies=installed_tool_dependencies, + missing_tool_dependencies=missing_tool_dependencies ) + containers_dicts.append( containers_dict ) # Handle tool dependencies chack box. if trans.app.config.tool_dependency_dir is None: if includes_tool_dependencies: @@ -1319,7 +1327,7 @@ includes_repository_dependencies=includes_repository_dependencies, install_repository_dependencies_check_box=install_repository_dependencies_check_box, new_tool_panel_section=new_tool_panel_section, - containers_dict=containers_dict, + containers_dicts=containers_dicts, shed_tool_conf=shed_tool_conf, shed_tool_conf_select_field=shed_tool_conf_select_field, tool_panel_section_select_field=tool_panel_section_select_field, @@ -1667,8 +1675,13 @@ message ++ "from the installed repository's <b>Repository Actions</b> menu. " status = 'error' shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) - repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) - containers_dict = shed_util.populate_containers_dict_from_repository_metadata( trans, tool_shed_url, tool_path, repository, reinstalling=False ) + repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) + containers_dict = shed_util.populate_containers_dict_from_repository_metadata( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + repository=repository, + reinstalling=False, + required_repo_info_dicts=None ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako', repository=repository, description=repository.description, diff -r 753130def2f89698bb95a554ce76c7ea8c5102d7 -r 3faa833c15b5162db69f061bdbd4e951ba2ffdc7 templates/admin/tool_shed_repository/select_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -20,18 +20,25 @@ # this case, the repository metadata is an empty dictionary, but one or both of includes_repository_dependencies # and includes_tool_dependencies may be True. If either of these are True but we have no metadata, we cannot install # repository dependencies on this pass. - if includes_repository_dependencies: - repository_dependencies = containers_dict[ 'repository_dependencies' ] - missing_repository_dependencies = containers_dict[ 'missing_repository_dependencies' ] - can_display_repository_dependencies = repository_dependencies or missing_repository_dependencies - else: - can_display_repository_dependencies = False - if includes_tool_dependencies: - tool_dependencies = containers_dict[ 'tool_dependencies' ] - missing_tool_dependencies = containers_dict[ 'missing_tool_dependencies' ] - can_display_tool_dependencies = tool_dependencies or missing_tool_dependencies - else: - can_display_tool_dependencies = False + + # TODO: do we need this? + can_display_repository_dependencies = False + can_display_tool_dependencies = False + + if includes_repository_dependencies and not can_display_repository_dependencies: + for containers_dict in containers_dicts: + repository_dependencies = containers_dict[ 'repository_dependencies' ] + missing_repository_dependencies = containers_dict[ 'missing_repository_dependencies' ] + if repository_dependencies or missing_repository_dependencies: + can_display_repository_dependencies = True + break + if includes_tool_dependencies and not can_display_tool_dependencies: + for containers_dict in containers_dicts: + tool_dependencies = containers_dict[ 'tool_dependencies' ] + missing_tool_dependencies = containers_dict[ 'missing_tool_dependencies' ] + if tool_dependencies or missing_tool_dependencies: + can_display_tool_dependencies = True + break %> %if message: @@ -56,7 +63,14 @@ <div class="toolFormBody"><form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='prepare_for_install', tool_shed_url=tool_shed_url, encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, includes_tool_dependencies=includes_tool_dependencies )}" method="post" ><div style="clear: both"></div> - <% readme_files_dict = containers_dict.get( 'readme_files', None ) %> + <% + if len( containers_dicts ) == 1: + containers_dict = containers_dicts[ 0 ] + readme_files_dict = containers_dict.get( 'readme_files', None ) + else: + containers_dict = None + readme_files_dict = None + %> %if readme_files_dict: <div class="form-row"><table class="colored" width="100%"> @@ -72,8 +86,15 @@ <th bgcolor="#EBD9B2">Confirm dependency installation</th></table></div> - ${render_dependencies_section( install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict )} - <div style="clear: both"></div> + %for index, containers_dict in enumerate( containers_dicts ): + %if index == 0: + ${render_dependencies_section( install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict )} + <div style="clear: both"></div> + %else: + ${render_dependencies_section( None, None, containers_dict )} + <div style="clear: both"></div> + %endif + %endfor %endif <div class="form-row"><table class="colored" width="100%"> diff -r 753130def2f89698bb95a554ce76c7ea8c5102d7 -r 3faa833c15b5162db69f061bdbd4e951ba2ffdc7 templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -207,13 +207,13 @@ if folder.description: folder_label = "%s<i> - %s</i>" % ( folder_label, folder.description ) else: - folder_label = "%s<i> - this repository's tools require handling of these missing dependencies</i>" % folder_label + folder_label = "%s<i> - repository tools require handling of these missing dependencies</i>" % folder_label col_span_str = 'colspan="5"' elif folder.label in [ 'Installed repository dependencies', 'Repository dependencies', 'Missing repository dependencies' ]: if folder.description: folder_label = "%s<i> - %s</i>" % ( folder_label, folder.description ) - else: - folder_label = "%s<i> - this repository requires installation of these additional repositories</i>" % folder_label + elif folder.label not in [ 'Installed repository dependencies' ]: + folder_label = "%s<i> - installation of these additional repositories is required</i>" % folder_label if trans.webapp.name == 'galaxy': col_span_str = 'colspan="4"' elif folder.label == 'Valid tools': @@ -228,7 +228,7 @@ if folder.description: folder_label = "%s<i> - %s</i>" % ( folder_label, folder.description ) else: - folder_label = "%s<i> - this repository's tools require handling of these dependencies</i>" % folder_label + folder_label = "%s<i> - repository tools require handling of these dependencies</i>" % folder_label col_span_str = 'colspan="4"' elif folder.workflows: if folder.description: @@ -467,6 +467,7 @@ <%def name="render_tool_dependency( tool_dependency, pad, parent, row_counter, row_is_header )"><% encoded_id = trans.security.encode_id( tool_dependency.id ) + is_missing = tool_dependency.installation_status not in [ 'Installed' ] if row_is_header: cell_type = 'th' else: @@ -506,12 +507,11 @@ ${version_str | h} </${cell_type}><${cell_type}>${tool_dependency.type | h}</${cell_type}> - %if tool_dependency.install_dir: + %if is_missing: + <${cell_type}>${tool_dependency.installation_status | h}</${cell_type}> + %elif tool_dependency.install_dir: <${cell_type}>${tool_dependency.install_dir | h}</${cell_type}> %endif - %if tool_dependency.installation_status not in [ 'Installed', None ]: - <${cell_type}>${tool_dependency.installation_status | h}</${cell_type}> - %endif </tr><% my_row = row_counter.count diff -r 753130def2f89698bb95a554ce76c7ea8c5102d7 -r 3faa833c15b5162db69f061bdbd4e951ba2ffdc7 templates/webapps/community/repository/preview_tools_in_changeset.mako --- a/templates/webapps/community/repository/preview_tools_in_changeset.mako +++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako @@ -41,7 +41,7 @@ <br/><br/><ul class="manage-table-actions"> - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to Galaxy</a></li><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> diff -r 753130def2f89698bb95a554ce76c7ea8c5102d7 -r 3faa833c15b5162db69f061bdbd4e951ba2ffdc7 templates/webapps/community/repository/tool_form.mako --- a/templates/webapps/community/repository/tool_form.mako +++ b/templates/webapps/community/repository/tool_form.mako @@ -124,7 +124,7 @@ %if trans.webapp.name == 'galaxy': <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to Galaxy</a></li><li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Browse repository</a></li></div><li><a class="action-button" id="tool_shed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li> diff -r 753130def2f89698bb95a554ce76c7ea8c5102d7 -r 3faa833c15b5162db69f061bdbd4e951ba2ffdc7 templates/webapps/community/repository/view_repository.mako --- a/templates/webapps/community/repository/view_repository.mako +++ b/templates/webapps/community/repository/view_repository.mako @@ -94,7 +94,7 @@ %endif %endif %else: - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to Galaxy</a></li><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> diff -r 753130def2f89698bb95a554ce76c7ea8c5102d7 -r 3faa833c15b5162db69f061bdbd4e951ba2ffdc7 templates/webapps/community/repository/view_tool_metadata.mako --- a/templates/webapps/community/repository/view_tool_metadata.mako +++ b/templates/webapps/community/repository/view_tool_metadata.mako @@ -43,7 +43,7 @@ %if trans.webapp.name == 'galaxy': <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to Galaxy</a></li><li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Browse repository</a></li></div><li><a class="action-button" id="tool_shed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li> diff -r 753130def2f89698bb95a554ce76c7ea8c5102d7 -r 3faa833c15b5162db69f061bdbd4e951ba2ffdc7 test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py @@ -72,7 +72,7 @@ self.preview_repository_in_tool_shed( repository_name, common.test_user_1_name, strings_displayed=strings_displayed ) def test_0015_install_freebayes_repository( self ): '''Install the freebayes repository without installing tool dependencies.''' - strings_displayed=[ 'set your tool_dependency_dir', 'can be automatically installed', 'Set the tool_dependency_dir' ] + strings_displayed=[ 'Never installed', 'can be automatically installed', 'Set the tool_dependency_dir' ] strings_displayed.extend( [ 'Handle', 'tool dependencies', 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18' ] ) self.install_repository( repository_name, common.test_user_1_name, diff -r 753130def2f89698bb95a554ce76c7ea8c5102d7 -r 3faa833c15b5162db69f061bdbd4e951ba2ffdc7 test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py --- a/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py +++ b/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py @@ -74,7 +74,7 @@ '''Install the emboss repository without installing tool dependencies.''' global repository_datatypes_count global base_datatypes_count - strings_displayed = [ 'Handle', 'Missing', 'tool dependencies', 'emboss', '5.0.0', 'package' ] + strings_displayed = [ 'Handle', 'Never installed', 'tool dependencies', 'emboss', '5.0.0', 'package' ] self.install_repository( 'emboss_0020', common.test_user_1_name, 'Test 0020 Basic Repository Dependencies', diff -r 753130def2f89698bb95a554ce76c7ea8c5102d7 -r 3faa833c15b5162db69f061bdbd4e951ba2ffdc7 test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py --- a/test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py +++ b/test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py @@ -113,7 +113,7 @@ global base_datatypes_count global running_standalone base_datatypes_count = int( self.get_datatypes_count() ) - strings_displayed = [ 'Handle', 'Missing', 'tool dependencies', 'emboss', '5.0.0', 'package' ] + strings_displayed = [ 'Handle', 'Never installed', 'tool dependencies', 'emboss', '5.0.0', 'package' ] self.install_repository( 'emboss_0030', common.test_user_1_name, 'Test 0030 Repository Dependency Revisions', diff -r 753130def2f89698bb95a554ce76c7ea8c5102d7 -r 3faa833c15b5162db69f061bdbd4e951ba2ffdc7 test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py --- a/test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py +++ b/test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py @@ -70,7 +70,7 @@ self.galaxy_logout() self.galaxy_login( email=common.admin_email, username=common.admin_username ) base_datatypes_count = int( self.get_datatypes_count() ) - strings_displayed = [ 'Handle', 'Missing', 'tool dependencies', 'emboss', '5.0.0', 'package' ] + strings_displayed = [ 'Handle', 'Never installed', 'tool dependencies', 'emboss', '5.0.0', 'package' ] self.install_repository( emboss_repository_name, common.test_user_1_name, 'Test 0020 Basic Repository Dependencies', diff -r 753130def2f89698bb95a554ce76c7ea8c5102d7 -r 3faa833c15b5162db69f061bdbd4e951ba2ffdc7 test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py --- a/test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py +++ b/test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py @@ -107,7 +107,7 @@ self.galaxy_logout() self.galaxy_login( email=common.admin_email, username=common.admin_username ) base_datatypes_count = int( self.get_datatypes_count() ) - strings_displayed = [ 'Handle', 'Missing', 'tool dependencies', 'emboss', '5.0.0', 'package' ] + strings_displayed = [ 'Handle', 'Never installed', 'tool dependencies', 'emboss', '5.0.0', 'package' ] self.install_repository( emboss_repository_name, common.test_user_1_name, 'Test 0030 Repository Dependency Revisions', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Update Yogeshwar Kelkar's Microsatellite tools.
by Bitbucket 11 Jan '13

11 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/753130def2f8/ changeset: 753130def2f8 user: dan date: 2013-01-11 15:48:47 summary: Update Yogeshwar Kelkar's Microsatellite tools. affected #: 9 files diff -r c802de6bf0ba697d9a5038ab41dfa1425f0c296f -r 753130def2f89698bb95a554ce76c7ea8c5102d7 test-data/regVariation/microsatellite/Galaxy17_masked_short.maf.gz Binary file test-data/regVariation/microsatellite/Galaxy17_masked_short.maf.gz has changed diff -r c802de6bf0ba697d9a5038ab41dfa1425f0c296f -r 753130def2f89698bb95a554ce76c7ea8c5102d7 test-data/regVariation/microsatellite/Galaxy17_short_raw.txt --- a/test-data/regVariation/microsatellite/Galaxy17_short_raw.txt +++ b/test-data/regVariation/microsatellite/Galaxy17_short_raw.txt @@ -1,703 +1,5 @@ ->calJac1 5 hg18 chr22 16069424 16069727 panTro2 chr22 16078237 16078538 ponAbe2 chr22 13770841 13771145 rheMac2 chr10 61855336 61855639 calJac1 Contig6986 129306 129617 mononucleotide [a][A] 2 113 + 134 [a]c[aaaaaaaaaaaaaaaaaaaa] indel/deletion c 2 1 ->panTro2 5 hg18 chr22 16069424 16069727 panTro2 chr22 16078237 16078538 ponAbe2 chr22 13770841 13771145 rheMac2 chr10 61855336 61855639 calJac1 Contig6986 129306 129617 mononucleotide A 16 285 + 293 aaaaaaaaa >panTro2 5 hg18 chr22 16069424 16069727 panTro2 chr22 16078237 16078538 ponAbe2 chr22 13770841 13771145 rheMac2 chr10 61855336 61855639 calJac1 Contig6986 129306 129617 mononucleotide [a][A] 16 301 + 316 [aa]t----[aaaaaaaaa] indel/deletion t 3 1 >ponAbe2 5 hg18 chr22 16069424 16069727 panTro2 chr22 16078237 16078538 ponAbe2 chr22 13770841 13771145 rheMac2 chr10 61855336 61855639 calJac1 Contig6986 129306 129617 mononucleotide A 16 285 + 293 aaaaaaaaa >calJac1 5 hg18 chr22 16069424 16069727 panTro2 chr22 16078237 16078538 ponAbe2 chr22 13770841 13771145 rheMac2 chr10 61855336 61855639 calJac1 Contig6986 129306 129617 mononucleotide A 3 285 + 302 aaaaaaaaa-------aa >hg18 5 hg18 chr22 16069424 16069727 panTro2 chr22 16078237 16078538 ponAbe2 chr22 13770841 13771145 rheMac2 chr10 61855336 61855639 calJac1 Contig6986 129306 129617 mononucleotide [a][A] 16 301 + 316 [aa]t--[aaaaaaaaaaa] indel/deletion t 3 1 >rheMac2 5 hg18 chr22 16069424 16069727 panTro2 chr22 16078237 16078538 ponAbe2 chr22 13770841 13771145 rheMac2 chr10 61855336 61855639 calJac1 Contig6986 129306 129617 mononucleotide A 18 308 + 320 aaaaaaaaaaaaa ->calJac1 7 hg18 chr22 16089475 16090837 panTro2 chr22 16100440 16101836 ponAbe2 chr22 13794262 13795648 rheMac2 chr10 61887207 61888593 calJac1 Contig5889 56093 57503 tetranucleotide AAGC 0 11 + 31 aag---------CAAGCAAGC ->calJac1 9 hg18 chr22 16090983 16091493 panTro2 chr22 16101982 16102495 ponAbe2 chr22 13795794 13796300 rheMac2 chr10 61888708 61889219 calJac1 Contig6986 137453 137956 tetranucleotide [TTTA][ttta] 6 488 + 505 [TTTAtttattta]tt[ttta] indel/deletion tt 13 1 ->hg18 10 hg18 chr22 16091493 16091818 panTro2 chr22 16102495 16102820 ponAbe2 chr22 13796300 13796625 rheMac2 chr10 61889519 61889823 calJac1 Contig6986 137956 138274 mononucleotide T 0 1 + 12 tttttttttttt >panTro2 10 hg18 chr22 16091493 16091818 panTro2 chr22 16102495 16102820 ponAbe2 chr22 13796300 13796625 rheMac2 chr10 61889519 61889823 calJac1 Contig6986 137956 138274 mononucleotide T 0 1 + 12 tttttttttttt >ponAbe2 10 hg18 chr22 16091493 16091818 panTro2 chr22 16102495 16102820 ponAbe2 chr22 13796300 13796625 rheMac2 chr10 61889519 61889823 calJac1 Contig6986 137956 138274 mononucleotide T 0 1 + 12 tttttttttttt >rheMac2 10 hg18 chr22 16091493 16091818 panTro2 chr22 16102495 16102820 ponAbe2 chr22 13796300 13796625 rheMac2 chr10 61889519 61889823 calJac1 Contig6986 137956 138274 mononucleotide T 0 1 + 13 ttttttttttttt >calJac1 10 hg18 chr22 16091493 16091818 panTro2 chr22 16102495 16102820 ponAbe2 chr22 13796300 13796625 rheMac2 chr10 61889519 61889823 calJac1 Contig6986 137956 138274 mononucleotide T 0 1 + 12 tttttttttttt ->rheMac2 10 hg18 chr22 16091493 16091818 panTro2 chr22 16102495 16102820 ponAbe2 chr22 13796300 13796625 rheMac2 chr10 61889519 61889823 calJac1 Contig6986 137956 138274 mononucleotide [t][T] 29 310 + 333 [tttt]c[ttttttttttttttttttt] indel/deletion c 5 1 ->hg18 15 hg18 chr22 16092941 16093413 panTro2 chr22 16103944 16104421 ponAbe2 chr22 13797750 13798215 rheMac2 chr10 61890946 61891409 calJac1 Contig6986 140254 140728 mononucleotide A 0 13 + 29 aaaaa------aaaAAA >rheMac2 15 hg18 chr22 16092941 16093413 panTro2 chr22 16103944 16104421 ponAbe2 chr22 13797750 13798215 rheMac2 chr10 61890946 61891409 calJac1 Contig6986 140254 140728 mononucleotide A 0 13 + 29 aaaaaaaa---AAAAAA ->panTro2 15 hg18 chr22 16092941 16093413 panTro2 chr22 16103944 16104421 ponAbe2 chr22 13797750 13798215 rheMac2 chr10 61890946 61891409 calJac1 Contig6986 140254 140728 mononucleotide A 2 35 + 43 aaaaaaaaa ->rheMac2 19 hg18 chr22 16094980 16095555 panTro2 chr22 16105989 16106564 ponAbe2 chr22 13799565 13800129 rheMac2 chr10 61893506 61894086 calJac1 Contig6986 142576 143125 trinucleotide CAC 6 206 + 220 CACCACCACCACCAC ->calJac1 21 hg18 chr22 16095954 16096670 panTro2 chr22 16106955 16107671 ponAbe2 chr22 13800518 13801234 rheMac2 chr10 61894621 61895293 calJac1 Contig13114 2 681 mononucleotide [A][A] 5 431 + 463 [AAAAA---------------------AAAAA]G[A] indel/deletion G 11 1 ->hg18 25 hg18 chr22 16097174 16098203 panTro2 chr22 16108182 16109208 ponAbe2 chr22 13805226 13806252 rheMac2 chr10 61895940 61897012 calJac1 Contig13114 1485 2637 mononucleotide A 12 135 + 225 aaaaaaaaaaaaaaaaa-------------------------------------------------------------------------a >panTro2 25 hg18 chr22 16097174 16098203 panTro2 chr22 16108182 16109208 ponAbe2 chr22 13805226 13806252 rheMac2 chr10 61895940 61897012 calJac1 Contig13114 1485 2637 mononucleotide A 12 135 + 223 aaaaaaaaaaaaaaa-------------------------------------------------------------------------a >ponAbe2 25 hg18 chr22 16097174 16098203 panTro2 chr22 16108182 16109208 ponAbe2 chr22 13805226 13806252 rheMac2 chr10 61895940 61897012 calJac1 Contig13114 1485 2637 mononucleotide A 13 135 + 226 aaaaaaaaaaaaaaaaaa-------------------------------------------------------------------------a ->calJac1 25 hg18 chr22 16097174 16098203 panTro2 chr22 16108182 16109208 ponAbe2 chr22 13805226 13806252 rheMac2 chr10 61895940 61897012 calJac1 Contig13114 1485 2637 mononucleotide [A][A][A] 8 270 + 285 [aaaaaAAAAAA]G[AA]T[A] indel/deletion,indel/deletion G,T 12,15 2 ->rheMac2 25 hg18 chr22 16097174 16098203 panTro2 chr22 16108182 16109208 ponAbe2 chr22 13805226 13806252 rheMac2 chr10 61895940 61897012 calJac1 Contig13114 1485 2637 mononucleotide T 128 394 + 409 tttttttttttttttt >hg18 25 hg18 chr22 16097174 16098203 panTro2 chr22 16108182 16109208 ponAbe2 chr22 13805226 13806252 rheMac2 chr10 61895940 61897012 calJac1 Contig13114 1485 2637 mononucleotide T 126 398 + 414 ttttttttttttttttt >panTro2 25 hg18 chr22 16097174 16098203 panTro2 chr22 16108182 16109208 ponAbe2 chr22 13805226 13806252 rheMac2 chr10 61895940 61897012 calJac1 Contig13114 1485 2637 mononucleotide T 128 398 + 413 tttttttttttttttt >ponAbe2 25 hg18 chr22 16097174 16098203 panTro2 chr22 16108182 16109208 ponAbe2 chr22 13805226 13806252 rheMac2 chr10 61895940 61897012 calJac1 Contig13114 1485 2637 mononucleotide T 126 398 + 408 ttttttttttt ->calJac1 25 hg18 chr22 16097174 16098203 panTro2 chr22 16108182 16109208 ponAbe2 chr22 13805226 13806252 rheMac2 chr10 61895940 61897012 calJac1 Contig13114 1485 2637 mononucleotide [T][t] 17 580 + 590 [ttttttttt]g[t] indel/deletion g 10 1 ->hg18 25 hg18 chr22 16097174 16098203 panTro2 chr22 16108182 16109208 ponAbe2 chr22 13805226 13806252 rheMac2 chr10 61895940 61897012 calJac1 Contig13114 1485 2637 tetranucleotide TGGA 149 866 + 877 TGGATGGATGGA >panTro2 25 hg18 chr22 16097174 16098203 panTro2 chr22 16108182 16109208 ponAbe2 chr22 13805226 13806252 rheMac2 chr10 61895940 61897012 calJac1 Contig13114 1485 2637 tetranucleotide TGGA 152 866 + 877 TGGATGGATGGA >ponAbe2 25 hg18 chr22 16097174 16098203 panTro2 chr22 16108182 16109208 ponAbe2 chr22 13805226 13806252 rheMac2 chr10 61895940 61897012 calJac1 Contig13114 1485 2637 tetranucleotide TGGA 156 866 + 883 TGGATGGATGGATGGATG ->calJac1 27 hg18 chr22 16102504 16103585 panTro2 chr22 16113512 16114587 ponAbe2 chr22 13810659 13811748 rheMac2 chr10 61901011 61902101 calJac1 Contig13114 9064 10114 mononucleotide A 58 1086 + 1126 aaaaaa---------------aaaaaaaaa---aaaaaaaa >rheMac2 27 hg18 chr22 16102504 16103585 panTro2 chr22 16113512 16114587 ponAbe2 chr22 13810659 13811748 rheMac2 chr10 61901011 61902101 calJac1 Contig13114 9064 10114 tetranucleotide AAAT 36 1087 + 1126 aaataaataaataaataaataaataaataaataaataaat ->calJac1 32 hg18 chr22 16113458 16114563 panTro2 chr22 16129884 16130987 ponAbe2 chr22 13832752 13833856 rheMac2 chr10 61913078 61914182 calJac1 Contig13114 13132 14307 dinucleotide AG 15 252 + 261 AGAGAGAGAG ->hg18 32 hg18 chr22 16113458 16114563 panTro2 chr22 16129884 16130987 ponAbe2 chr22 13832752 13833856 rheMac2 chr10 61913078 61914182 calJac1 Contig13114 13132 14307 mononucleotide A 120 1210 + 1225 aaaaaaaaaaaaaaaa >panTro2 32 hg18 chr22 16113458 16114563 panTro2 chr22 16129884 16130987 ponAbe2 chr22 13832752 13833856 rheMac2 chr10 61913078 61914182 calJac1 Contig13114 13132 14307 mononucleotide A 124 1210 + 1227 aaaaaaaaaaaaaaaaaa >rheMac2 32 hg18 chr22 16113458 16114563 panTro2 chr22 16129884 16130987 ponAbe2 chr22 13832752 13833856 rheMac2 chr10 61913078 61914182 calJac1 Contig13114 13132 14307 mononucleotide A 124 1210 + 1228 aaaaaaaaaaaaaaaaaaa >calJac1 32 hg18 chr22 16113458 16114563 panTro2 chr22 16129884 16130987 ponAbe2 chr22 13832752 13833856 rheMac2 chr10 61913078 61914182 calJac1 Contig13114 13132 14307 mononucleotide A 50 1210 + 1225 aaaaaaaaaaaaaaaa >ponAbe2 32 hg18 chr22 16113458 16114563 panTro2 chr22 16129884 16130987 ponAbe2 chr22 13832752 13833856 rheMac2 chr10 61913078 61914182 calJac1 Contig13114 13132 14307 mononucleotide A 124 1214 + 1228 aaaaaaaaaaaaaaa ->panTro2 33 hg18 chr22 16114590 16114938 panTro2 chr22 16131014 16131370 ponAbe2 chr22 13833883 13834239 rheMac2 chr10 61914209 61914553 calJac1 Contig13114 14643 14954 mononucleotide [a][A] 2 139 + 160 [a]c[aaaaaaaaaaaaaaaaaaaa] indel/deletion c 2 1 >ponAbe2 33 hg18 chr22 16114590 16114938 panTro2 chr22 16131014 16131370 ponAbe2 chr22 13833883 13834239 rheMac2 chr10 61914209 61914553 calJac1 Contig13114 14643 14954 mononucleotide [a][A] 2 139 + 160 [a]c[aaaa-aaaaaaaaaaaaaaa] indel/deletion c 2 1 ->hg18 33 hg18 chr22 16114590 16114938 panTro2 chr22 16131014 16131370 ponAbe2 chr22 13833883 13834239 rheMac2 chr10 61914209 61914553 calJac1 Contig13114 14643 14954 mononucleotide [A][a][a] 13 314 + 333 [aaaaaaaaaaaa]g[aa]t[aaaa] indel/deletion,indel/deletion g,t 13,16 2 >panTro2 33 hg18 chr22 16114590 16114938 panTro2 chr22 16131014 16131370 ponAbe2 chr22 13833883 13834239 rheMac2 chr10 61914209 61914553 calJac1 Contig13114 14643 14954 mononucleotide [A][a][a] 6 314 + 334 [aaaaaaaaaaaaa]g[aa]t[aaaa] indel/deletion,indel/deletion g,t 14,17 2 >ponAbe2 33 hg18 chr22 16114590 16114938 panTro2 chr22 16131014 16131370 ponAbe2 chr22 13833883 13834239 rheMac2 chr10 61914209 61914553 calJac1 Contig13114 14643 14954 mononucleotide A 4 314 + 333 aaaaaaaaaaaaaaa-aaaa >rheMac2 33 hg18 chr22 16114590 16114938 panTro2 chr22 16131014 16131370 ponAbe2 chr22 13833883 13834239 rheMac2 chr10 61914209 61914553 calJac1 Contig13114 14643 14954 mononucleotide [a][A] 19 314 + 326 [aa]g[aaaaaaaaaa] indel/deletion g 3 1 >calJac1 33 hg18 chr22 16114590 16114938 panTro2 chr22 16131014 16131370 ponAbe2 chr22 13833883 13834239 rheMac2 chr10 61914209 61914553 calJac1 Contig13114 14643 14954 tetranucleotide TAAA 21 318 + 333 aaataaataaat-aaa ->rheMac2 34 hg18 chr22 16115000 16115212 panTro2 chr22 16131432 16131644 ponAbe2 chr22 13834301 13834513 rheMac2 chr10 61914657 61914870 calJac1 Contig13114 14954 15124 mononucleotide A 1 198 + 206 aaaaaaaaa ->calJac1 37 hg18 chr22 16118223 16119141 panTro2 chr22 16134653 16135572 ponAbe2 chr22 13837634 13838553 rheMac2 chr10 61918520 61919424 calJac1 Contig13114 15842 16747 tetranucleotide AAAC 1 182 + 193 AAACAAACAAAC ->hg18 37 hg18 chr22 16118223 16119141 panTro2 chr22 16134653 16135572 ponAbe2 chr22 13837634 13838553 rheMac2 chr10 61918520 61919424 calJac1 Contig13114 15842 16747 mononucleotide T 7 568 + 577 TTTTTTTTTT >panTro2 37 hg18 chr22 16118223 16119141 panTro2 chr22 16134653 16135572 ponAbe2 chr22 13837634 13838553 rheMac2 chr10 61918520 61919424 calJac1 Contig13114 15842 16747 mononucleotide T 6 568 + 577 TTTTTTTTTT >ponAbe2 37 hg18 chr22 16118223 16119141 panTro2 chr22 16134653 16135572 ponAbe2 chr22 13837634 13838553 rheMac2 chr10 61918520 61919424 calJac1 Contig13114 15842 16747 mononucleotide T 5 568 + 576 TTTTTTTTT >rheMac2 37 hg18 chr22 16118223 16119141 panTro2 chr22 16134653 16135572 ponAbe2 chr22 13837634 13838553 rheMac2 chr10 61918520 61919424 calJac1 Contig13114 15842 16747 mononucleotide T 22 568 + 579 TTTTTTTTTTTT ->ponAbe2 37 hg18 chr22 16118223 16119141 panTro2 chr22 16134653 16135572 ponAbe2 chr22 13837634 13838553 rheMac2 chr10 61918520 61919424 calJac1 Contig13114 15842 16747 tetranucleotide GAGG 8 821 + 833 GAGGGAGGGAGGG ->hg18 38 hg18 chr22 16119141 16119363 panTro2 chr22 16135572 16135794 ponAbe2 chr22 13838553 13838774 rheMac2 chr10 61919424 61919654 calJac1 Contig13114 16747 16966 dinucleotide [TC][TC] 0 21 + 34 [TCT]G[TCTCTCTCTC] indel/deletion G 4 1 >panTro2 38 hg18 chr22 16119141 16119363 panTro2 chr22 16135572 16135794 ponAbe2 chr22 13838553 13838774 rheMac2 chr10 61919424 61919654 calJac1 Contig13114 16747 16966 dinucleotide [TC][TC] 0 21 + 34 [TCT]G[TCTCTCTCTC] indel/deletion G 4 1 >ponAbe2 38 hg18 chr22 16119141 16119363 panTro2 chr22 16135572 16135794 ponAbe2 chr22 13838553 13838774 rheMac2 chr10 61919424 61919654 calJac1 Contig13114 16747 16966 dinucleotide [TC][TC] 0 21 + 34 [TCT]G[TCTCTCTCTC] indel/deletion G 4 1 >rheMac2 38 hg18 chr22 16119141 16119363 panTro2 chr22 16135572 16135794 ponAbe2 chr22 13838553 13838774 rheMac2 chr10 61919424 61919654 calJac1 Contig13114 16747 16966 dinucleotide [TC][TC] 0 21 + 34 [TCT]G[TCTCTCTCTC] indel/deletion G 4 1 >calJac1 38 hg18 chr22 16119141 16119363 panTro2 chr22 16135572 16135794 ponAbe2 chr22 13838553 13838774 rheMac2 chr10 61919424 61919654 calJac1 Contig13114 16747 16966 dinucleotide [TC][TC] 0 21 + 34 [TCT]G[TCTCTCTCTC] indel/deletion G 4 1 ->rheMac2 45 hg18 chr22 16122069 16122736 panTro2 chr22 16138858 16139525 ponAbe2 chr22 13842141 13842809 rheMac2 chr10 61922407 61923076 calJac1 Contig13114 21049 21852 mononucleotide [A][a] 176 830 + 843 [aaaaaaaaaaaa]t[a] indel/deletion t 13 1 ->hg18 46 hg18 chr22 16122736 16122975 panTro2 chr22 16139525 16139765 ponAbe2 chr22 13842809 13843053 rheMac2 chr10 61923595 61923879 calJac1 Contig13114 21852 22093 mononucleotide [A][a] 4 158 + 172 [aaaaaaaaaaaa]g[aa] indel/deletion g 13 1 >panTro2 46 hg18 chr22 16122736 16122975 panTro2 chr22 16139525 16139765 ponAbe2 chr22 13842809 13843053 rheMac2 chr10 61923595 61923879 calJac1 Contig13114 21852 22093 mononucleotide [A][a] 4 158 + 173 [aaaaaaaaaaaaa]g[aa] indel/deletion g 14 1 >ponAbe2 46 hg18 chr22 16122736 16122975 panTro2 chr22 16139525 16139765 ponAbe2 chr22 13842809 13843053 rheMac2 chr10 61923595 61923879 calJac1 Contig13114 21852 22093 mononucleotide [A][a] 4 158 + 177 [aaaaaaaaaaaaaaaaa]g[aa] indel/deletion g 18 1 >rheMac2 46 hg18 chr22 16122736 16122975 panTro2 chr22 16139525 16139765 ponAbe2 chr22 13842809 13843053 rheMac2 chr10 61923595 61923879 calJac1 Contig13114 21852 22093 mononucleotide [a][A][A][A][A][A][A][A][A][A] 1 159 + 214 [aa]c[aaaaaaaaaa]g[aaaaaaa]g[aaaaaa]C[AA]G[AAAAA]C[AAAAA]C[AAAA]G[AAAA]G[AA] indel/deletion,insertion,insertion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion c,g,g,C,G,C,C,G,G 3,14,22,29,32,38,44,49,54 9 >calJac1 46 hg18 chr22 16122736 16122975 panTro2 chr22 16139525 16139765 ponAbe2 chr22 13842809 13843053 rheMac2 chr10 61923595 61923879 calJac1 Contig13114 21852 22093 mononucleotide [A][a] 46 200 + 214 [aaaaaaaaaaaa]g[aa] indel/deletion g 13 1 ->rheMac2 49 hg18 chr22 16123366 16124069 panTro2 chr22 16140156 16140859 ponAbe2 chr22 13843444 13844147 rheMac2 chr10 61924270 61924987 calJac1 Contig13114 22630 23283 mononucleotide [A][a] 0 154 + 169 [aaaaaaaaaaaaaa]g[a] indel/deletion g 15 1 >ponAbe2 49 hg18 chr22 16123366 16124069 panTro2 chr22 16140156 16140859 ponAbe2 chr22 13843444 13844147 rheMac2 chr10 61924270 61924987 calJac1 Contig13114 22630 23283 mononucleotide [A][A] 15 157 + 169 [aaaaaaaaaaa]G[A] indel/deletion G 12 1 ->calJac1 51 hg18 chr22 16124376 16124775 panTro2 chr22 16141166 16141565 ponAbe2 chr22 13844454 13844853 rheMac2 chr10 61925295 61925715 calJac1 Contig13114 24029 24487 mononucleotide [T][T][T] 0 41 + 64 [TTTT]C[TTT]C[ttttttttttttttt] indel/deletion,indel/deletion C,C 5,9 3 ->ponAbe2 51 hg18 chr22 16124376 16124775 panTro2 chr22 16141166 16141565 ponAbe2 chr22 13844454 13844853 rheMac2 chr10 61925295 61925715 calJac1 Contig13114 24029 24487 tetranucleotide AAAT 59 245 + 257 TAAATAAATAAAT >rheMac2 51 hg18 chr22 16124376 16124775 panTro2 chr22 16141166 16141565 ponAbe2 chr22 13844454 13844853 rheMac2 chr10 61925295 61925715 calJac1 Contig13114 24029 24487 tetranucleotide AAAT 59 245 + 257 TAAATAAATAAAT >calJac1 51 hg18 chr22 16124376 16124775 panTro2 chr22 16141166 16141565 ponAbe2 chr22 13844454 13844853 rheMac2 chr10 61925295 61925715 calJac1 Contig13114 24029 24487 tetranucleotide AAAT 2 245 + 257 TAAATAAATAAAT ->rheMac2 54 hg18 chr22 16125401 16125766 panTro2 chr22 16142191 16142556 ponAbe2 chr22 13845480 13845851 rheMac2 chr10 61927123 61927443 calJac1 Contig13114 25531 25820 compound.dinucleotide [CCCT][TC].[ct][Tc][Tc][TC] 0 16 + 120 [CCctccctccctccttctctctctctc--------------------------------------------------tctctgtc--tctttctctctctctctc] NA.indel/deletion,indel/deletion,indel/deletion NA.,g,t NA.3,20,26 NA.3 16.29 47.68 [CCCTCCCTCCCTCC]t[TCTCTCTCTCTCTCTCT].[ct][Tctctctctctctctct]g[Tctct]t[TCTCTCTCTCTCTC] >calJac1 54 hg18 chr22 16125401 16125766 panTro2 chr22 16142191 16142556 ponAbe2 chr22 13845480 13845851 rheMac2 chr10 61927123 61927443 calJac1 Contig13114 25531 25820 tetranucleotide [CCCT][tccc] 0 16 + 36 [ccctccctccctcc]t[tccctc] indel/deletion t 15 1 >hg18 54 hg18 chr22 16125401 16125766 panTro2 chr22 16142191 16142556 ponAbe2 chr22 13845480 13845851 rheMac2 chr10 61927123 61927443 calJac1 Contig13114 25531 25820 tetranucleotide.dinucleotide CCCT.[ct][Tc][TC] 0 78 + 120 [CCctccctccctccttctctgtc------tctctctctctctc] NA.indel/deletion,indel/deletion NA.,g NA.3,8 NA.2 78.91 91.114 CCCTCCCTCCCTCC.[ct][Tctct]g[TCTCTCTCTCTCTCTC] >panTro2 54 hg18 chr22 16125401 16125766 panTro2 chr22 16142191 16142556 ponAbe2 chr22 13845480 13845851 rheMac2 chr10 61927123 61927443 calJac1 Contig13114 25531 25820 tetranucleotide.dinucleotide CCCT.[ct][Tc][TC][ct] 0 78 + 120 [ccctccctccctccttctctgtc------tctctctcgctctc] NA.indel/deletion,indel/deletion,indel/deletion NA.,g,g NA.3,8,19 NA.3 78.91 91.114 CCCTCCCTCCCTCC.[ct][Tctct]g[TCTCTCTCTC]g[ctctC] >ponAbe2 54 hg18 chr22 16125401 16125766 panTro2 chr22 16142191 16142556 ponAbe2 chr22 13845480 13845851 rheMac2 chr10 61927123 61927443 calJac1 Contig13114 25531 25820 tetranucleotide.dinucleotide CCCT.[ct][Tc][TC][TC][tc] 0 78 + 120 [CCctccctccctccttctctgtctctctttctctctctctttc] NA.indel/deletion,indel/deletion,indel/substitution,indel/deletion NA.,g,t,t NA.3,8,16,28 NA.4 78.91 91.120 CCCTCCCTCCCTCC.[ct][Tctct]g[TCTCTCT]t[TCTCTCTCTCT]t[tc] ->rheMac2 55 hg18 chr22 16125821 16125949 panTro2 chr22 16142611 16142739 ponAbe2 chr22 13845906 13846034 rheMac2 chr10 61927498 61927626 calJac1 Contig13114 25875 26003 dinucleotide [GA][AG] 0 104 + 115 [GAGAGAGAGA][AG] indel/deletion 11 1 ->hg18 57 hg18 chr22 16126296 16126489 panTro2 chr22 16143086 16143279 ponAbe2 chr22 13846381 13846574 rheMac2 chr10 61927972 61928162 calJac1 Contig13114 26449 26628 trinucleotide [taa][TAA][AAT] 2 155 + 185 [taataataa]cag[taataataataataa][AATA] indel/deletion,indel/deletion cag, 10,28 2 >panTro2 57 hg18 chr22 16126296 16126489 panTro2 chr22 16143086 16143279 ponAbe2 chr22 13846381 13846574 rheMac2 chr10 61927972 61928162 calJac1 Contig13114 26449 26628 trinucleotide [taa][TAA][AAT] 2 155 + 185 [taataataa]cag[taataataataataa][AATA] indel/deletion,indel/deletion cag, 10,28 2 >ponAbe2 57 hg18 chr22 16126296 16126489 panTro2 chr22 16143086 16143279 ponAbe2 chr22 13846381 13846574 rheMac2 chr10 61927972 61928162 calJac1 Contig13114 26449 26628 trinucleotide [taa][TAA][AAT] 2 155 + 185 [taataataa]gag[taataataataataa][AATA] indel/deletion,indel/deletion gag, 10,28 2 ->ponAbe2 62 hg18 chr22 16128863 16129047 panTro2 chr22 16145665 16145849 ponAbe2 chr22 13848947 13849124 rheMac2 chr10 61930525 61930726 calJac1 Contig13114 30055 30231 tetranucleotide ACAA 9 153 + 165 acaaacaaacaaa >hg18 62 hg18 chr22 16128863 16129047 panTro2 chr22 16145665 16145849 ponAbe2 chr22 13848947 13849124 rheMac2 chr10 61930525 61930726 calJac1 Contig13114 30055 30231 tetranucleotide CAAA 10 154 + 181 caaaca--------aacaaacaaacaaa >rheMac2 62 hg18 chr22 16128863 16129047 panTro2 chr22 16145665 16145849 ponAbe2 chr22 13848947 13849124 rheMac2 chr10 61930525 61930726 calJac1 Contig13114 30055 30231 tetranucleotide [CAAA][AACA] 1 154 + 181 [caaacaaacaaac]g[aacaaacaaacaaa] indel/substitution g 14 1 ->hg18 65 hg18 chr22 16129408 16129537 panTro2 chr22 16146210 16146336 ponAbe2 chr22 13851107 13851239 rheMac2 chr10 61931080 61931197 calJac1 Contig13114 30556 30686 mononucleotide [A][A] 0 28 + 52 [AAAAAAA]G---[AAAAAAAAAAAAAA] insertion G 8 1 >panTro2 65 hg18 chr22 16129408 16129537 panTro2 chr22 16146210 16146336 ponAbe2 chr22 13851107 13851239 rheMac2 chr10 61931080 61931197 calJac1 Contig13114 30556 30686 mononucleotide [A][A] 0 28 + 52 [AAAAAAA]G------[AAAAAAAAAAA] insertion G 8 1 >ponAbe2 65 hg18 chr22 16129408 16129537 panTro2 chr22 16146210 16146336 ponAbe2 chr22 13851107 13851239 rheMac2 chr10 61931080 61931197 calJac1 Contig13114 30556 30686 mononucleotide A 0 28 + 52 aaaaaaaaaaaaaaaaaaaaaaaaa >calJac1 65 hg18 chr22 16129408 16129537 panTro2 chr22 16146210 16146336 ponAbe2 chr22 13851107 13851239 rheMac2 chr10 61931080 61931197 calJac1 Contig13114 30556 30686 mononucleotide [A][A] 0 28 + 51 [aaaaaaaaaaaa]c[aaaaaaaaaaa] insertion c 13 1 ->hg18 68 hg18 chr22 16129966 16130165 panTro2 chr22 16146765 16146964 ponAbe2 chr22 13851668 13851867 rheMac2 chr10 61931627 61931825 calJac1 Contig13114 31737 31931 tetranucleotide AAGG 4 21 + 32 AAGGAAGGAAGG >panTro2 68 hg18 chr22 16129966 16130165 panTro2 chr22 16146765 16146964 ponAbe2 chr22 13851668 13851867 rheMac2 chr10 61931627 61931825 calJac1 Contig13114 31737 31931 tetranucleotide AAGG 4 21 + 32 AAGGAAGGAAGG >ponAbe2 68 hg18 chr22 16129966 16130165 panTro2 chr22 16146765 16146964 ponAbe2 chr22 13851668 13851867 rheMac2 chr10 61931627 61931825 calJac1 Contig13114 31737 31931 tetranucleotide AAGG 4 21 + 32 AAGGAAGGAAGG >rheMac2 68 hg18 chr22 16129966 16130165 panTro2 chr22 16146765 16146964 ponAbe2 chr22 13851668 13851867 rheMac2 chr10 61931627 61931825 calJac1 Contig13114 31737 31931 tetranucleotide AAGG 5 21 + 32 AAGGAAGGAAGG ->rheMac2 70 hg18 chr22 16130388 16130720 panTro2 chr22 16147174 16147507 ponAbe2 chr22 13852091 13852425 rheMac2 chr10 61932049 61932359 calJac1 Contig13114 32153 32482 mononucleotide C 25 289 + 301 CCCCCCCCCCCCC ->calJac1 72 hg18 chr22 16131964 16132665 panTro2 chr22 16148745 16149456 ponAbe2 chr22 13853665 13854383 rheMac2 chr10 61935354 61936080 calJac1 Contig13114 33032 33737 tetranucleotide TTTG 27 167 + 178 tttgtttgtttg ->ponAbe2 72 hg18 chr22 16131964 16132665 panTro2 chr22 16148745 16149456 ponAbe2 chr22 13853665 13854383 rheMac2 chr10 61935354 61936080 calJac1 Contig13114 33032 33737 mononucleotide [t][T] 10 352 + 362 [t]a[ttttttttt] indel/deletion a 2 1 ->rheMac2 72 hg18 chr22 16131964 16132665 panTro2 chr22 16148745 16149456 ponAbe2 chr22 13853665 13854383 rheMac2 chr10 61935354 61936080 calJac1 Contig13114 33032 33737 mononucleotide T 34 515 + 525 TTTTTTTTTTT ->calJac1 72 hg18 chr22 16131964 16132665 panTro2 chr22 16148745 16149456 ponAbe2 chr22 13853665 13854383 rheMac2 chr10 61935354 61936080 calJac1 Contig13114 33032 33737 tetranucleotide TTTA 39 530 + 564 tttatttattta-----------tttatttattta >hg18 72 hg18 chr22 16131964 16132665 panTro2 chr22 16148745 16149456 ponAbe2 chr22 13853665 13854383 rheMac2 chr10 61935354 61936080 calJac1 Contig13114 33032 33737 tetranucleotide [tatt][TTTA] 40 531 + 564 [ttatt]--[ttta-----------tttatttattta] indel/deletion 6 1 >panTro2 72 hg18 chr22 16131964 16132665 panTro2 chr22 16148745 16149456 ponAbe2 chr22 13853665 13854383 rheMac2 chr10 61935354 61936080 calJac1 Contig13114 33032 33737 tetranucleotide [tatt][TTTA] 30 531 + 564 [ttatt]--[ttta-----------tttatttattta] indel/deletion 6 1 >ponAbe2 72 hg18 chr22 16131964 16132665 panTro2 chr22 16148745 16149456 ponAbe2 chr22 13853665 13854383 rheMac2 chr10 61935354 61936080 calJac1 Contig13114 33032 33737 tetranucleotide [tatt][TTTA] 24 531 + 564 [ttatt]--[ttta-----------tttatttattta] indel/deletion 6 1 >rheMac2 72 hg18 chr22 16131964 16132665 panTro2 chr22 16148745 16149456 ponAbe2 chr22 13853665 13854383 rheMac2 chr10 61935354 61936080 calJac1 Contig13114 33032 33737 mononucleotide T 36 554 + 571 ttttttttttt--ttttt ->hg18 73 hg18 chr22 16132665 16133124 panTro2 chr22 16149456 16149917 ponAbe2 chr22 13854383 13854844 rheMac2 chr10 61935354 61935806 calJac1 Contig13114 33737 34150 tetranucleotide [GTTT][gttT] 0 159 + 178 [ttgtttgtttgttt]a[tgttt] indel/deletion a 15 1 >panTro2 73 hg18 chr22 16132665 16133124 panTro2 chr22 16149456 16149917 ponAbe2 chr22 13854383 13854844 rheMac2 chr10 61935354 61935806 calJac1 Contig13114 33737 34150 tetranucleotide [GTTT][gttT] 0 159 + 178 [ttgtttgtttgttt]a[tgttt] indel/deletion a 15 1 >ponAbe2 73 hg18 chr22 16132665 16133124 panTro2 chr22 16149456 16149917 ponAbe2 chr22 13854383 13854844 rheMac2 chr10 61935354 61935806 calJac1 Contig13114 33737 34150 tetranucleotide [GTTT][gttT] 0 159 + 178 [ttgtttgtttgttt]a[tgttt] indel/deletion a 15 1 ->hg18 74 hg18 chr22 16133347 16133775 panTro2 chr22 16150141 16150569 ponAbe2 chr22 13855071 13855499 rheMac2 chr10 61936725 61937155 calJac1 Contig13114 34318 34739 tetranucleotide CCTC 0 209 + 220 CCTCCCTCCCTC >panTro2 74 hg18 chr22 16133347 16133775 panTro2 chr22 16150141 16150569 ponAbe2 chr22 13855071 13855499 rheMac2 chr10 61936725 61937155 calJac1 Contig13114 34318 34739 tetranucleotide CCTC 0 209 + 220 CCTCCCTCCCTC >ponAbe2 74 hg18 chr22 16133347 16133775 panTro2 chr22 16150141 16150569 ponAbe2 chr22 13855071 13855499 rheMac2 chr10 61936725 61937155 calJac1 Contig13114 34318 34739 tetranucleotide CCTC 0 209 + 220 CCTCCCTCCCTC >rheMac2 74 hg18 chr22 16133347 16133775 panTro2 chr22 16150141 16150569 ponAbe2 chr22 13855071 13855499 rheMac2 chr10 61936725 61937155 calJac1 Contig13114 34318 34739 tetranucleotide CCTC 0 209 + 220 CCTCCCTCCCTC ->rheMac2 78 hg18 chr22 16134760 16134871 panTro2 chr22 16151554 16151662 ponAbe2 chr22 13856483 13856596 rheMac2 chr10 61938139 61938249 calJac1 Contig19362 1709 1820 mononucleotide A 2 101 + 115 aaaaa---aaaaaaa >calJac1 78 hg18 chr22 16134760 16134871 panTro2 chr22 16151554 16151662 ponAbe2 chr22 13856483 13856596 rheMac2 chr10 61938139 61938249 calJac1 Contig19362 1709 1820 mononucleotide A 4 101 + 115 aaaaaaaaaaaaaaa >hg18 78 hg18 chr22 16134760 16134871 panTro2 chr22 16151554 16151662 ponAbe2 chr22 13856483 13856596 rheMac2 chr10 61938139 61938249 calJac1 Contig19362 1709 1820 mononucleotide A 0 102 + 111 aaaaaaaaaa >ponAbe2 78 hg18 chr22 16134760 16134871 panTro2 chr22 16151554 16151662 ponAbe2 chr22 13856483 13856596 rheMac2 chr10 61938139 61938249 calJac1 Contig19362 1709 1820 mononucleotide A 2 102 + 115 aaaaaaaaaaaaaa ->calJac1 80 hg18 chr22 16139975 16140074 panTro2 chr22 16160385 16160484 ponAbe2 chr22 13865832 13865931 rheMac2 chr10 61947469 61947563 calJac1 Contig12391 263 319 mononucleotide [T][T] 1 9 + 23 [TTTTTTTTTT]A[TTTT] indel/deletion A 11 1 ->calJac1 81 hg18 chr22 16140571 16140723 panTro2 chr22 16160932 16161084 ponAbe2 chr22 13866427 13866579 rheMac2 chr10 61948011 61948154 calJac1 Contig12391 837 988 tetranucleotide [ATAA][TAAA] 10 137 + 155 [taaaTAAATAAATAA][TAAA] indel/deletion 16 1 ->hg18 82 hg18 chr22 16141188 16141332 panTro2 chr22 16161549 16161696 ponAbe2 chr22 13866625 13866769 rheMac2 chr10 61948604 61948758 calJac1 Contig12391 996 1068 mononucleotide A 0 103 + 117 aaaaaaaaaaaaaaa >panTro2 82 hg18 chr22 16141188 16141332 panTro2 chr22 16161549 16161696 ponAbe2 chr22 13866625 13866769 rheMac2 chr10 61948604 61948758 calJac1 Contig12391 996 1068 mononucleotide A 0 103 + 124 aaa---aaaaaaaaaaaaaaaa >ponAbe2 82 hg18 chr22 16141188 16141332 panTro2 chr22 16161549 16161696 ponAbe2 chr22 13866625 13866769 rheMac2 chr10 61948604 61948758 calJac1 Contig12391 996 1068 mononucleotide A 0 103 + 116 aaaaaaaaaaaaaa ->rheMac2 82 hg18 chr22 16141188 16141332 panTro2 chr22 16161549 16161696 ponAbe2 chr22 13866625 13866769 rheMac2 chr10 61948604 61948758 calJac1 Contig12391 996 1068 mononucleotide T 0 138 + 152 TTTTTTTTTTTTTTT >hg18 82 hg18 chr22 16141188 16141332 panTro2 chr22 16161549 16161696 ponAbe2 chr22 13866625 13866769 rheMac2 chr10 61948604 61948758 calJac1 Contig12391 996 1068 mononucleotide T 6 139 + 148 TTTTTTTTTT >panTro2 82 hg18 chr22 16141188 16141332 panTro2 chr22 16161549 16161696 ponAbe2 chr22 13866625 13866769 rheMac2 chr10 61948604 61948758 calJac1 Contig12391 996 1068 mononucleotide T 3 139 + 148 TTTTTTTTTT >ponAbe2 82 hg18 chr22 16141188 16141332 panTro2 chr22 16161549 16161696 ponAbe2 chr22 13866625 13866769 rheMac2 chr10 61948604 61948758 calJac1 Contig12391 996 1068 mononucleotide T 7 139 + 149 TTTTTTTTTTT >calJac1 82 hg18 chr22 16141188 16141332 panTro2 chr22 16161549 16161696 ponAbe2 chr22 13866625 13866769 rheMac2 chr10 61948604 61948758 calJac1 Contig12391 996 1068 mononucleotide T 79 139 + 150 TTTTTTTTTTTT ->hg18 88 hg18 chr22 16146883 16147079 panTro2 chr22 16167267 16167463 ponAbe2 chr22 13873058 13873254 rheMac2 chr10 61955020 61955216 calJac1 Contig11249 1024 1191 dinucleotide [Ta][TA] 0 179 + 196 [tatat]g[tatatatatata] indel/deletion g 6 1 >panTro2 88 hg18 chr22 16146883 16147079 panTro2 chr22 16167267 16167463 ponAbe2 chr22 13873058 13873254 rheMac2 chr10 61955020 61955216 calJac1 Contig11249 1024 1191 dinucleotide TA 0 179 + 196 tatatatatatatatata >ponAbe2 88 hg18 chr22 16146883 16147079 panTro2 chr22 16167267 16167463 ponAbe2 chr22 13873058 13873254 rheMac2 chr10 61955020 61955216 calJac1 Contig11249 1024 1191 dinucleotide TA 0 179 + 196 tatatatatatatatata >rheMac2 88 hg18 chr22 16146883 16147079 panTro2 chr22 16167267 16167463 ponAbe2 chr22 13873058 13873254 rheMac2 chr10 61955020 61955216 calJac1 Contig11249 1024 1191 dinucleotide AT 0 180 + 196 atatatatatatatata ->hg18 89 hg18 chr22 16147079 16147276 panTro2 chr22 16167463 16167663 ponAbe2 chr22 13873254 13873448 rheMac2 chr10 61955729 61955915 calJac1 Contig11249 1191 1369 mononucleotide [t][T] 0 1 + 21 [t]a-----[tttttttttttttt] indel/deletion a 2 1 >panTro2 89 hg18 chr22 16147079 16147276 panTro2 chr22 16167463 16167663 ponAbe2 chr22 13873254 13873448 rheMac2 chr10 61955729 61955915 calJac1 Contig11249 1191 1369 mononucleotide [t][T] 0 1 + 21 [t]a[ttttttttttttttttttt] indel/deletion a 2 1 >ponAbe2 89 hg18 chr22 16147079 16147276 panTro2 chr22 16167463 16167663 ponAbe2 chr22 13873254 13873448 rheMac2 chr10 61955729 61955915 calJac1 Contig11249 1191 1369 mononucleotide [t][T] 0 1 + 21 [t]a--------[ttttttttttt] indel/deletion a 2 1 >calJac1 89 hg18 chr22 16147079 16147276 panTro2 chr22 16167463 16167663 ponAbe2 chr22 13873254 13873448 rheMac2 chr10 61955729 61955915 calJac1 Contig11249 1191 1369 mononucleotide T 0 1 + 10 tttttttttt ->rheMac2 89 hg18 chr22 16147079 16147276 panTro2 chr22 16167463 16167663 ponAbe2 chr22 13873254 13873448 rheMac2 chr10 61955729 61955915 calJac1 Contig11249 1191 1369 mononucleotide [t][T] 8 178 + 188 [t]a[ttttttttt] indel/deletion a 2 1 ->rheMac2 95 hg18 chr22 16150676 16150875 panTro2 chr22 16171411 16171610 ponAbe2 chr22 13877198 13877397 rheMac2 chr10 61959701 61959903 calJac1 Contig12391 7283 7494 mononucleotide T 15 207 + 217 ttttttttttt ->calJac1 96 hg18 chr22 16150875 16151031 panTro2 chr22 16171610 16171766 ponAbe2 chr22 13877397 13877553 rheMac2 chr10 61959903 61960059 calJac1 Contig12391 7633 7784 mononucleotide T 0 127 + 141 tttt-----tttttt ->hg18 97 hg18 chr22 16151135 16151786 panTro2 chr22 16171870 16172515 ponAbe2 chr22 13877657 13878308 rheMac2 chr10 61960163 61960814 calJac1 Contig11249 6667 7327 mononucleotide [T][t][t] 8 488 + 503 [tttttttttt]c[ttt]g[t] indel/deletion,indel/deletion c,g 11,15 2 >panTro2 97 hg18 chr22 16151135 16151786 panTro2 chr22 16171870 16172515 ponAbe2 chr22 13877657 13878308 rheMac2 chr10 61960163 61960814 calJac1 Contig11249 6667 7327 mononucleotide [T][t][t] 13 488 + 502 [ttttttttt]c[ttt]g[t] indel/deletion,indel/deletion c,g 10,14 2 >ponAbe2 97 hg18 chr22 16151135 16151786 panTro2 chr22 16171870 16172515 ponAbe2 chr22 13877657 13878308 rheMac2 chr10 61960163 61960814 calJac1 Contig11249 6667 7327 mononucleotide [T][T] 8 488 + 501 [TTTTTTTTTT]C[TTT] indel/deletion C 11 1 >rheMac2 97 hg18 chr22 16151135 16151786 panTro2 chr22 16171870 16172515 ponAbe2 chr22 13877657 13878308 rheMac2 chr10 61960163 61960814 calJac1 Contig11249 6667 7327 mononucleotide [T][T] 8 488 + 498 [TTTTTTTTT]C[T] indel/deletion C 10 1 >calJac1 97 hg18 chr22 16151135 16151786 panTro2 chr22 16171870 16172515 ponAbe2 chr22 13877657 13878308 rheMac2 chr10 61960163 61960814 calJac1 Contig11249 6667 7327 mononucleotide T 1 488 + 498 TTTTTTTTTTT ->panTro2 98 hg18 chr22 16151786 16152355 panTro2 chr22 16172515 16173078 ponAbe2 chr22 13878308 13878876 rheMac2 chr10 61960814 61961383 calJac1 Contig12391 10267 10830 mononucleotide A 0 299 + 309 aaaaaaaaaaa >ponAbe2 98 hg18 chr22 16151786 16152355 panTro2 chr22 16172515 16173078 ponAbe2 chr22 13878308 13878876 rheMac2 chr10 61960814 61961383 calJac1 Contig12391 10267 10830 mononucleotide A 0 299 + 315 aaaaaaaaaaaaaaaaa >rheMac2 98 hg18 chr22 16151786 16152355 panTro2 chr22 16172515 16173078 ponAbe2 chr22 13878308 13878876 rheMac2 chr10 61960814 61961383 calJac1 Contig12391 10267 10830 mononucleotide A 0 299 + 307 aaaaaaaaa >hg18 98 hg18 chr22 16151786 16152355 panTro2 chr22 16172515 16173078 ponAbe2 chr22 13878308 13878876 rheMac2 chr10 61960814 61961383 calJac1 Contig12391 10267 10830 mononucleotide A 3 303 + 315 aaaaaaaaaaaaa ->calJac1 98 hg18 chr22 16151786 16152355 panTro2 chr22 16172515 16173078 ponAbe2 chr22 13878308 13878876 rheMac2 chr10 61960814 61961383 calJac1 Contig12391 10267 10830 tetranucleotide [aaat][AAAT] 19 322 + 348 [aaat]ta[aaataaat----aaataaaTA] indel/deletion ta 5 1 >rheMac2 98 hg18 chr22 16151786 16152355 panTro2 chr22 16172515 16173078 ponAbe2 chr22 13878308 13878876 rheMac2 chr10 61960814 61961383 calJac1 Contig12391 10267 10830 tetranucleotide [AAAt][AAAT] 8 328 + 348 [aaataaa]c[aaaTAAATAAATA] indel/deletion c 8 1 ->ponAbe2 98 hg18 chr22 16151786 16152355 panTro2 chr22 16172515 16173078 ponAbe2 chr22 13878308 13878876 rheMac2 chr10 61960814 61961383 calJac1 Contig12391 10267 10830 mononucleotide T 22 582 + 590 ttttttttt >rheMac2 98 hg18 chr22 16151786 16152355 panTro2 chr22 16172515 16173078 ponAbe2 chr22 13878308 13878876 rheMac2 chr10 61960814 61961383 calJac1 Contig12391 10267 10830 mononucleotide [T][T] 27 582 + 596 [ttttttttt]c[ttttt] insertion c 10 1 >calJac1 98 hg18 chr22 16151786 16152355 panTro2 chr22 16172515 16173078 ponAbe2 chr22 13878308 13878876 rheMac2 chr10 61960814 61961383 calJac1 Contig12391 10267 10830 mononucleotide T 27 582 + 590 TTTTTTTTT >hg18 98 hg18 chr22 16151786 16152355 panTro2 chr22 16172515 16173078 ponAbe2 chr22 13878308 13878876 rheMac2 chr10 61960814 61961383 calJac1 Contig12391 10267 10830 mononucleotide T 25 583 + 594 tttttttttttt >panTro2 98 hg18 chr22 16151786 16152355 panTro2 chr22 16172515 16173078 ponAbe2 chr22 13878308 13878876 rheMac2 chr10 61960814 61961383 calJac1 Contig12391 10267 10830 mononucleotide T 32 583 + 595 ttttttttttttt ->calJac1 100 hg18 chr22 16165740 16166035 panTro2 chr22 16187216 16187511 ponAbe2 chr22 13894503 13894798 rheMac2 chr10 61975717 61976012 calJac1 Contig12391 17383 17855 mononucleotide [t][T][t][t] 5 332 + 360 [t]a[tttttttttt]c[tttt]c[ttttttttttt] indel/deletion,indel/deletion,indel/deletion a,c,c 2,13,18 3 ->hg18 104 hg18 chr22 16166472 16167032 panTro2 chr22 16187948 16188522 ponAbe2 chr22 13895235 13895793 rheMac2 chr10 61976448 61977034 calJac1 Contig12391 18412 18952 tetranucleotide TTTG 0 200 + 212 TTTGTTTGT-TTG >hg18 104 hg18 chr22 16166472 16167032 panTro2 chr22 16187948 16188522 ponAbe2 chr22 13895235 13895793 rheMac2 chr10 61976448 61977034 calJac1 Contig12391 18412 18952 trinucleotide GTT 1 221 + 248 Gttgttgttgt------------tgttg >panTro2 104 hg18 chr22 16166472 16167032 panTro2 chr22 16187948 16188522 ponAbe2 chr22 13895235 13895793 rheMac2 chr10 61976448 61977034 calJac1 Contig12391 18412 18952 tetranucleotide TTTG 0 200 + 212 TTTGTTTGT-TTG >panTro2 104 hg18 chr22 16166472 16167032 panTro2 chr22 16187948 16188522 ponAbe2 chr22 13895235 13895793 rheMac2 chr10 61976448 61977034 calJac1 Contig12391 18412 18952 trinucleotide GTT 1 221 + 248 Gttgttgttgt------------tgttg >ponAbe2 104 hg18 chr22 16166472 16167032 panTro2 chr22 16187948 16188522 ponAbe2 chr22 13895235 13895793 rheMac2 chr10 61976448 61977034 calJac1 Contig12391 18412 18952 tetranucleotide TTTG 0 200 + 212 TTTGTTTGT-TTG >ponAbe2 104 hg18 chr22 16166472 16167032 panTro2 chr22 16187948 16188522 ponAbe2 chr22 13895235 13895793 rheMac2 chr10 61976448 61977034 calJac1 Contig12391 18412 18952 trinucleotide GTT 1 221 + 248 Gttgttgttgt------------tgttg >calJac1 104 hg18 chr22 16166472 16167032 panTro2 chr22 16187948 16188522 ponAbe2 chr22 13895235 13895793 rheMac2 chr10 61976448 61977034 calJac1 Contig12391 18412 18952 mononucleotide [t][t][T] 14 220 + 247 [t]g[tt]a[ttttt--------------tttt] indel/deletion,indel/deletion g,a 2,5 2 >rheMac2 104 hg18 chr22 16166472 16167032 panTro2 chr22 16187948 16188522 ponAbe2 chr22 13895235 13895793 rheMac2 chr10 61976448 61977034 calJac1 Contig12391 18412 18952 trinucleotide [gtt][TTG][tgt] 1 221 + 248 [gttgtt]a[ttgttgttgttgttg]a[tgttg] indel/deletion,indel/deletion a,a 7,23 2 ->hg18 104 hg18 chr22 16166472 16167032 panTro2 chr22 16187948 16188522 ponAbe2 chr22 13895235 13895793 rheMac2 chr10 61976448 61977034 calJac1 Contig12391 18412 18952 mononucleotide [t][T][t] 31 412 + 445 [t]a--------------[tttttttttttttttt]g[t] indel/deletion,indel/deletion a,g 2,19 2 >panTro2 104 hg18 chr22 16166472 16167032 panTro2 chr22 16187948 16188522 ponAbe2 chr22 13895235 13895793 rheMac2 chr10 61976448 61977034 calJac1 Contig12391 18412 18952 mononucleotide [T][t] 31 415 + 445 [ttttttttttttttttttttttttttttt]g[t] indel/deletion g 30 1 >ponAbe2 104 hg18 chr22 16166472 16167032 panTro2 chr22 16187948 16188522 ponAbe2 chr22 13895235 13895793 rheMac2 chr10 61976448 61977034 calJac1 Contig12391 18412 18952 mononucleotide [T][t] 34 415 + 432 [tttttttttttttttt]g[t] indel/deletion g 17 1 >rheMac2 104 hg18 chr22 16166472 16167032 panTro2 chr22 16187948 16188522 ponAbe2 chr22 13895235 13895793 rheMac2 chr10 61976448 61977034 calJac1 Contig12391 18412 18952 mononucleotide [T][t] 1 415 + 430 [tttttttttttttt]g[t] indel/deletion g 15 1 >calJac1 104 hg18 chr22 16166472 16167032 panTro2 chr22 16187948 16188522 ponAbe2 chr22 13895235 13895793 rheMac2 chr10 61976448 61977034 calJac1 Contig12391 18412 18952 mononucleotide T 54 424 + 442 ttttttttttttttttttt ->hg18 104 hg18 chr22 16166472 16167032 panTro2 chr22 16187948 16188522 ponAbe2 chr22 13895235 13895793 rheMac2 chr10 61976448 61977034 calJac1 Contig12391 18412 18952 tetranucleotide [TTTG][GTTT] 46 582 + 603 [TTTGTTTG][TTGTTTGTTTGTTT] indel/substitution 9 1 >ponAbe2 104 hg18 chr22 16166472 16167032 panTro2 chr22 16187948 16188522 ponAbe2 chr22 13895235 13895793 rheMac2 chr10 61976448 61977034 calJac1 Contig12391 18412 18952 tetranucleotide [TTTG][GTTT] 48 582 + 603 [TTTGTTTG][TTGTTTGTTTGTTT] indel/substitution 9 1 ->calJac1 105 hg18 chr22 16167032 16168313 panTro2 chr22 16188522 16189796 ponAbe2 chr22 13895793 13897066 rheMac2 chr10 61977034 61978235 calJac1 Contig12391 19268 20510 mononucleotide [T][T][T] 0 45 + 64 [T]C[ttttttt]c[tttttttttt] indel/deletion,insertion C,c 2,10 2 >ponAbe2 105 hg18 chr22 16167032 16168313 panTro2 chr22 16188522 16189796 ponAbe2 chr22 13895793 13897066 rheMac2 chr10 61977034 61978235 calJac1 Contig12391 19268 20510 trinucleotide [Gtt][TTG][ttg] 0 50 + 74 [Gtt]t---[ttgttgttgttg]ttt[ttg] indel/deletion,indel/deletion t,ttt 4,17 2 >rheMac2 105 hg18 chr22 16167032 16168313 panTro2 chr22 16188522 16189796 ponAbe2 chr22 13895793 13897066 rheMac2 chr10 61977034 61978235 calJac1 Contig12391 19268 20510 trinucleotide [GTT][GTT][ttg] 0 51 + 76 [GTT]TTt[ttgttgttgttgttgtt][ttg] indel/deletion,indel/deletion TTt, 4,24 2 >hg18 105 hg18 chr22 16167032 16168313 panTro2 chr22 16188522 16189796 ponAbe2 chr22 13895793 13897066 rheMac2 chr10 61977034 61978235 calJac1 Contig12391 19268 20510 trinucleotide [TTG][ttg] 0 54 + 74 [ttgttgttgttgttg]ttt[ttg] indel/deletion ttt 16 1 >panTro2 105 hg18 chr22 16167032 16168313 panTro2 chr22 16188522 16189796 ponAbe2 chr22 13895793 13897066 rheMac2 chr10 61977034 61978235 calJac1 Contig12391 19268 20510 trinucleotide [TTG][ttg] 0 54 + 74 [ttgttgttgttgttg]ttt[ttg] indel/deletion ttt 16 1 ->ponAbe2 105 hg18 chr22 16167032 16168313 panTro2 chr22 16188522 16189796 ponAbe2 chr22 13895793 13897066 rheMac2 chr10 61977034 61978235 calJac1 Contig12391 19268 20510 mononucleotide A 11 1276 + 1284 aaaaaaaaa >rheMac2 105 hg18 chr22 16167032 16168313 panTro2 chr22 16188522 16189796 ponAbe2 chr22 13895793 13897066 rheMac2 chr10 61977034 61978235 calJac1 Contig12391 19268 20510 mononucleotide A 83 1276 + 1284 aaaaaaaaa >calJac1 105 hg18 chr22 16167032 16168313 panTro2 chr22 16188522 16189796 ponAbe2 chr22 13895793 13897066 rheMac2 chr10 61977034 61978235 calJac1 Contig12391 19268 20510 mononucleotide A 42 1276 + 1284 aaaaaaaaa ->ponAbe2 106 hg18 chr22 16169890 16170045 panTro2 chr22 16191272 16191427 ponAbe2 chr22 13898766 13898941 rheMac2 chr10 61979989 61980162 calJac1 Contig12391 20528 20667 tetranucleotide ATGT 0 164 + 175 atgtatgtatgt ->hg18 108 hg18 chr22 16170691 16171260 panTro2 chr22 16192073 16192651 ponAbe2 chr22 13901664 13902239 rheMac2 chr10 61980939 61981513 calJac1 Contig12391 21512 22179 mononucleotide [T][T] 11 478 + 587 [T]C--------------------------------------------------------------------------------------------------[tttttttttt] indel/deletion C 2 1 >panTro2 108 hg18 chr22 16170691 16171260 panTro2 chr22 16192073 16192651 ponAbe2 chr22 13901664 13902239 rheMac2 chr10 61980939 61981513 calJac1 Contig12391 21512 22179 mononucleotide [T][T] 11 478 + 587 [T]C[ttt-----------------------------------------------------------------------------------------tttttttttttttttt] indel/deletion C 2 1 >ponAbe2 108 hg18 chr22 16170691 16171260 panTro2 chr22 16192073 16192651 ponAbe2 chr22 13901664 13902239 rheMac2 chr10 61980939 61981513 calJac1 Contig12391 21512 22179 mononucleotide [T][T] 11 478 + 587 [T]C--------------------------------------------------------------------------------------------[tttttttttttttttt] indel/deletion C 2 1 >rheMac2 108 hg18 chr22 16170691 16171260 panTro2 chr22 16192073 16192651 ponAbe2 chr22 13901664 13902239 rheMac2 chr10 61980939 61981513 calJac1 Contig12391 21512 22179 mononucleotide [T][T] 12 480 + 496 [ttt]c[ttttttttttttt] indel/deletion C 4 1 >calJac1 108 hg18 chr22 16170691 16171260 panTro2 chr22 16192073 16192651 ponAbe2 chr22 13901664 13902239 rheMac2 chr10 61980939 61981513 calJac1 Contig12391 21512 22179 dinucleotide CA 14 560 + 569 CACACACACA >calJac1 108 hg18 chr22 16170691 16171260 panTro2 chr22 16192073 16192651 ponAbe2 chr22 13901664 13902239 rheMac2 chr10 61980939 61981513 calJac1 Contig12391 21512 22179 mononucleotide [t][T] 14 574 + 587 [tt]c[ttttttttttt] indel/deletion c 3 1 ->calJac1 115 hg18 chr22 16174763 16175207 panTro2 chr22 16197174 16197613 ponAbe2 chr22 13905656 13906090 rheMac2 chr10 61985283 61985741 calJac1 Contig12391 25501 26010 mononucleotide A 1 284 + 301 aaaa---aaaaaaaaaaa >rheMac2 115 hg18 chr22 16174763 16175207 panTro2 chr22 16197174 16197613 ponAbe2 chr22 13905656 13906090 rheMac2 chr10 61985283 61985741 calJac1 Contig12391 25501 26010 mononucleotide [A][A][A][A][A][A][A] 0 285 + 346 [aaaaaaaaaaaaaaaaa]g[aaa]g[aaa]g[aaa]g[aaa]g[a----------------------aa]g[aa] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion G,G,G,G,G,G 18,22,26,30,34,38 6 ->hg18 117 hg18 chr22 16175439 16175904 panTro2 chr22 16197845 16198310 ponAbe2 chr22 13906321 13906786 rheMac2 chr10 61985966 61986429 calJac1 Contig12391 26553 27022 dinucleotide GT 7 98 + 108 GTGTGTGTGTG >panTro2 117 hg18 chr22 16175439 16175904 panTro2 chr22 16197845 16198310 ponAbe2 chr22 13906321 13906786 rheMac2 chr10 61985966 61986429 calJac1 Contig12391 26553 27022 dinucleotide GT 7 98 + 108 GTGTGTGTGTG >ponAbe2 117 hg18 chr22 16175439 16175904 panTro2 chr22 16197845 16198310 ponAbe2 chr22 13906321 13906786 rheMac2 chr10 61985966 61986429 calJac1 Contig12391 26553 27022 dinucleotide GT 7 98 + 108 GTGTGTGTGTG ->calJac1 125 hg18 chr22 16190506 16190908 panTro2 chr22 16213866 16214268 ponAbe2 chr22 13922209 13922582 rheMac2 chr10 62000830 62001238 calJac1 Contig12391 35279 35667 mononucleotide A 6 341 + 365 aaaaaaa---------------aaa >hg18 125 hg18 chr22 16190506 16190908 panTro2 chr22 16213866 16214268 ponAbe2 chr22 13922209 13922582 rheMac2 chr10 62000830 62001238 calJac1 Contig12391 35279 35667 mononucleotide [A][A][a][a] 1 342 + 373 [aaaaa]g------[aaaaaaaaaa]g[aaaa]g[aaaa] insertion,indel/deletion,indel/deletion g,g,g 6,17,22 3 >panTro2 125 hg18 chr22 16190506 16190908 panTro2 chr22 16213866 16214268 ponAbe2 chr22 13922209 13922582 rheMac2 chr10 62000830 62001238 calJac1 Contig12391 35279 35667 mononucleotide [A][A][a][a] 1 342 + 373 [aaaaa]g------[aaaaaaaaaa]g[aaaa]g[aaaa] insertion,indel/deletion,indel/deletion g,g,g 6,17,22 3 >ponAbe2 125 hg18 chr22 16190506 16190908 panTro2 chr22 16213866 16214268 ponAbe2 chr22 13922209 13922582 rheMac2 chr10 62000830 62001238 calJac1 Contig12391 35279 35667 mononucleotide [A][A][a][a] 33 342 + 373 [aaaaa]g---[aaaaaaaaaaaaa]g[aaaa]g[aaaa] insertion,indel/deletion,indel/deletion g,g,g 6,20,25 3 >rheMac2 125 hg18 chr22 16190506 16190908 panTro2 chr22 16213866 16214268 ponAbe2 chr22 13922209 13922582 rheMac2 chr10 62000830 62001238 calJac1 Contig12391 35279 35667 mononucleotide A 1 342 + 373 aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa ->calJac1 127 hg18 chr22 16191000 16191114 panTro2 chr22 16214926 16215032 ponAbe2 chr22 13932603 13932717 rheMac2 chr10 62001330 62001444 calJac1 Contig12391 36142 36264 mononucleotide [A][a][a] 0 102 + 121 [aaaaaaaaaa]g[aaaa]g[aaaa] indel/deletion,indel/deletion g,g 11,16 2 ->hg18 129 hg18 chr22 16196830 16197535 panTro2 chr22 16220191 16220893 ponAbe2 chr22 13938662 13939373 rheMac2 chr10 62008861 62009550 calJac1 Contig12391 37461 38167 mononucleotide T 0 7 + 15 TTTTTTTTT ->hg18 129 hg18 chr22 16196830 16197535 panTro2 chr22 16220191 16220893 ponAbe2 chr22 13938662 13939373 rheMac2 chr10 62008861 62009550 calJac1 Contig12391 37461 38167 mononucleotide A 0 100 + 118 AAAAAAAAAAAAAAAAAAA >panTro2 129 hg18 chr22 16196830 16197535 panTro2 chr22 16220191 16220893 ponAbe2 chr22 13938662 13939373 rheMac2 chr10 62008861 62009550 calJac1 Contig12391 37461 38167 mononucleotide A 3 100 + 116 AAAAAAAAAAAAAAAAA >rheMac2 129 hg18 chr22 16196830 16197535 panTro2 chr22 16220191 16220893 ponAbe2 chr22 13938662 13939373 rheMac2 chr10 62008861 62009550 calJac1 Contig12391 37461 38167 mononucleotide A 3 100 + 112 AAAAAAAAAAAAA >calJac1 129 hg18 chr22 16196830 16197535 panTro2 chr22 16220191 16220893 ponAbe2 chr22 13938662 13939373 rheMac2 chr10 62008861 62009550 calJac1 Contig12391 37461 38167 mononucleotide [A][A] 3 100 + 120 [AAAAAAAAAAAAAAAAAA]G[AA] indel/deletion G 19 1 >ponAbe2 129 hg18 chr22 16196830 16197535 panTro2 chr22 16220191 16220893 ponAbe2 chr22 13938662 13939373 rheMac2 chr10 62008861 62009550 calJac1 Contig12391 37461 38167 mononucleotide A 15 113 + 121 AAAAAAAAA ->hg18 129 hg18 chr22 16196830 16197535 panTro2 chr22 16220191 16220893 ponAbe2 chr22 13938662 13939373 rheMac2 chr10 62008861 62009550 calJac1 Contig12391 37461 38167 mononucleotide T 3 245 + 253 TTTTTTTTT >panTro2 129 hg18 chr22 16196830 16197535 panTro2 chr22 16220191 16220893 ponAbe2 chr22 13938662 13939373 rheMac2 chr10 62008861 62009550 calJac1 Contig12391 37461 38167 mononucleotide T 8 245 + 255 TTTTTTTTTTT ->hg18 129 hg18 chr22 16196830 16197535 panTro2 chr22 16220191 16220893 ponAbe2 chr22 13938662 13939373 rheMac2 chr10 62008861 62009550 calJac1 Contig12391 37461 38167 tetranucleotide [TTTA][attt] 14 494 + 523 [tatttatttatttatttatttattta][attt] indel/deletion 27 1 >panTro2 129 hg18 chr22 16196830 16197535 panTro2 chr22 16220191 16220893 ponAbe2 chr22 13938662 13939373 rheMac2 chr10 62008861 62009550 calJac1 Contig12391 37461 38167 tetranucleotide [TATT][TTAT] 13 494 + 515 [TATTTATTTATTTA]C[TTATTTA] indel/deletion C 15 1 >ponAbe2 129 hg18 chr22 16196830 16197535 panTro2 chr22 16220191 16220893 ponAbe2 chr22 13938662 13939373 rheMac2 chr10 62008861 62009550 calJac1 Contig12391 37461 38167 tetranucleotide [TTTA][attt] 24 494 + 539 [tatttatttatttatttatttatttatttatttatttattta][attt] indel/deletion 43 1 >rheMac2 129 hg18 chr22 16196830 16197535 panTro2 chr22 16220191 16220893 ponAbe2 chr22 13938662 13939373 rheMac2 chr10 62008861 62009550 calJac1 Contig12391 37461 38167 tetranucleotide [TATT][attt] 18 494 + 511 [TAtttatttatt]cc[attt] indel/deletion cc 13 1 >calJac1 129 hg18 chr22 16196830 16197535 panTro2 chr22 16220191 16220893 ponAbe2 chr22 13938662 13939373 rheMac2 chr10 62008861 62009550 calJac1 Contig12391 37461 38167 tetranucleotide [ATTT][attt] 28 516 + 539 [tttatttatttatttattt]c[attt] indel/deletion c 20 1 ->ponAbe2 131 hg18 chr22 16198189 16199039 panTro2 chr22 16221545 16222403 ponAbe2 chr22 13944495 13945357 rheMac2 chr10 62010152 62011003 calJac1 Contig12391 38430 39272 trinucleotide TGT 0 90 + 108 tgttgttgttgttgttgtt ->calJac1 131 hg18 chr22 16198189 16199039 panTro2 chr22 16221545 16222403 ponAbe2 chr22 13944495 13945357 rheMac2 chr10 62010152 62011003 calJac1 Contig12391 38430 39272 trinucleotide AGG 17 449 + 461 aggaggag-gagg ->rheMac2 132 hg18 chr22 16199039 16199336 panTro2 chr22 16222403 16222700 ponAbe2 chr22 13945357 13945655 rheMac2 chr10 62011003 62011301 calJac1 Contig12391 39400 39701 mononucleotide T 0 1 + 22 tttttttttttttt-------t >calJac1 132 hg18 chr22 16199039 16199336 panTro2 chr22 16222403 16222700 ponAbe2 chr22 13945357 13945655 rheMac2 chr10 62011003 62011301 calJac1 Contig12391 39400 39701 compound [T][AT] 0 2 + 24 [tttttttttttt][atatatatata] ->calJac1 135 hg18 chr22 16199632 16199819 panTro2 chr22 16222996 16223183 ponAbe2 chr22 13945951 13946138 rheMac2 chr10 62011597 62011784 calJac1 Contig12391 40779 41074 mononucleotide A 0 1 + 13 aaaaaaaaaaaaa ->ponAbe2 136 hg18 chr22 16199819 16200697 panTro2 chr22 16223183 16224061 ponAbe2 chr22 13946138 13947018 rheMac2 chr10 62012092 62012972 calJac1 Contig12391 41074 41995 mononucleotide T 4 180 + 188 ttttttttt ->panTro2 138 hg18 chr22 16201986 16202524 panTro2 chr22 16225483 16225980 ponAbe2 chr22 13948291 13948792 rheMac2 chr10 62014265 62014739 calJac1 Contig12391 43430 43840 compound [AAGA][AGGA] 10 237 + 356 [agaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaaga]--------------------------------------------[aaggaaggaagGA] >hg18 138 hg18 chr22 16201986 16202524 panTro2 chr22 16225483 16225980 ponAbe2 chr22 13948291 13948792 rheMac2 chr10 62014265 62014739 calJac1 Contig12391 43430 43840 compound [GAAA][GAAG] 11 238 + 356 [gaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag][gaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagga] >rheMac2 138 hg18 chr22 16201986 16202524 panTro2 chr22 16225483 16225980 ponAbe2 chr22 13948291 13948792 rheMac2 chr10 62014265 62014739 calJac1 Contig12391 43430 43840 mononucleotide [A][A][A][A][A] 2 239 + 289 [aaaaaaaaaaa-------------------aaaaa]g[aaa]g[aaa]g[aaa]g[aaa] indel/deletion,indel/deletion,indel/deletion,indel/deletion G,G,G,G 17,21,25,29 4 ->panTro2 140 hg18 chr22 16203068 16203903 panTro2 chr22 16226525 16227364 ponAbe2 chr22 13949336 13950176 rheMac2 chr10 62015298 62016134 calJac1 Contig12391 44275 45043 tetranucleotide [attt][TTTA][ttta] 20 659 + 714 [attt]--------[tttattta--------------tttatttatttattta]tt[ttta] indel/deletion,indel/deletion ,tt 5,29 2 >calJac1 140 hg18 chr22 16203068 16203903 panTro2 chr22 16226525 16227364 ponAbe2 chr22 13949336 13950176 rheMac2 chr10 62015298 62016134 calJac1 Contig12391 44275 45043 tetranucleotide TTTA 114 667 + 678 TTTATTTATTTA >hg18 140 hg18 chr22 16203068 16203903 panTro2 chr22 16226525 16227364 ponAbe2 chr22 13949336 13950176 rheMac2 chr10 62015298 62016134 calJac1 Contig12391 44275 45043 mononucleotide [T][T] 32 679 + 699 [T]G[ttttttttttttttttttt] indel/deletion G 2 1 >ponAbe2 140 hg18 chr22 16203068 16203903 panTro2 chr22 16226525 16227364 ponAbe2 chr22 13949336 13950176 rheMac2 chr10 62015298 62016134 calJac1 Contig12391 44275 45043 mononucleotide T 41 692 + 713 tttttttttttttttttttttt >rheMac2 140 hg18 chr22 16203068 16203903 panTro2 chr22 16226525 16227364 ponAbe2 chr22 13949336 13950176 rheMac2 chr10 62015298 62016134 calJac1 Contig12391 44275 45043 mononucleotide T 45 694 + 705 tttttttttttt ->hg18 142 hg18 chr22 16208436 16208903 panTro2 chr22 16234374 16234849 ponAbe2 chr22 13958770 13959228 rheMac2 chr10 62019211 62019670 calJac1 Contig8598 2 468 trinucleotide CAA 9 142 + 173 c--------aacaacaacaacaacaacaacaa >panTro2 142 hg18 chr22 16208436 16208903 panTro2 chr22 16234374 16234849 ponAbe2 chr22 13958770 13959228 rheMac2 chr10 62019211 62019670 calJac1 Contig8598 2 468 trinucleotide [CAA][AAC] 9 142 + 173 [caacaacaa][aacaacaacaacaacaacaacaa] indel/substitution 10 1 >ponAbe2 142 hg18 chr22 16208436 16208903 panTro2 chr22 16234374 16234849 ponAbe2 chr22 13958770 13959228 rheMac2 chr10 62019211 62019670 calJac1 Contig8598 2 468 trinucleotide CAA 9 142 + 175 c--------aacaacaacaacaaC---------A >rheMac2 142 hg18 chr22 16208436 16208903 panTro2 chr22 16234374 16234849 ponAbe2 chr22 13958770 13959228 rheMac2 chr10 62019211 62019670 calJac1 Contig8598 2 468 trinucleotide [caa][CAA] 9 142 + 173 [c--------aa]a[aacaacaacaac------aa] indel/deletion a 4 1 ->hg18 144 hg18 chr22 16212241 16212557 panTro2 chr22 16238311 16238619 ponAbe2 chr22 13962393 13962694 rheMac2 chr10 62023116 62023428 calJac1 Contig8598 2068 2374 mononucleotide [T][T][T][T][T] 0 1 + 31 [tt]c[ttt]c[ttt]----c[ttt]c[tttttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion C,C,C,C 3,7,11,15 4 >panTro2 144 hg18 chr22 16212241 16212557 panTro2 chr22 16238311 16238619 ponAbe2 chr22 13962393 13962694 rheMac2 chr10 62023116 62023428 calJac1 Contig8598 2068 2374 mononucleotide [T][T][T] 0 1 + 31 [tt]c[ttt]c[ttt---------tttttttttttt] indel/deletion,indel/deletion C,C 3,7 2 >ponAbe2 144 hg18 chr22 16212241 16212557 panTro2 chr22 16238311 16238619 ponAbe2 chr22 13962393 13962694 rheMac2 chr10 62023116 62023428 calJac1 Contig8598 2068 2374 mononucleotide T 0 1 + 31 t------------------tttttttttttt >rheMac2 144 hg18 chr22 16212241 16212557 panTro2 chr22 16238311 16238619 ponAbe2 chr22 13962393 13962694 rheMac2 chr10 62023116 62023428 calJac1 Contig8598 2068 2374 mononucleotide [T][t][t][T] 0 1 + 31 [Tttt]c[tttt]c[tttt]c[tttttttttttttttt] indel/deletion,indel/deletion,indel/deletion c,c,c 5,10,15 3 >calJac1 144 hg18 chr22 16212241 16212557 panTro2 chr22 16238311 16238619 ponAbe2 chr22 13962393 13962694 rheMac2 chr10 62023116 62023428 calJac1 Contig8598 2068 2374 mononucleotide T 0 1 + 13 ttttttttttttt ->calJac1 144 hg18 chr22 16212241 16212557 panTro2 chr22 16238311 16238619 ponAbe2 chr22 13962393 13962694 rheMac2 chr10 62023116 62023428 calJac1 Contig8598 2068 2374 mononucleotide [T][T] 24 315 + 338 [T]------G[ttttttttt--ttttt] indel/deletion G 2 1 >rheMac2 144 hg18 chr22 16212241 16212557 panTro2 chr22 16238311 16238619 ponAbe2 chr22 13962393 13962694 rheMac2 chr10 62023116 62023428 calJac1 Contig8598 2068 2374 mononucleotide T 22 316 + 325 tttttttttt >hg18 144 hg18 chr22 16212241 16212557 panTro2 chr22 16238311 16238619 ponAbe2 chr22 13962393 13962694 rheMac2 chr10 62023116 62023428 calJac1 Contig8598 2068 2374 mononucleotide T 22 319 + 340 ttttttttttttt--ttttttt >panTro2 144 hg18 chr22 16212241 16212557 panTro2 chr22 16238311 16238619 ponAbe2 chr22 13962393 13962694 rheMac2 chr10 62023116 62023428 calJac1 Contig8598 2068 2374 mononucleotide T 30 323 + 340 ttttttttt--ttttttt >ponAbe2 144 hg18 chr22 16212241 16212557 panTro2 chr22 16238311 16238619 ponAbe2 chr22 13962393 13962694 rheMac2 chr10 62023116 62023428 calJac1 Contig8598 2068 2374 mononucleotide T 37 324 + 340 tttttttt--ttttttt ->hg18 145 hg18 chr22 16212725 16213164 panTro2 chr22 16238804 16239243 ponAbe2 chr22 13962844 13963280 rheMac2 chr10 62023588 62024020 calJac1 Contig8598 2395 2813 mononucleotide T 0 1 + 9 ttttttttt >ponAbe2 145 hg18 chr22 16212725 16213164 panTro2 chr22 16238804 16239243 ponAbe2 chr22 13962844 13963280 rheMac2 chr10 62023588 62024020 calJac1 Contig8598 2395 2813 mononucleotide T 0 1 + 9 ttttttttt >rheMac2 145 hg18 chr22 16212725 16213164 panTro2 chr22 16238804 16239243 ponAbe2 chr22 13962844 13963280 rheMac2 chr10 62023588 62024020 calJac1 Contig8598 2395 2813 mononucleotide T 0 1 + 9 ttttttttt ->calJac1 145 hg18 chr22 16212725 16213164 panTro2 chr22 16238804 16239243 ponAbe2 chr22 13962844 13963280 rheMac2 chr10 62023588 62024020 calJac1 Contig8598 2395 2813 tetranucleotide [TAAA][AAAT] 25 425 + 443 [TAAAT]GA[aaataaataaat] indel/deletion GA 6 1 ->calJac1 149 hg18 chr22 16217706 16218316 panTro2 chr22 16243445 16244027 ponAbe2 chr22 13967560 13968167 rheMac2 chr10 62028422 62029025 calJac1 Contig8598 3706 4276 mononucleotide [A][A][A][a] 0 15 + 36 [A]C[AAAAAAAAAA]G[AAAAA]g[aaa] indel/deletion,insertion,indel/deletion C,G,g 2,13,19 3 ->hg18 149 hg18 chr22 16217706 16218316 panTro2 chr22 16243445 16244027 ponAbe2 chr22 13967560 13968167 rheMac2 chr10 62028422 62029025 calJac1 Contig8598 3706 4276 tetranucleotide TTTA 29 175 + 199 tt-----tatttatttatttattta >panTro2 149 hg18 chr22 16217706 16218316 panTro2 chr22 16243445 16244027 ponAbe2 chr22 13967560 13968167 rheMac2 chr10 62028422 62029025 calJac1 Contig8598 3706 4276 tetranucleotide TTTA 29 175 + 199 tt-----tatttatttatttattta >ponAbe2 149 hg18 chr22 16217706 16218316 panTro2 chr22 16243445 16244027 ponAbe2 chr22 13967560 13968167 rheMac2 chr10 62028422 62029025 calJac1 Contig8598 3706 4276 tetranucleotide TTTA 29 175 + 199 tt-----tatttatttatttattta >rheMac2 149 hg18 chr22 16217706 16218316 panTro2 chr22 16243445 16244027 ponAbe2 chr22 13967560 13968167 rheMac2 chr10 62028422 62029025 calJac1 Contig8598 3706 4276 tetranucleotide [TTTA][TTTA] 29 177 + 204 [TTTA]ATT[TTTATTTATTTATTTA-TTTA] indel/deletion ATT 5 1 ->hg18 155 hg18 chr22 16219990 16220414 panTro2 chr22 16245699 16246117 ponAbe2 chr22 13969816 13970238 rheMac2 chr10 62030679 62031140 calJac1 Contig8598 6795 7177 mononucleotide [t][T][t][t] 0 100 + 135 [t]c[ttttttttt]c[tttt]c-----[tttttttttttttt] indel/deletion,indel/deletion,indel/deletion c,c,c 2,12,17 3 >panTro2 155 hg18 chr22 16219990 16220414 panTro2 chr22 16245699 16246117 ponAbe2 chr22 13969816 13970238 rheMac2 chr10 62030679 62031140 calJac1 Contig8598 6795 7177 mononucleotide [t][T][t][t] 0 100 + 135 [t]c[ttttttttt]c[tttt]c------[ttttttttttttt] indel/deletion,indel/deletion,indel/deletion c,c,c 2,12,17 3 >ponAbe2 155 hg18 chr22 16219990 16220414 panTro2 chr22 16245699 16246117 ponAbe2 chr22 13969816 13970238 rheMac2 chr10 62030679 62031140 calJac1 Contig8598 6795 7177 mononucleotide [t][T][t][t][t] 0 100 + 135 [t]c[ttttttttt]c[tttt]c-------[tttt]c[ttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion c,c,c,c 2,12,17,22 4 >rheMac2 155 hg18 chr22 16219990 16220414 panTro2 chr22 16245699 16246117 ponAbe2 chr22 13969816 13970238 rheMac2 chr10 62030679 62031140 calJac1 Contig8598 6795 7177 mononucleotide [t][T][T][t][t] 0 100 + 134 [t]c[TTTtttttttt]c[ttttt]c[tttt]c[tttttttttt] indel/deletion,insertion,indel/deletion,indel/deletion c,c,c,c 2,14,20,25 4 ->rheMac2 155 hg18 chr22 16219990 16220414 panTro2 chr22 16245699 16246117 ponAbe2 chr22 13969816 13970238 rheMac2 chr10 62030679 62031140 calJac1 Contig8598 6795 7177 mononucleotide [t][T] 0 283 + 308 [tttt]c[ttttttttttttttttttttt] indel/deletion c 5 1 ->hg18 156 hg18 chr22 16223924 16224124 panTro2 chr22 16249588 16249792 ponAbe2 chr22 13973628 13973840 rheMac2 chr10 62031420 62031634 calJac1 Contig8598 13275 13538 mononucleotide [T][T][T][T] 12 19 + 85 [tt]c[tt]c------------------------------------[tttttttttttt]g-----[ttttttt] indel/deletion,indel/deletion,indel/deletion C,C,g 3,6,19 3 >panTro2 156 hg18 chr22 16223924 16224124 panTro2 chr22 16249588 16249792 ponAbe2 chr22 13973628 13973840 rheMac2 chr10 62031420 62031634 calJac1 Contig8598 13275 13538 mononucleotide [T][T][T][T] 12 19 + 85 [TT]C[tt]c[tttttt------------------------------tttttttttttt]g-----[ttttttt] indel/deletion,indel/deletion,indel/deletion C,C,g 3,6,25 3 >rheMac2 156 hg18 chr22 16223924 16224124 panTro2 chr22 16249588 16249792 ponAbe2 chr22 13973628 13973840 rheMac2 chr10 62031420 62031634 calJac1 Contig8598 13275 13538 mononucleotide T 12 19 + 85 t-----------------------------------------ttttttttttttt-----ttttttt ->rheMac2 158 hg18 chr22 16224263 16224530 panTro2 chr22 16249941 16250208 ponAbe2 chr22 13974206 13974502 rheMac2 chr10 62032002 62032299 calJac1 Contig8598 14010 14300 tetranucleotide TTTA 0 1 + 15 tttatttatttattt >calJac1 158 hg18 chr22 16224263 16224530 panTro2 chr22 16249941 16250208 ponAbe2 chr22 13974206 13974502 rheMac2 chr10 62032002 62032299 calJac1 Contig8598 14010 14300 mononucleotide [t][T] 0 1 + 14 [ttt]c[tttttttttt] indel/deletion c 4 1 ->rheMac2 159 hg18 chr22 16224677 16224938 panTro2 chr22 16250355 16250616 ponAbe2 chr22 13974502 13974852 rheMac2 chr10 62032299 62032645 calJac1 Contig5161 112118 112449 tetranucleotide AGTG 2 287 + 298 AGTGAGTGAGTG >calJac1 159 hg18 chr22 16224677 16224938 panTro2 chr22 16250355 16250616 ponAbe2 chr22 13974502 13974852 rheMac2 chr10 62032299 62032645 calJac1 Contig5161 112118 112449 tetranucleotide AGTG 21 287 + 298 AGTGAGTGAGTG ->panTro2 161 hg18 chr22 16226311 16226620 panTro2 chr22 16251979 16252283 ponAbe2 chr22 13978219 13978526 rheMac2 chr10 62035571 62035869 calJac1 Contig5161 114821 115140 mononucleotide [A][A] 0 119 + 134 [aaaaa]t[a-aaaaaaaa] insertion t 6 1 ->calJac1 161 hg18 chr22 16226311 16226620 panTro2 chr22 16251979 16252283 ponAbe2 chr22 13978219 13978526 rheMac2 chr10 62035571 62035869 calJac1 Contig5161 114821 115140 mononucleotide [A][A][A] 1 297 + 326 [aaaa----aaaaaaaaa]g[aaa]g[aaaa--aa] indel/deletion,indel/deletion G,G 14,18 3 >rheMac2 161 hg18 chr22 16226311 16226620 panTro2 chr22 16251979 16252283 ponAbe2 chr22 13978219 13978526 rheMac2 chr10 62035571 62035869 calJac1 Contig5161 114821 115140 mononucleotide A 15 300 + 321 a----aaa-----aaaaaaaaa >hg18 161 hg18 chr22 16226311 16226620 panTro2 chr22 16251979 16252283 ponAbe2 chr22 13978219 13978526 rheMac2 chr10 62035571 62035869 calJac1 Contig5161 114821 115140 tetranucleotide [AAAC][acAA] 15 301 + 326 [aaacaaacaaacaaac]aa[aaac--aa] indel/deletion aa 17 1 >panTro2 161 hg18 chr22 16226311 16226620 panTro2 chr22 16251979 16252283 ponAbe2 chr22 13978219 13978526 rheMac2 chr10 62035571 62035869 calJac1 Contig5161 114821 115140 tetranucleotide [AAAC][acAA] 16 301 + 322 [aaacaaacaaac]aa[aaac--aa] indel/deletion aa 13 1 >ponAbe2 161 hg18 chr22 16226311 16226620 panTro2 chr22 16251979 16252283 ponAbe2 chr22 13978219 13978526 rheMac2 chr10 62035571 62035869 calJac1 Contig5161 114821 115140 tetranucleotide [AAAC][cAAA] 15 301 + 321 [aaacaaacaaac]aa[aaacaaa] indel/deletion aa 13 1 ->ponAbe2 162 hg18 chr22 16227098 16227503 panTro2 chr22 16252762 16253167 ponAbe2 chr22 13979003 13979424 rheMac2 chr10 62036676 62037079 calJac1 Contig8598 14300 14717 mononucleotide [T][T] 0 2 + 24 [ttt]c-[tttttttttttttttttt] indel/deletion C 4 1 >rheMac2 162 hg18 chr22 16227098 16227503 panTro2 chr22 16252762 16253167 ponAbe2 chr22 13979003 13979424 rheMac2 chr10 62036676 62037079 calJac1 Contig8598 14300 14717 mononucleotide [T][T] 1 4 + 24 [T]C[ttttttttttttttttttt] indel/deletion C 2 1 >calJac1 162 hg18 chr22 16227098 16227503 panTro2 chr22 16252762 16253167 ponAbe2 chr22 13979003 13979424 rheMac2 chr10 62036676 62037079 calJac1 Contig8598 14300 14717 mononucleotide [T][T] 1 4 + 24 [tttttttttttt]c[tttttttt] insertion c 13 1 ->calJac1 165 hg18 chr22 16228260 16228396 panTro2 chr22 16253924 16254059 ponAbe2 chr22 13980392 13980517 rheMac2 chr10 62037848 62037990 calJac1 Contig8598 16160 16266 mononucleotide T 0 15 + 26 tttttttttttt >hg18 165 hg18 chr22 16228260 16228396 panTro2 chr22 16253924 16254059 ponAbe2 chr22 13980392 13980517 rheMac2 chr10 62037848 62037990 calJac1 Contig8598 16160 16266 mononucleotide T 0 17 + 27 ttttttttttt >panTro2 165 hg18 chr22 16228260 16228396 panTro2 chr22 16253924 16254059 ponAbe2 chr22 13980392 13980517 rheMac2 chr10 62037848 62037990 calJac1 Contig8598 16160 16266 mononucleotide T 0 17 + 26 tttttttttt >rheMac2 165 hg18 chr22 16228260 16228396 panTro2 chr22 16253924 16254059 ponAbe2 chr22 13980392 13980517 rheMac2 chr10 62037848 62037990 calJac1 Contig8598 16160 16266 mononucleotide T 0 17 + 33 ttttttttttttttttt ->calJac1 168 hg18 chr22 16229440 16230269 panTro2 chr22 16255104 16255954 ponAbe2 chr22 13981564 13982413 rheMac2 chr10 62039050 62039880 calJac1 Contig8598 16457 17326 mononucleotide [g][G][G] 5 249 + 270 [gg]c[ggggggggggg]c[ggggggg] indel/deletion,insertion c,c 3,15 2 ->hg18 175 hg18 chr22 16233182 16233601 panTro2 chr22 16260165 16260580 ponAbe2 chr22 13986986 13987405 rheMac2 chr10 62044268 62044622 calJac1 Contig8598 21789 22171 mononucleotide A 0 156 + 164 aaaaaaaaa >panTro2 175 hg18 chr22 16233182 16233601 panTro2 chr22 16260165 16260580 ponAbe2 chr22 13986986 13987405 rheMac2 chr10 62044268 62044622 calJac1 Contig8598 21789 22171 mononucleotide A 2 156 + 164 aaaaaaaaa ->rheMac2 179 hg18 chr22 16234686 16235223 panTro2 chr22 16261665 16262213 ponAbe2 chr22 13988489 13989025 rheMac2 chr10 62045948 62046471 calJac1 Contig8598 23785 24303 mononucleotide T 20 308 + 319 TTTTTTTTTTTT ->hg18 179 hg18 chr22 16234686 16235223 panTro2 chr22 16261665 16262213 ponAbe2 chr22 13988489 13989025 rheMac2 chr10 62045948 62046471 calJac1 Contig8598 23785 24303 dinucleotide TA 8 379 + 391 ATATATATATATA >panTro2 179 hg18 chr22 16234686 16235223 panTro2 chr22 16261665 16262213 ponAbe2 chr22 13988489 13989025 rheMac2 chr10 62045948 62046471 calJac1 Contig8598 23785 24303 compound [AT][T] 17 379 + 416 [atatatatatatatatatat][tttttttttttttttttt] >ponAbe2 179 hg18 chr22 16234686 16235223 panTro2 chr22 16261665 16262213 ponAbe2 chr22 13988489 13989025 rheMac2 chr10 62045948 62046471 calJac1 Contig8598 23785 24303 dinucleotide TA 5 379 + 391 ATATATATATATA >rheMac2 179 hg18 chr22 16234686 16235223 panTro2 chr22 16261665 16262213 ponAbe2 chr22 13988489 13989025 rheMac2 chr10 62045948 62046471 calJac1 Contig8598 23785 24303 dinucleotide TA 24 379 + 393 ATATATATATATATA ->hg18 182 hg18 chr22 16236431 16236646 panTro2 chr22 16263936 16264150 ponAbe2 chr22 13990466 13990670 rheMac2 chr10 62048270 62048476 calJac1 Contig8598 25457 25586 mononucleotide [t][T][T] 0 142 + 169 [tttt]c[ttttttttt]g-[tttttttttttt] indel/deletion,insertion c,g 5,15 2 >panTro2 182 hg18 chr22 16236431 16236646 panTro2 chr22 16263936 16264150 ponAbe2 chr22 13990466 13990670 rheMac2 chr10 62048270 62048476 calJac1 Contig8598 25457 25586 mononucleotide [t][T][T] 2 142 + 169 [tttt]c[ttttttttt]g[ttttttttttttt] indel/deletion,insertion c,g 5,15 2 >ponAbe2 182 hg18 chr22 16236431 16236646 panTro2 chr22 16263936 16264150 ponAbe2 chr22 13990466 13990670 rheMac2 chr10 62048270 62048476 calJac1 Contig8598 25457 25586 mononucleotide [t][T] 2 142 + 169 [tttt]c[t----------tttttttttttt] indel/deletion c 5 1 ->rheMac2 184 hg18 chr22 16237257 16237500 panTro2 chr22 16264760 16264997 ponAbe2 chr22 13991279 13991518 rheMac2 chr10 62049087 62049331 calJac1 Contig8598 26694 26972 mononucleotide [T][T][T][T][T] 0 107 + 163 [TT]C[TT]------------------C[TTT]C[ttt]c[ttttttt------------tttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion C,C,C,C 3,6,10,14 4 >hg18 184 hg18 chr22 16237257 16237500 panTro2 chr22 16264760 16264997 ponAbe2 chr22 13991279 13991518 rheMac2 chr10 62049087 62049331 calJac1 Contig8598 26694 26972 mononucleotide T 18 136 + 163 tt-ttttttt------------tttttt >panTro2 184 hg18 chr22 16237257 16237500 panTro2 chr22 16264760 16264997 ponAbe2 chr22 13991279 13991518 rheMac2 chr10 62049087 62049331 calJac1 Contig8598 26694 26972 mononucleotide T 18 136 + 157 ttttt------------ttttt >ponAbe2 184 hg18 chr22 16237257 16237500 panTro2 chr22 16264760 16264997 ponAbe2 chr22 13991279 13991518 rheMac2 chr10 62049087 62049331 calJac1 Contig8598 26694 26972 mononucleotide T 18 136 + 158 ttttt------------tttttt ->calJac1 185 hg18 chr22 16237500 16238220 panTro2 chr22 16264997 16265713 ponAbe2 chr22 13991518 13992244 rheMac2 chr10 62049331 62050045 calJac1 Contig8598 26972 27594 mononucleotide T 19 349 + 458 ttt-------------------------------------------------------------------------------------------tttttttttttttttt ->calJac1 187 hg18 chr22 16238900 16239214 panTro2 chr22 16266394 16266703 ponAbe2 chr22 13993220 13993527 rheMac2 chr10 62050418 62050725 calJac1 Contig3684 48435 48748 mononucleotide T 0 1 + 14 tttttttttttttt ->rheMac2 188 hg18 chr22 16239214 16239736 panTro2 chr22 16266703 16267225 ponAbe2 chr22 13993527 13994045 rheMac2 chr10 62050725 62051262 calJac1 Contig8598 28048 28552 mononucleotide T 0 1 + 9 TTTTTTTTT ->hg18 188 hg18 chr22 16239214 16239736 panTro2 chr22 16266703 16267225 ponAbe2 chr22 13993527 13994045 rheMac2 chr10 62050725 62051262 calJac1 Contig8598 28048 28552 dinucleotide [GT][TG] 9 322 + 368 [gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt]T[TG] indel/deletion T 45 1 >ponAbe2 188 hg18 chr22 16239214 16239736 panTro2 chr22 16266703 16267225 ponAbe2 chr22 13993527 13994045 rheMac2 chr10 62050725 62051262 calJac1 Contig8598 28048 28552 dinucleotide [GT][TG] 7 322 + 362 [gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt]T[TG] indel/deletion T 39 1 >rheMac2 188 hg18 chr22 16239214 16239736 panTro2 chr22 16266703 16267225 ponAbe2 chr22 13993527 13994045 rheMac2 chr10 62050725 62051262 calJac1 Contig8598 28048 28552 dinucleotide [GT][TG] 2 324 + 376 [gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt]T[TG] indel/deletion T 51 1 >panTro2 188 hg18 chr22 16239214 16239736 panTro2 chr22 16266703 16267225 ponAbe2 chr22 13993527 13994045 rheMac2 chr10 62050725 62051262 calJac1 Contig8598 28048 28552 dinucleotide [GT][TG] 17 332 + 376 [gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt]T[TG] indel/deletion T 43 1 >calJac1 188 hg18 chr22 16239214 16239736 panTro2 chr22 16266703 16267225 ponAbe2 chr22 13993527 13994045 rheMac2 chr10 62050725 62051262 calJac1 Contig8598 28048 28552 tetranucleotide GTGC 34 356 + 367 gtgcgtgcgtgc ->hg18 194 hg18 chr22 16241314 16241567 panTro2 chr22 16268807 16269060 ponAbe2 chr22 13995632 13995885 rheMac2 chr10 62053142 62053390 calJac1 Contig8598 30076 30327 mononucleotide T 0 1 + 9 TTTTTTTTT >panTro2 194 hg18 chr22 16241314 16241567 panTro2 chr22 16268807 16269060 ponAbe2 chr22 13995632 13995885 rheMac2 chr10 62053142 62053390 calJac1 Contig8598 30076 30327 mononucleotide T 0 1 + 9 TTTTTTTTT >ponAbe2 194 hg18 chr22 16241314 16241567 panTro2 chr22 16268807 16269060 ponAbe2 chr22 13995632 13995885 rheMac2 chr10 62053142 62053390 calJac1 Contig8598 30076 30327 mononucleotide T 0 1 + 9 ttttttttt ->calJac1 195 hg18 chr22 16241567 16242186 panTro2 chr22 16269060 16269682 ponAbe2 chr22 13995885 13996514 rheMac2 chr10 62053390 62053997 calJac1 Contig3684 51192 51806 mononucleotide [t][T][T] 2 258 + 284 [tttt]c[tttttttttttt]---c[tttttt] indel/deletion,insertion c,c 5,18 2 >ponAbe2 195 hg18 chr22 16241567 16242186 panTro2 chr22 16269060 16269682 ponAbe2 chr22 13995885 13996514 rheMac2 chr10 62053390 62053997 calJac1 Contig3684 51192 51806 mononucleotide T 1 262 + 284 ttttttttttttttttttttttt >rheMac2 195 hg18 chr22 16241567 16242186 panTro2 chr22 16269060 16269682 ponAbe2 chr22 13995885 13996514 rheMac2 chr10 62053390 62053997 calJac1 Contig3684 51192 51806 mononucleotide T 3 262 + 284 ttttttttttttt--------tt >hg18 195 hg18 chr22 16241567 16242186 panTro2 chr22 16269060 16269682 ponAbe2 chr22 13995885 13996514 rheMac2 chr10 62053390 62053997 calJac1 Contig3684 51192 51806 mononucleotide [T][T] 0 263 + 284 [tttttttttttt]-g[tttttttt] insertion g 13 1 >panTro2 195 hg18 chr22 16241567 16242186 panTro2 chr22 16269060 16269682 ponAbe2 chr22 13995885 13996514 rheMac2 chr10 62053390 62053997 calJac1 Contig3684 51192 51806 mononucleotide [T][t][t] 0 263 + 284 [tttttttttt]g[t--ttt]c[tttt] indel/deletion,indel/deletion g,c 11,16 2 ->hg18 195 hg18 chr22 16241567 16242186 panTro2 chr22 16269060 16269682 ponAbe2 chr22 13995885 13996514 rheMac2 chr10 62053390 62053997 calJac1 Contig3684 51192 51806 mononucleotide T 9 442 + 455 tttttttttttttt >panTro2 195 hg18 chr22 16241567 16242186 panTro2 chr22 16269060 16269682 ponAbe2 chr22 13995885 13996514 rheMac2 chr10 62053390 62053997 calJac1 Contig3684 51192 51806 mononucleotide T 10 442 + 457 tttttttttttttttt >ponAbe2 195 hg18 chr22 16241567 16242186 panTro2 chr22 16269060 16269682 ponAbe2 chr22 13995885 13996514 rheMac2 chr10 62053390 62053997 calJac1 Contig3684 51192 51806 mononucleotide T 9 442 + 465 tttttttttttttttttttttttt >rheMac2 195 hg18 chr22 16241567 16242186 panTro2 chr22 16269060 16269682 ponAbe2 chr22 13995885 13996514 rheMac2 chr10 62053390 62053997 calJac1 Contig3684 51192 51806 mononucleotide [T][T] 12 442 + 464 [ttttttttttttttttttttt]g[t] indel/deletion G 22 1 ->hg18 195 hg18 chr22 16241567 16242186 panTro2 chr22 16269060 16269682 ponAbe2 chr22 13995885 13996514 rheMac2 chr10 62053390 62053997 calJac1 Contig3684 51192 51806 dinucleotide GA 19 625 + 636 GAGAGAGAGAGA >panTro2 195 hg18 chr22 16241567 16242186 panTro2 chr22 16269060 16269682 ponAbe2 chr22 13995885 13996514 rheMac2 chr10 62053390 62053997 calJac1 Contig3684 51192 51806 dinucleotide GA 18 625 + 638 GAGAGAGAGAGAGA >rheMac2 195 hg18 chr22 16241567 16242186 panTro2 chr22 16269060 16269682 ponAbe2 chr22 13995885 13996514 rheMac2 chr10 62053390 62053997 calJac1 Contig3684 51192 51806 dinucleotide GA 31 625 + 636 GAGAGAGAGAGA ->hg18 196 hg18 chr22 16246769 16248076 panTro2 chr22 16274313 16275611 ponAbe2 chr22 14003658 14004956 rheMac2 chr10 62058856 62060193 calJac1 Contig8598 36855 38078 mononucleotide [T][T] 24 1000 + 1010 [TTTTTTTTT]C[T] indel/deletion C 10 1 >panTro2 196 hg18 chr22 16246769 16248076 panTro2 chr22 16274313 16275611 ponAbe2 chr22 14003658 14004956 rheMac2 chr10 62058856 62060193 calJac1 Contig8598 36855 38078 mononucleotide [T][T] 28 1000 + 1011 [TTTTTTTTTT]C[T] indel/deletion C 11 1 >ponAbe2 196 hg18 chr22 16246769 16248076 panTro2 chr22 16274313 16275611 ponAbe2 chr22 14003658 14004956 rheMac2 chr10 62058856 62060193 calJac1 Contig8598 36855 38078 mononucleotide [T][T] 26 1000 + 1010 [TTTTTTTTT]C[T] indel/deletion C 10 1 ->panTro2 196 hg18 chr22 16246769 16248076 panTro2 chr22 16274313 16275611 ponAbe2 chr22 14003658 14004956 rheMac2 chr10 62058856 62060193 calJac1 Contig8598 36855 38078 mononucleotide [T][T][t] 31 1090 + 1132 [ttt]g[ttttt------------------ttttttttttt]g---[t] indel/deletion,indel/deletion G,g 4,21 2 >ponAbe2 196 hg18 chr22 16246769 16248076 panTro2 chr22 16274313 16275611 ponAbe2 chr22 14003658 14004956 rheMac2 chr10 62058856 62060193 calJac1 Contig8598 36855 38078 mononucleotide [T][t] 28 1090 + 1132 [tttttt---------------------ttttttttttt]g---[t] indel/deletion g 18 1 >rheMac2 196 hg18 chr22 16246769 16248076 panTro2 chr22 16274313 16275611 ponAbe2 chr22 14003658 14004956 rheMac2 chr10 62058856 62060193 calJac1 Contig8598 36855 38078 tetranucleotide [tgtt][TTTG] 20 1099 + 1128 [tttgtt][tttgtttgtttgtttgtttgtttg] indel/deletion 7 1 ->hg18 197 hg18 chr22 16249002 16250461 panTro2 chr22 16276537 16277996 ponAbe2 chr22 14006230 14007705 rheMac2 chr10 62061120 62062622 calJac1 Contig8598 38273 39710 tetranucleotide CTGC 1 231 + 245 CTGCCTGCCTGCCTG >hg18 197 hg18 chr22 16249002 16250461 panTro2 chr22 16276537 16277996 ponAbe2 chr22 14006230 14007705 rheMac2 chr10 62061120 62062622 calJac1 Contig8598 38273 39710 tetranucleotide GCTA 1 250 + 262 GCTAGCTAGCTAG >panTro2 197 hg18 chr22 16249002 16250461 panTro2 chr22 16276537 16277996 ponAbe2 chr22 14006230 14007705 rheMac2 chr10 62061120 62062622 calJac1 Contig8598 38273 39710 tetranucleotide CTGC 1 231 + 245 CTGCCTGCCTGCCTG >panTro2 197 hg18 chr22 16249002 16250461 panTro2 chr22 16276537 16277996 ponAbe2 chr22 14006230 14007705 rheMac2 chr10 62061120 62062622 calJac1 Contig8598 38273 39710 tetranucleotide GCTA 1 250 + 262 GCTAGCTAGCTAG >ponAbe2 197 hg18 chr22 16249002 16250461 panTro2 chr22 16276537 16277996 ponAbe2 chr22 14006230 14007705 rheMac2 chr10 62061120 62062622 calJac1 Contig8598 38273 39710 compound [CTGC][CTAG] 1 231 + 266 [CTGCCTGCCTGCCTGCCTG]T[CTAGCTAGCTAGCTAG] ->calJac1 197 hg18 chr22 16249002 16250461 panTro2 chr22 16276537 16277996 ponAbe2 chr22 14006230 14007705 rheMac2 chr10 62061120 62062622 calJac1 Contig8598 38273 39710 mononucleotide T 75 375 + 384 tttttttttt ->hg18 197 hg18 chr22 16249002 16250461 panTro2 chr22 16276537 16277996 ponAbe2 chr22 14006230 14007705 rheMac2 chr10 62061120 62062622 calJac1 Contig8598 38273 39710 tetranucleotide [TAtt][TTTA] 16 520 + 561 [TAt------------------t]cttt[tttatttatttattta] indel/deletion cttt 5 1 >panTro2 197 hg18 chr22 16249002 16250461 panTro2 chr22 16276537 16277996 ponAbe2 chr22 14006230 14007705 rheMac2 chr10 62061120 62062622 calJac1 Contig8598 38273 39710 tetranucleotide [TAtt][TTTA] 16 520 + 561 [TAt------------------t]cttt[tttatttatttattta] indel/deletion cttt 5 1 >rheMac2 197 hg18 chr22 16249002 16250461 panTro2 chr22 16276537 16277996 ponAbe2 chr22 14006230 14007705 rheMac2 chr10 62061120 62062622 calJac1 Contig8598 38273 39710 compound [TC][TC][T] 24 523 + 567 [tctctctctct]t[tctctctctctctctct][tttttttttt-ttttt] >ponAbe2 197 hg18 chr22 16249002 16250461 panTro2 chr22 16276537 16277996 ponAbe2 chr22 14006230 14007705 rheMac2 chr10 62061120 62062622 calJac1 Contig8598 38273 39710 tetranucleotide TTTA 20 546 + 561 tttatttatttattta ->hg18 199 hg18 chr22 16250795 16251998 panTro2 chr22 16278328 16279532 ponAbe2 chr22 14008037 14009248 rheMac2 chr10 62062957 62064160 calJac1 Contig8598 40481 41603 tetranucleotide TGGT 39 416 + 429 T--GGTTGGTTGGT >panTro2 199 hg18 chr22 16250795 16251998 panTro2 chr22 16278328 16279532 ponAbe2 chr22 14008037 14009248 rheMac2 chr10 62062957 62064160 calJac1 Contig8598 40481 41603 tetranucleotide TGGT 39 416 + 429 T--GGTTGGTTGGT ->calJac1 199 hg18 chr22 16250795 16251998 panTro2 chr22 16278328 16279532 ponAbe2 chr22 14008037 14009248 rheMac2 chr10 62062957 62064160 calJac1 Contig8598 40481 41603 tetranucleotide TTAT 37 859 + 921 ttattt-----------------------------------------------atttatttat ->hg18 199 hg18 chr22 16250795 16251998 panTro2 chr22 16278328 16279532 ponAbe2 chr22 14008037 14009248 rheMac2 chr10 62062957 62064160 calJac1 Contig8598 40481 41603 tetranucleotide TTTG 49 954 + 965 tttgtttgtttg >panTro2 199 hg18 chr22 16250795 16251998 panTro2 chr22 16278328 16279532 ponAbe2 chr22 14008037 14009248 rheMac2 chr10 62062957 62064160 calJac1 Contig8598 40481 41603 tetranucleotide TTTG 49 954 + 965 tttgtttgtttg >ponAbe2 199 hg18 chr22 16250795 16251998 panTro2 chr22 16278328 16279532 ponAbe2 chr22 14008037 14009248 rheMac2 chr10 62062957 62064160 calJac1 Contig8598 40481 41603 tetranucleotide TTTG 41 954 + 969 tttgtttgtttgtttg >rheMac2 199 hg18 chr22 16250795 16251998 panTro2 chr22 16278328 16279532 ponAbe2 chr22 14008037 14009248 rheMac2 chr10 62062957 62064160 calJac1 Contig8598 40481 41603 tetranucleotide TTTG 53 958 + 969 tttgtttgtttg ->hg18 201 hg18 chr22 16255241 16255814 panTro2 chr22 16286157 16286718 ponAbe2 chr22 14015382 14015951 rheMac2 chr10 62071121 62071690 calJac1 Contig8598 58064 58635 mononucleotide [t][T] 0 1 + 12 [t]c[tttttttttt] indel/deletion c 2 1 >ponAbe2 201 hg18 chr22 16255241 16255814 panTro2 chr22 16286157 16286718 ponAbe2 chr22 14015382 14015951 rheMac2 chr10 62071121 62071690 calJac1 Contig8598 58064 58635 mononucleotide T 0 1 + 12 tttttttttttt >calJac1 201 hg18 chr22 16255241 16255814 panTro2 chr22 16286157 16286718 ponAbe2 chr22 14015382 14015951 rheMac2 chr10 62071121 62071690 calJac1 Contig8598 58064 58635 mononucleotide [t][T] 0 1 + 12 [t]c[tttttttttt] indel/deletion c 2 1 ->hg18 202 hg18 chr22 16255814 16256479 panTro2 chr22 16286718 16287385 ponAbe2 chr22 14015951 14016622 rheMac2 chr10 62071690 62072342 calJac1 Contig8598 58931 59629 mononucleotide [a][A][a] 2 157 + 178 [aaaa]t--[aaaaaaaa-aaa]c[aa] indel/deletion,indel/deletion t,c 5,17 2 >ponAbe2 202 hg18 chr22 16255814 16256479 panTro2 chr22 16286718 16287385 ponAbe2 chr22 14015951 14016622 rheMac2 chr10 62071690 62072342 calJac1 Contig8598 58931 59629 mononucleotide [a][A][a] 2 157 + 178 [aaaa]t--[aaaaaaaa-a]c[aaaa] indel/deletion,indel/deletion t,c 5,15 2 >panTro2 202 hg18 chr22 16255814 16256479 panTro2 chr22 16286718 16287385 ponAbe2 chr22 14015951 14016622 rheMac2 chr10 62071690 62072342 calJac1 Contig8598 58931 59629 mononucleotide [A][a] 2 163 + 178 [aaaaaaaaa-aaa]c[aa] indel/deletion c 13 1 ->hg18 202 hg18 chr22 16255814 16256479 panTro2 chr22 16286718 16287385 ponAbe2 chr22 14015951 14016622 rheMac2 chr10 62071690 62072342 calJac1 Contig8598 58931 59629 mononucleotide [A][A] 6 326 + 432 [aaaaaaaaaaaaaa-----------------------------------aaa]C[A----------------------------------------------------A] indel/deletion C 18 1 >panTro2 202 hg18 chr22 16255814 16256479 panTro2 chr22 16286718 16287385 ponAbe2 chr22 14015951 14016622 rheMac2 chr10 62071690 62072342 calJac1 Contig8598 58931 59629 mononucleotide [A][A] 4 326 + 428 [aaaaaaaaaa-----------------------------------aaa]C[A----------------------------------------------------A] indel/deletion C 14 1 >ponAbe2 202 hg18 chr22 16255814 16256479 panTro2 chr22 16286718 16287385 ponAbe2 chr22 14015951 14016622 rheMac2 chr10 62071690 62072342 calJac1 Contig8598 58931 59629 mononucleotide A 6 326 + 430 aaaaaaaaaaaa-----------------------------------aaaaa----------------------------------------------------a ->hg18 202 hg18 chr22 16255814 16256479 panTro2 chr22 16286718 16287385 ponAbe2 chr22 14015951 14016622 rheMac2 chr10 62071690 62072342 calJac1 Contig8598 58931 59629 tetranucleotide [caaa][AAAC] 97 720 + 743 [caaa][aaacaaac--------aaaC] indel/deletion 5 1 >ponAbe2 202 hg18 chr22 16255814 16256479 panTro2 chr22 16286718 16287385 ponAbe2 chr22 14015951 14016622 rheMac2 chr10 62071690 62072342 calJac1 Contig8598 58931 59629 tetranucleotide [caaa][AAAC][aaaC] 98 720 + 743 [caaa][aaacaaacaaac]-aaa[aaaC] indel/deletion,indel/deletion ,aaa 5,17 2 >rheMac2 202 hg18 chr22 16255814 16256479 panTro2 chr22 16286718 16287385 ponAbe2 chr22 14015951 14016622 rheMac2 chr10 62071690 62072342 calJac1 Contig8598 58931 59629 tetranucleotide [caaa][AAAC][aaaC] 118 720 + 743 [caaa][aaacaaacaaac]aaaa[aaaC] indel/deletion,indel/deletion ,aaaa 5,17 2 ->panTro2 203 hg18 chr22 16256534 16257407 panTro2 chr22 16287440 16288315 ponAbe2 chr22 14016678 14017546 rheMac2 chr10 62072393 62073266 calJac1 Contig8598 59629 60461 tetranucleotide [attt][TTAT][TTTA] 1 478 + 507 [tttattt]tt[tttatttat][tttatttattta] indel/deletion,indel/substitution tt, 8,19 2 >ponAbe2 203 hg18 chr22 16256534 16257407 panTro2 chr22 16287440 16288315 ponAbe2 chr22 14016678 14017546 rheMac2 chr10 62072393 62073266 calJac1 Contig8598 59629 60461 tetranucleotide [TTAT][TTTA] 11 483 + 507 [tttatttatttat][tttatttattta] indel/substitution 14 1 >hg18 203 hg18 chr22 16256534 16257407 panTro2 chr22 16287440 16288315 ponAbe2 chr22 14016678 14017546 rheMac2 chr10 62072393 62073266 calJac1 Contig8598 59629 60461 tetranucleotide [TTAT][TTTA] 3 487 + 507 [tttatttat][tttatttattta] indel/substitution 10 1 ->calJac1 203 hg18 chr22 16256534 16257407 panTro2 chr22 16287440 16288315 ponAbe2 chr22 14016678 14017546 rheMac2 chr10 62072393 62073266 calJac1 Contig8598 59629 60461 tetranucleotide [Gttt][GTTT] 29 668 + 690 [Gttt][tttgtttgtttgtttgttt] indel/deletion 5 1 ->rheMac2 203 hg18 chr22 16256534 16257407 panTro2 chr22 16287440 16288315 ponAbe2 chr22 14016678 14017546 rheMac2 chr10 62072393 62073266 calJac1 Contig8598 59629 60461 mononucleotide A 47 859 + 867 aaaaaaaaa ->ponAbe2 203 hg18 chr22 16256534 16257407 panTro2 chr22 16287440 16288315 ponAbe2 chr22 14016678 14017546 rheMac2 chr10 62072393 62073266 calJac1 Contig8598 59629 60461 trinucleotide TTA 60 910 + 922 attattattatta ->hg18 204 hg18 chr22 16257705 16259185 panTro2 chr22 16288613 16290086 ponAbe2 chr22 14017845 14019314 rheMac2 chr10 62073266 62074724 calJac1 Contig8598 60657 62123 mononucleotide [g][G] 25 413 + 423 [g]t[ggggggggg] indel/deletion t 2 1 ->calJac1 207 hg18 chr22 16259955 16260383 panTro2 chr22 16290856 16291208 ponAbe2 chr22 14020086 14020506 rheMac2 chr10 62075859 62076287 calJac1 Contig8598 62897 63325 tetranucleotide AAAG 7 253 + 264 AAAGAAAGAAAG ->calJac1 208 hg18 chr22 16260643 16260812 panTro2 chr22 16291468 16291637 ponAbe2 chr22 14020758 14020925 rheMac2 chr10 62076523 62076691 calJac1 Contig8598 63370 63540 mononucleotide T 0 1 + 15 ttttttttttttttt ->rheMac2 210 hg18 chr22 16265802 16266450 panTro2 chr22 16296841 16297486 ponAbe2 chr22 14027380 14028026 rheMac2 chr10 62081962 62082612 calJac1 Contig8598 65374 65993 mononucleotide [A][a] 28 662 + 678 [aaaaaaaaaaaaaa]g[aa] indel/deletion g 15 1 ->rheMac2 214 hg18 chr22 16266954 16268986 panTro2 chr22 16297990 16300025 ponAbe2 chr22 14028533 14030619 rheMac2 chr10 62083122 62085192 calJac1 Contig8598 66505 68550 trinucleotide TTG 1 125 + 160 TTGTTGTTG-------------------TTGTTGTT ->ponAbe2 214 hg18 chr22 16266954 16268986 panTro2 chr22 16297990 16300025 ponAbe2 chr22 14028533 14030619 rheMac2 chr10 62083122 62085192 calJac1 Contig8598 66505 68550 tetranucleotide [caaa][AAAC][aaaC] 44 606 + 653 [c-aaa]a[aaacaaacaaac]aaaa[aaa----------------------C] indel/deletion,indel/deletion a,aaaa 5,18 2 >hg18 214 hg18 chr22 16266954 16268986 panTro2 chr22 16297990 16300025 ponAbe2 chr22 14028533 14030619 rheMac2 chr10 62083122 62085192 calJac1 Contig8598 66505 68550 mononucleotide A 70 607 + 618 aaaaaaaaaaaa >panTro2 214 hg18 chr22 16266954 16268986 panTro2 chr22 16297990 16300025 ponAbe2 chr22 14028533 14030619 rheMac2 chr10 62083122 62085192 calJac1 Contig8598 66505 68550 mononucleotide A 70 607 + 630 aaaaaaaaaaaaaaaaaaaaaaaa >rheMac2 214 hg18 chr22 16266954 16268986 panTro2 chr22 16297990 16300025 ponAbe2 chr22 14028533 14030619 rheMac2 chr10 62083122 62085192 calJac1 Contig8598 66505 68550 mononucleotide [A][A][A] 72 608 + 651 [aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa]G[AAA]G[A] indel/deletion,indel/deletion G,G 39,43 2 >calJac1 214 hg18 chr22 16266954 16268986 panTro2 chr22 16297990 16300025 ponAbe2 chr22 14028533 14030619 rheMac2 chr10 62083122 62085192 calJac1 Contig8598 66505 68550 tetranucleotide AAAT 35 609 + 627 aaataaataaataaataaa ->calJac1 214 hg18 chr22 16266954 16268986 panTro2 chr22 16297990 16300025 ponAbe2 chr22 14028533 14030619 rheMac2 chr10 62083122 62085192 calJac1 Contig8598 66505 68550 tetranucleotide [TCAT][tcat] 97 1448 + 1466 [tcattcattcat]ctg[tcat] indel/deletion ctg 13 1 ->panTro2 216 hg18 chr22 16269459 16269691 panTro2 chr22 16301340 16301568 ponAbe2 chr22 14031907 14032132 rheMac2 chr10 62086416 62086630 calJac1 Contig8598 69225 69415 mononucleotide [T][T][T][T] 0 25 + 55 [TT]G[t----ttttttttt]g[tttttt]g[tttttt] indel/deletion,insertion,insertion G,g,g 3,14,21 3 >rheMac2 216 hg18 chr22 16269459 16269691 panTro2 chr22 16301340 16301568 ponAbe2 chr22 14031907 14032132 rheMac2 chr10 62086416 62086630 calJac1 Contig8598 69225 69415 mononucleotide [T][T] 0 25 + 55 [T]C[t-----tttt-------------tttttt] indel/deletion C 2 1 ->calJac1 221 hg18 chr22 16273790 16274088 panTro2 chr22 16305670 16305968 ponAbe2 chr22 14035861 14036159 rheMac2 chr10 62090087 62090384 calJac1 Contig8598 73112 73397 mononucleotide [C][C][C] 2 98 + 118 [CCCCCCCCC]G[CC]T[CCCCCCCC] indel/deletion,indel/deletion G,T 10,13 2 ->ponAbe2 222 hg18 chr22 16276467 16277725 panTro2 chr22 16308354 16309612 ponAbe2 chr22 14038536 14039761 rheMac2 chr10 62092714 62093976 calJac1 Contig8598 73397 74645 mononucleotide A 0 61 + 69 AAAAAAAAA >calJac1 222 hg18 chr22 16276467 16277725 panTro2 chr22 16308354 16309612 ponAbe2 chr22 14038536 14039761 rheMac2 chr10 62092714 62093976 calJac1 Contig8598 73397 74645 mononucleotide A 0 61 + 69 AAAAAAAAA ->hg18 222 hg18 chr22 16276467 16277725 panTro2 chr22 16308354 16309612 ponAbe2 chr22 14038536 14039761 rheMac2 chr10 62092714 62093976 calJac1 Contig8598 73397 74645 mononucleotide [A][A] 15 580 + 597 [AAAAAAAA-------A]C[A] indel/deletion C 10 1 >panTro2 222 hg18 chr22 16276467 16277725 panTro2 chr22 16308354 16309612 ponAbe2 chr22 14038536 14039761 rheMac2 chr10 62092714 62093976 calJac1 Contig8598 73397 74645 mononucleotide [A][A] 16 580 + 598 [AAAAAAAAA-------A]C[A] indel/deletion C 11 1 >rheMac2 222 hg18 chr22 16276467 16277725 panTro2 chr22 16308354 16309612 ponAbe2 chr22 14038536 14039761 rheMac2 chr10 62092714 62093976 calJac1 Contig8598 73397 74645 dinucleotide AC 13 588 + 599 ACACACACACAC ->panTro2 225 hg18 chr22 16284518 16285899 panTro2 chr22 16316018 16317398 ponAbe2 chr22 14048552 14049949 rheMac2 chr10 62100755 62102158 calJac1 Contig8598 78743 80063 trinucleotide TGG 4 350 + 361 tggtggtggtgg ->calJac1 225 hg18 chr22 16284518 16285899 panTro2 chr22 16316018 16317398 ponAbe2 chr22 14048552 14049949 rheMac2 chr10 62100755 62102158 calJac1 Contig8598 78743 80063 mononucleotide [A][a] 46 724 + 735 [aaaaaaaaa]c[aa] indel/deletion c 10 1 ->hg18 225 hg18 chr22 16284518 16285899 panTro2 chr22 16316018 16317398 ponAbe2 chr22 14048552 14049949 rheMac2 chr10 62100755 62102158 calJac1 Contig8598 78743 80063 mononucleotide [T][t] 11 896 + 909 [ttttttttttt]c[tt] indel/deletion c 12 1 >panTro2 225 hg18 chr22 16284518 16285899 panTro2 chr22 16316018 16317398 ponAbe2 chr22 14048552 14049949 rheMac2 chr10 62100755 62102158 calJac1 Contig8598 78743 80063 mononucleotide [T][t] 11 896 + 908 [tttttttttt]c[tt] indel/deletion c 11 1 >rheMac2 225 hg18 chr22 16284518 16285899 panTro2 chr22 16316018 16317398 ponAbe2 chr22 14048552 14049949 rheMac2 chr10 62100755 62102158 calJac1 Contig8598 78743 80063 mononucleotide [T][T][T][T][T][T][T][T] 10 896 + 934 [tt]a[ttt]a[ttt]a[ttt]a[ttt]a[ttt]a[ttt]a[tttttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion A,A,A,A,A,A,A 3,7,11,15,19,23,27 7 >ponAbe2 225 hg18 chr22 16284518 16285899 panTro2 chr22 16316018 16317398 ponAbe2 chr22 14048552 14049949 rheMac2 chr10 62100755 62102158 calJac1 Contig8598 78743 80063 mononucleotide [T][t] 30 915 + 930 [ttttttttttttt]c[tt] indel/deletion c 14 1 ->hg18 227 hg18 chr22 16287537 16287863 panTro2 chr22 16319035 16319364 ponAbe2 chr22 14052155 14052489 rheMac2 chr10 62103486 62103821 calJac1 Contig8598 81384 81809 dinucleotide TG 70 377 + 396 tgtgtgtgtgtgtgtgtgtg >panTro2 227 hg18 chr22 16287537 16287863 panTro2 chr22 16319035 16319364 ponAbe2 chr22 14052155 14052489 rheMac2 chr10 62103486 62103821 calJac1 Contig8598 81384 81809 dinucleotide TG 67 377 + 396 tgtgtgtgtgtgtgtgtgtg >ponAbe2 227 hg18 chr22 16287537 16287863 panTro2 chr22 16319035 16319364 ponAbe2 chr22 14052155 14052489 rheMac2 chr10 62103486 62103821 calJac1 Contig8598 81384 81809 dinucleotide TG 62 377 + 396 tgtgtgtgtgtgtgtgtgtg >calJac1 227 hg18 chr22 16287537 16287863 panTro2 chr22 16319035 16319364 ponAbe2 chr22 14052155 14052489 rheMac2 chr10 62103486 62103821 calJac1 Contig8598 81384 81809 dinucleotide GT 3 396 + 428 gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg ->hg18 230 hg18 chr22 16289549 16290414 panTro2 chr22 16321054 16321919 ponAbe2 chr22 14053573 14054441 rheMac2 chr10 62105626 62106415 calJac1 Contig8598 83453 84273 dinucleotide [Ta][TA][at] 2 364 + 381 [tat]t[tatatatatata][at] indel/deletion,indel/deletion t, 4,17 2 >panTro2 230 hg18 chr22 16289549 16290414 panTro2 chr22 16321054 16321919 ponAbe2 chr22 14053573 14054441 rheMac2 chr10 62105626 62106415 calJac1 Contig8598 83453 84273 dinucleotide [Ta][TA][at] 2 364 + 381 [tat]t[tatatatatata][at] indel/deletion,indel/deletion t, 4,17 2 >ponAbe2 230 hg18 chr22 16289549 16290414 panTro2 chr22 16321054 16321919 ponAbe2 chr22 14053573 14054441 rheMac2 chr10 62105626 62106415 calJac1 Contig8598 83453 84273 dinucleotide [Ta][TA][at] 6 364 + 381 [tat]t[tatatatatata][at] indel/deletion,indel/deletion t, 4,17 2 ->calJac1 231 hg18 chr22 16290414 16290680 panTro2 chr22 16321919 16322185 ponAbe2 chr22 14054441 14054710 rheMac2 chr10 62106415 62106684 calJac1 Contig8598 84273 84537 tetranucleotide CTTT 2 102 + 113 CTTTCTTTCTTT ->hg18 232 hg18 chr22 16290680 16291038 panTro2 chr22 16322185 16322556 ponAbe2 chr22 14054710 14055076 rheMac2 chr10 62106684 62107041 calJac1 Contig8598 84537 84871 mononucleotide [A][A] 0 61 + 71 [AAAAAAAAA]G[A] indel/deletion G 10 1 >panTro2 232 hg18 chr22 16290680 16291038 panTro2 chr22 16322185 16322556 ponAbe2 chr22 14054710 14055076 rheMac2 chr10 62106684 62107041 calJac1 Contig8598 84537 84871 mononucleotide [A][A] 0 61 + 71 [AAAAAAAAA]G[A] indel/deletion G 10 1 >rheMac2 232 hg18 chr22 16290680 16291038 panTro2 chr22 16322185 16322556 ponAbe2 chr22 14054710 14055076 rheMac2 chr10 62106684 62107041 calJac1 Contig8598 84537 84871 mononucleotide [A][A] 13 61 + 77 [AAAAAAAAAAAAAAA]G[A] indel/deletion G 16 1 >calJac1 232 hg18 chr22 16290680 16291038 panTro2 chr22 16322185 16322556 ponAbe2 chr22 14054710 14055076 rheMac2 chr10 62106684 62107041 calJac1 Contig8598 84537 84871 mononucleotide A 13 61 + 73 AAAAAAAAAAAAA ->hg18 232 hg18 chr22 16290680 16291038 panTro2 chr22 16322185 16322556 ponAbe2 chr22 14054710 14055076 rheMac2 chr10 62106684 62107041 calJac1 Contig8598 84537 84871 mononucleotide [T][T] 4 138 + 159 [T]A[TT----------TTTTTTTT] indel/deletion A 2 1 ->calJac1 234 hg18 chr22 16291640 16291694 panTro2 chr22 16323032 16323086 ponAbe2 chr22 14055488 14055549 rheMac2 chr10 62107688 62107826 calJac1 Contig8598 85281 85342 mononucleotide [t][T][T][T] 85 118 + 146 [ttt]g[tttttt]c[ttttt]c[tttttttttttt] indel/deletion,insertion,insertion g,c,c 4,11,17 3 ->hg18 236 hg18 chr22 16292285 16294278 panTro2 chr22 16323677 16325680 ponAbe2 chr22 14056140 14058141 rheMac2 chr10 62108411 62110398 calJac1 Contig8598 86533 88374 mononucleotide A 15 921 + 930 AAAAAAAA-A >panTro2 236 hg18 chr22 16292285 16294278 panTro2 chr22 16323677 16325680 ponAbe2 chr22 14056140 14058141 rheMac2 chr10 62108411 62110398 calJac1 Contig8598 86533 88374 mononucleotide A 5 921 + 930 AAAAAAAA-A >rheMac2 236 hg18 chr22 16292285 16294278 panTro2 chr22 16323677 16325680 ponAbe2 chr22 14056140 14058141 rheMac2 chr10 62108411 62110398 calJac1 Contig8598 86533 88374 mononucleotide [A][A][A] 11 922 + 944 [AAAAAAAAAAAAAAA-AA]G[AA]G[A] indel/deletion,indel/deletion G,G 18,21 2 ->hg18 236 hg18 chr22 16292285 16294278 panTro2 chr22 16323677 16325680 ponAbe2 chr22 14056140 14058141 rheMac2 chr10 62108411 62110398 calJac1 Contig8598 86533 88374 mononucleotide [T][T][T][T][T] 53 2002 + 2029 [tttttT]C[TTT]C[TTT]C[TTT]C[TTTTTTTTT] indel/deletion,indel/deletion,indel/deletion,indel/deletion C,C,C,C 7,11,15,19 4 >panTro2 236 hg18 chr22 16292285 16294278 panTro2 chr22 16323677 16325680 ponAbe2 chr22 14056140 14058141 rheMac2 chr10 62108411 62110398 calJac1 Contig8598 86533 88374 mononucleotide [T][T][T][T][T] 43 2002 + 2029 [tttttt]c[ttt]c[ttt]c[ttt]c[ttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion C,C,C,C 7,11,15,19 4 >rheMac2 236 hg18 chr22 16292285 16294278 panTro2 chr22 16323677 16325680 ponAbe2 chr22 14056140 14058141 rheMac2 chr10 62108411 62110398 calJac1 Contig8598 86533 88374 mononucleotide [T][T] 49 2002 + 2029 [tttttt]g[ttt----------tttttttt] insertion g 7 1 >ponAbe2 236 hg18 chr22 16292285 16294278 panTro2 chr22 16323677 16325680 ponAbe2 chr22 14056140 14058141 rheMac2 chr10 62108411 62110398 calJac1 Contig8598 86533 88374 tetranucleotide TTTC 44 2005 + 2020 tttctttctttctttc ->hg18 239 hg18 chr22 16294635 16294954 panTro2 chr22 16326037 16326354 ponAbe2 chr22 14058520 14058839 rheMac2 chr10 62111104 62111426 calJac1 Contig8598 88700 89018 mononucleotide [A][A] 0 95 + 121 [aaaaaaaaaaaaaaaaaaaaaaaaa]C[A] indel/deletion C 26 1 >panTro2 239 hg18 chr22 16294635 16294954 panTro2 chr22 16326037 16326354 ponAbe2 chr22 14058520 14058839 rheMac2 chr10 62111104 62111426 calJac1 Contig8598 88700 89018 mononucleotide [A][A] 0 95 + 119 [aaaaaaaaaaaaaaaaaaaaaaa]T[A] indel/deletion T 24 1 >rheMac2 239 hg18 chr22 16294635 16294954 panTro2 chr22 16326037 16326354 ponAbe2 chr22 14058520 14058839 rheMac2 chr10 62111104 62111426 calJac1 Contig8598 88700 89018 mononucleotide [A][A] 6 95 + 131 [a---------aaaaaaaaaaaaaaaaaaaaaaaaa]T[A] indel/deletion T 27 1 >ponAbe2 239 hg18 chr22 16294635 16294954 panTro2 chr22 16326037 16326354 ponAbe2 chr22 14058520 14058839 rheMac2 chr10 62111104 62111426 calJac1 Contig8598 88700 89018 mononucleotide A 10 106 + 125 aaaaaaaaaaaaaaaaaaaa ->rheMac2 239 hg18 chr22 16294635 16294954 panTro2 chr22 16326037 16326354 ponAbe2 chr22 14058520 14058839 rheMac2 chr10 62111104 62111426 calJac1 Contig8598 88700 89018 mononucleotide [T][T] 15 170 + 180 [TTTTTTTTT]C[T] indel/deletion C 10 1 ->calJac1 241 hg18 chr22 16295654 16295859 panTro2 chr22 16327038 16327243 ponAbe2 chr22 14059543 14059748 rheMac2 chr10 62112149 62112350 calJac1 Contig8598 89376 89570 tetranucleotide GGTG 6 101 + 120 GGTGG--------GTGGGTG ->panTro2 243 hg18 chr22 16296671 16296979 panTro2 chr22 16328055 16328364 ponAbe2 chr22 14060559 14060874 rheMac2 chr10 62113159 62113474 calJac1 Contig8598 90350 90654 mononucleotide A 4 107 + 115 AAAAAAAAA >ponAbe2 243 hg18 chr22 16296671 16296979 panTro2 chr22 16328055 16328364 ponAbe2 chr22 14060559 14060874 rheMac2 chr10 62113159 62113474 calJac1 Contig8598 90350 90654 mononucleotide [A][A] 0 107 + 117 [AAAAAAAAA]G[A] indel/deletion G 10 1 ->ponAbe2 246 hg18 chr22 16297445 16297842 panTro2 chr22 16328830 16329230 ponAbe2 chr22 14061338 14061743 rheMac2 chr10 62113911 62114314 calJac1 Contig8598 91120 91486 tetranucleotide ACCC 0 131 + 144 acccacccacccac >rheMac2 246 hg18 chr22 16297445 16297842 panTro2 chr22 16328830 16329230 ponAbe2 chr22 14061338 14061743 rheMac2 chr10 62113911 62114314 calJac1 Contig8598 91120 91486 tetranucleotide ACCC 4 131 + 142 acccacccaccc ->hg18 246 hg18 chr22 16297445 16297842 panTro2 chr22 16328830 16329230 ponAbe2 chr22 14061338 14061743 rheMac2 chr10 62113911 62114314 calJac1 Contig8598 91120 91486 mononucleotide T 1 220 + 231 tttttttttttt >panTro2 246 hg18 chr22 16297445 16297842 panTro2 chr22 16328830 16329230 ponAbe2 chr22 14061338 14061743 rheMac2 chr10 62113911 62114314 calJac1 Contig8598 91120 91486 mononucleotide T 2 220 + 232 ttttttttttttt >ponAbe2 246 hg18 chr22 16297445 16297842 panTro2 chr22 16328830 16329230 ponAbe2 chr22 14061338 14061743 rheMac2 chr10 62113911 62114314 calJac1 Contig8598 91120 91486 mononucleotide T 1 220 + 236 t---ttttttttttttt >ponAbe2 246 hg18 chr22 16297445 16297842 panTro2 chr22 16328830 16329230 ponAbe2 chr22 14061338 14061743 rheMac2 chr10 62113911 62114314 calJac1 Contig8598 91120 91486 mononucleotide T 6 243 + 251 ttttttttt >calJac1 246 hg18 chr22 16297445 16297842 panTro2 chr22 16328830 16329230 ponAbe2 chr22 14061338 14061743 rheMac2 chr10 62113911 62114314 calJac1 Contig8598 91120 91486 mononucleotide [T][T] 26 220 + 244 [tttttttttttt]g[t------ttttt] insertion g 13 1 ->ponAbe2 246 hg18 chr22 16297445 16297842 panTro2 chr22 16328830 16329230 ponAbe2 chr22 14061338 14061743 rheMac2 chr10 62113911 62114314 calJac1 Contig8598 91120 91486 trinucleotide TTC 6 305 + 317 ttcttcttcttct ->calJac1 247 hg18 chr22 16297885 16298166 panTro2 chr22 16329273 16329554 ponAbe2 chr22 14061786 14062066 rheMac2 chr10 62114356 62114623 calJac1 Contig8598 91520 91825 mononucleotide [T][T][T] 3 19 + 41 [TTT]C[TTTTTTTTTT]C------[TT] indel/deletion,indel/deletion C,C 4,15 2 ->ponAbe2 247 hg18 chr22 16297885 16298166 panTro2 chr22 16329273 16329554 ponAbe2 chr22 14061786 14062066 rheMac2 chr10 62114356 62114623 calJac1 Contig8598 91520 91825 mononucleotide.dinucleotide T.[TA][TA] 6 180 + 236 [TTTTTTTTT---------------------------------AAGTATATATATATA] NA.indel/deletion NA.AG NA.3 NA.1 174.182 182.197 TTTTTTTTT.[TA]AG[TATATATATATA] ->calJac1 248 hg18 chr22 16298166 16298735 panTro2 chr22 16329554 16330125 ponAbe2 chr22 14062066 14062645 rheMac2 chr10 62114623 62115219 calJac1 Contig8598 92222 92786 mononucleotide [T][T][T][T] 0 43 + 94 [TTTT--------TTTTT]A[T-------------T]G[TTTTT----------T]A[T] indel/deletion,indel/deletion,indel/deletion A,G,A 10,13,20 3 >hg18 248 hg18 chr22 16298166 16298735 panTro2 chr22 16329554 16330125 ponAbe2 chr22 14062066 14062645 rheMac2 chr10 62114623 62115219 calJac1 Contig8598 92222 92786 mononucleotide T 0 47 + 73 TTTTTTT-------------TTTTTTT >panTro2 248 hg18 chr22 16298166 16298735 panTro2 chr22 16329554 16330125 ponAbe2 chr22 14062066 14062645 rheMac2 chr10 62114623 62115219 calJac1 Contig8598 92222 92786 mononucleotide T 0 47 + 73 TTTTTTT-------------TTTTTTT >ponAbe2 248 hg18 chr22 16298166 16298735 panTro2 chr22 16329554 16330125 ponAbe2 chr22 14062066 14062645 rheMac2 chr10 62114623 62115219 calJac1 Contig8598 92222 92786 mononucleotide T 0 47 + 72 TTTTTT-------------TTTTTTT >rheMac2 248 hg18 chr22 16298166 16298735 panTro2 chr22 16329554 16330125 ponAbe2 chr22 14062066 14062645 rheMac2 chr10 62114623 62115219 calJac1 Contig8598 92222 92786 mononucleotide [T][T][T] 0 52 + 71 [TTTTTTTTTT]G[TTTT]A[TTTT] indel/deletion,indel/deletion G,A 11,16 2 ->hg18 248 hg18 chr22 16298166 16298735 panTro2 chr22 16329554 16330125 ponAbe2 chr22 14062066 14062645 rheMac2 chr10 62114623 62115219 calJac1 Contig8598 92222 92786 mononucleotide [a][A][a] 36 454 + 468 [a]c[aaaaaaaaa]--t[a] indel/deletion,indel/deletion c,t 2,12 2 >panTro2 248 hg18 chr22 16298166 16298735 panTro2 chr22 16329554 16330125 ponAbe2 chr22 14062066 14062645 rheMac2 chr10 62114623 62115219 calJac1 Contig8598 92222 92786 mononucleotide [A][A] 36 454 + 468 [A]C[AAAAAAAAA---A] indel/deletion C 2 1 >ponAbe2 248 hg18 chr22 16298166 16298735 panTro2 chr22 16329554 16330125 ponAbe2 chr22 14062066 14062645 rheMac2 chr10 62114623 62115219 calJac1 Contig8598 92222 92786 mononucleotide [A][A][A] 30 454 + 468 [A]C[AAAAAAAAA]--T[A] indel/deletion,indel/deletion C,T 2,12 2 >rheMac2 248 hg18 chr22 16298166 16298735 panTro2 chr22 16329554 16330125 ponAbe2 chr22 14062066 14062645 rheMac2 chr10 62114623 62115219 calJac1 Contig8598 92222 92786 mononucleotide [a][A][A] 14 454 + 468 [a]c[aaaaaaAAAAA]T[A] indel/deletion,indel/deletion c,T 2,14 2 ->calJac1 251 hg18 chr22 16299942 16300101 panTro2 chr22 16331331 16331483 ponAbe2 chr22 14063849 14063993 rheMac2 chr10 62115542 62115705 calJac1 Contig8598 94004 94146 mononucleotide T 20 51 + 62 tttttttttttt >ponAbe2 251 hg18 chr22 16299942 16300101 panTro2 chr22 16331331 16331483 ponAbe2 chr22 14063849 14063993 rheMac2 chr10 62115542 62115705 calJac1 Contig8598 94004 94146 mononucleotide [G][g] 7 58 + 87 [GGGGGGGG---------------GGG]C[ggg] indel/deletion C 12 1 ->hg18 252 hg18 chr22 16300101 16300939 panTro2 chr22 16331483 16332323 ponAbe2 chr22 14063993 14064832 rheMac2 chr10 62115705 62116536 calJac1 Contig8598 94146 94971 tetranucleotide TGAA 8 567 + 583 TGAATGAATGAATGAAT >panTro2 252 hg18 chr22 16300101 16300939 panTro2 chr22 16331483 16332323 ponAbe2 chr22 14063993 14064832 rheMac2 chr10 62115705 62116536 calJac1 Contig8598 94146 94971 tetranucleotide TGAA 8 567 + 583 TGAATGAATGAATGAAT >ponAbe2 252 hg18 chr22 16300101 16300939 panTro2 chr22 16331483 16332323 ponAbe2 chr22 14063993 14064832 rheMac2 chr10 62115705 62116536 calJac1 Contig8598 94146 94971 tetranucleotide TGAA 11 567 + 583 TGAATGAATGAATGAAT ->calJac1 254 hg18 chr22 16301918 16302211 panTro2 chr22 16333303 16333596 ponAbe2 chr22 14065777 14066071 rheMac2 chr10 62117566 62117857 calJac1 Contig17313 2 291 trinucleotide GAA 18 275 + 291 AAGAAGAAGAAGAAGAA ->rheMac2 256 hg18 chr22 16302445 16303446 panTro2 chr22 16333828 16334831 ponAbe2 chr22 14066304 14067303 rheMac2 chr10 62118089 62119086 calJac1 Contig17313 523 1521 mononucleotide A 0 158 + 166 AAAAAAAAA ->hg18 257 hg18 chr22 16303446 16303697 panTro2 chr22 16334831 16335086 ponAbe2 chr22 14067303 14067555 rheMac2 chr10 62119086 62119349 calJac1 Contig17313 1521 1775 mononucleotide A 4 220 + 245 aaaaaa-------------aaaa-aa >panTro2 257 hg18 chr22 16303446 16303697 panTro2 chr22 16334831 16335086 ponAbe2 chr22 14067303 14067555 rheMac2 chr10 62119086 62119349 calJac1 Contig17313 1521 1775 mononucleotide A 0 220 + 245 aaaaaa-------------aaaa-aa >ponAbe2 257 hg18 chr22 16303446 16303697 panTro2 chr22 16334831 16335086 ponAbe2 chr22 14067303 14067555 rheMac2 chr10 62119086 62119349 calJac1 Contig17313 1521 1775 mononucleotide [A][A] 4 220 + 245 [aaaaaa-------------aaaa]C[AA] indel/deletion C 11 1 >rheMac2 257 hg18 chr22 16303446 16303697 panTro2 chr22 16334831 16335086 ponAbe2 chr22 14067303 14067555 rheMac2 chr10 62119086 62119349 calJac1 Contig17313 1521 1775 tetranucleotide [AAAC][aaaC] 7 225 + 247 [aaacaaacaaacaaac]aa[aa-aC] indel/deletion aa 17 1 ->hg18 258 hg18 chr22 16321388 16321681 panTro2 chr22 16355870 16356163 ponAbe2 chr22 14085613 14085906 rheMac2 chr10 62143053 62143347 calJac1 Contig17313 8224 8526 mononucleotide [A][A][A][A][a] 0 10 + 56 [aaa]t[aa]t[aa]t[aaaaaaaa-------------------------aa]g[a] indel/deletion,indel/deletion,indel/deletion,indel/deletion T,T,T,g 4,7,10,21 5 >calJac1 258 hg18 chr22 16321388 16321681 panTro2 chr22 16355870 16356163 ponAbe2 chr22 14085613 14085906 rheMac2 chr10 62143053 62143347 calJac1 Contig17313 8224 8526 mononucleotide A 2 10 + 27 aaa----aaaaaaaaaaa >panTro2 258 hg18 chr22 16321388 16321681 panTro2 chr22 16355870 16356163 ponAbe2 chr22 14085613 14085906 rheMac2 chr10 62143053 62143347 calJac1 Contig17313 8224 8526 trinucleotide AAT 7 18 + 29 AATAATAATAAT >ponAbe2 258 hg18 chr22 16321388 16321681 panTro2 chr22 16355870 16356163 ponAbe2 chr22 14085613 14085906 rheMac2 chr10 62143053 62143347 calJac1 Contig17313 8224 8526 trinucleotide AAT 7 18 + 29 aataataataat ->ponAbe2 260 hg18 chr22 16323504 16324215 panTro2 chr22 16357708 16358419 ponAbe2 chr22 14090165 14090884 rheMac2 chr10 62147336 62148024 calJac1 Contig17313 11750 12456 dinucleotide [TC][tc][ct] 1 51 + 69 [tctctctctct][tctct]g[ct] indel/deletion,indel/deletion ,g 12,17 2 ->panTro2 260 hg18 chr22 16323504 16324215 panTro2 chr22 16357708 16358419 ponAbe2 chr22 14090165 14090884 rheMac2 chr10 62147336 62148024 calJac1 Contig17313 11750 12456 mononucleotide T 7 537 + 555 ttttttttttttttttttt >ponAbe2 260 hg18 chr22 16323504 16324215 panTro2 chr22 16357708 16358419 ponAbe2 chr22 14090165 14090884 rheMac2 chr10 62147336 62148024 calJac1 Contig17313 11750 12456 mononucleotide [t][t][T] 12 538 + 568 [t]a[ttt]c[t-ttttttttttttttttttttttt] indel/deletion,indel/deletion a,c 2,6 2 >hg18 260 hg18 chr22 16323504 16324215 panTro2 chr22 16357708 16358419 ponAbe2 chr22 14090165 14090884 rheMac2 chr10 62147336 62148024 calJac1 Contig17313 11750 12456 mononucleotide T 20 551 + 568 tttttttttttttttttt ->hg18 261 hg18 chr22 16327506 16327745 panTro2 chr22 16362145 16362384 ponAbe2 chr22 14094639 14094887 rheMac2 chr10 62150170 62150407 calJac1 Contig25039 5336 5588 mononucleotide T 0 59 + 67 ttttttttt >panTro2 261 hg18 chr22 16327506 16327745 panTro2 chr22 16362145 16362384 ponAbe2 chr22 14094639 14094887 rheMac2 chr10 62150170 62150407 calJac1 Contig25039 5336 5588 mononucleotide T 0 59 + 67 ttttttttt >ponAbe2 261 hg18 chr22 16327506 16327745 panTro2 chr22 16362145 16362384 ponAbe2 chr22 14094639 14094887 rheMac2 chr10 62150170 62150407 calJac1 Contig25039 5336 5588 mononucleotide [t][T] 0 59 + 75 [ttt]c[ttttttttttttt] indel/deletion c 4 1 ->hg18 263 hg18 chr22 16328382 16328665 panTro2 chr22 16363021 16363297 ponAbe2 chr22 14095534 14095808 rheMac2 chr10 62150849 62151126 calJac1 Contig25039 6012 6242 mononucleotide [T][T] 4 255 + 274 [TT]G[TTTTTTTTTTTTTTTTT] indel/deletion G 3 1 >panTro2 263 hg18 chr22 16328382 16328665 panTro2 chr22 16363021 16363297 ponAbe2 chr22 14095534 14095808 rheMac2 chr10 62150849 62151126 calJac1 Contig25039 6012 6242 mononucleotide [T][T] 3 255 + 274 [TT]G--------[TTTTTTTTT] indel/deletion G 3 1 ->calJac1 265 hg18 chr22 16329045 16329222 panTro2 chr22 16363677 16363854 ponAbe2 chr22 14096185 14096362 rheMac2 chr10 62151508 62151686 calJac1 Contig25478 2315 2491 dinucleotide [AC][AC] 2 114 + 127 [ACA]G[ACACACACAC] indel/deletion G 4 1 >hg18 265 hg18 chr22 16329045 16329222 panTro2 chr22 16363677 16363854 ponAbe2 chr22 14096185 14096362 rheMac2 chr10 62151508 62151686 calJac1 Contig25478 2315 2491 dinucleotide AC 1 118 + 127 ACACACACAC >panTro2 265 hg18 chr22 16329045 16329222 panTro2 chr22 16363677 16363854 ponAbe2 chr22 14096185 14096362 rheMac2 chr10 62151508 62151686 calJac1 Contig25478 2315 2491 dinucleotide AC 1 118 + 127 ACACACACAC ->ponAbe2 270 hg18 chr22 16330420 16330904 panTro2 chr22 16365050 16365526 ponAbe2 chr22 14097691 14098183 rheMac2 chr10 62152864 62153342 calJac1 Contig9043 2 456 trinucleotide [GTT][TTG][gtt][Gtt] 7 140 + 175 [GTT]TT[ttgttgttgttgttgttgttg][gttgtt][TGtt] indel/deletion,indel/deletion,indel/deletion TT,, 4,27,33 3 >rheMac2 270 hg18 chr22 16330420 16330904 panTro2 chr22 16365050 16365526 ponAbe2 chr22 14097691 14098183 rheMac2 chr10 62152864 62153342 calJac1 Contig9043 2 456 trinucleotide [TTG][ttg] 11 145 + 168 [ttgttgttgttgttgt--t][ttgtt] indel/deletion 18 1 >hg18 270 hg18 chr22 16330420 16330904 panTro2 chr22 16365050 16365526 ponAbe2 chr22 14097691 14098183 rheMac2 chr10 62152864 62153342 calJac1 Contig9043 2 456 tetranucleotide [tgtt][TTTG][GTTT] 8 151 + 184 [ttgtt]g[TTGT--TTGTTTGTTTGTTTG]A[TTGTTT] indel/deletion,indel/deletion g,A 6,26 2 >panTro2 270 hg18 chr22 16330420 16330904 panTro2 chr22 16365050 16365526 ponAbe2 chr22 14097691 14098183 rheMac2 chr10 62152864 62153342 calJac1 Contig9043 2 456 tetranucleotide [TGTT][GTTT] 8 151 + 184 [TTGTT]G[TTGt--ttgtttgt--------ttgttt] indel/deletion G 6 1 ->hg18 272 hg18 chr22 16331445 16331734 panTro2 chr22 16366067 16366356 ponAbe2 chr22 14099015 14099291 rheMac2 chr10 62153876 62154160 calJac1 Contig9043 1289 1552 mononucleotide [T][T] 1 165 + 179 [TTTTTT--TTT]C[TTT] indel/deletion C 10 1 >panTro2 272 hg18 chr22 16331445 16331734 panTro2 chr22 16366067 16366356 ponAbe2 chr22 14099015 14099291 rheMac2 chr10 62153876 62154160 calJac1 Contig9043 1289 1552 mononucleotide [T][T] 1 165 + 179 [TTTTTT--TTT]C[TTT] indel/deletion C 10 1 >ponAbe2 272 hg18 chr22 16331445 16331734 panTro2 chr22 16366067 16366356 ponAbe2 chr22 14099015 14099291 rheMac2 chr10 62153876 62154160 calJac1 Contig9043 1289 1552 mononucleotide [T][T] 4 165 + 179 [TTTTTT--TTT]C[TTT] indel/deletion C 10 1 >calJac1 272 hg18 chr22 16331445 16331734 panTro2 chr22 16366067 16366356 ponAbe2 chr22 14099015 14099291 rheMac2 chr10 62153876 62154160 calJac1 Contig9043 1289 1552 mononucleotide [T][T] 4 165 + 179 [TTTTTT--TTT]C[TTT] indel/deletion C 10 1 ->hg18 279 hg18 chr22 16333362 16334120 panTro2 chr22 16367983 16368743 ponAbe2 chr22 14101275 14102033 rheMac2 chr10 62156110 62156889 calJac1 Contig9043 4122 4889 tetranucleotide TTAT 9 520 + 553 ttatttat--------------------ttattt >panTro2 279 hg18 chr22 16333362 16334120 panTro2 chr22 16367983 16368743 ponAbe2 chr22 14101275 14102033 rheMac2 chr10 62156110 62156889 calJac1 Contig9043 4122 4889 tetranucleotide TTAT 7 520 + 553 ttatttat--------------------ttattt >ponAbe2 279 hg18 chr22 16333362 16334120 panTro2 chr22 16367983 16368743 ponAbe2 chr22 14101275 14102033 rheMac2 chr10 62156110 62156889 calJac1 Contig9043 4122 4889 tetranucleotide TTAT 9 520 + 553 TTATTTAT--------------------TTAttt >rheMac2 279 hg18 chr22 16333362 16334120 panTro2 chr22 16367983 16368743 ponAbe2 chr22 14101275 14102033 rheMac2 chr10 62156110 62156889 calJac1 Contig9043 4122 4889 tetranucleotide [TTAT][ttat] 7 520 + 553 [ttatttatttatttatttatttattta]c[ttattt] indel/deletion c 28 1 ->rheMac2 280 hg18 chr22 16334120 16335613 panTro2 chr22 16368743 16370234 ponAbe2 chr22 14102033 14103528 rheMac2 chr10 62156889 62158396 calJac1 Contig9043 5235 6731 trinucleotide TTG 7 391 + 402 ttgttgttgttg ->ponAbe2 280 hg18 chr22 16334120 16335613 panTro2 chr22 16368743 16370234 ponAbe2 chr22 14102033 14103528 rheMac2 chr10 62156889 62158396 calJac1 Contig9043 5235 6731 tetranucleotide [TTGT][TTTG] 39 1228 + 1248 [TTTGT]GCtt[tttgtttgtttg] indel/deletion GCtt 6 1 >hg18 280 hg18 chr22 16334120 16335613 panTro2 chr22 16368743 16370234 ponAbe2 chr22 14102033 14103528 rheMac2 chr10 62156889 62158396 calJac1 Contig9043 5235 6731 tetranucleotide [Gttt][TTTG] 43 1232 + 1248 [TGttt][tttgtttgtttg] indel/deletion 6 1 >panTro2 280 hg18 chr22 16334120 16335613 panTro2 chr22 16368743 16370234 ponAbe2 chr22 14102033 14103528 rheMac2 chr10 62156889 62158396 calJac1 Contig9043 5235 6731 tetranucleotide [Gttt][TTTG] 43 1232 + 1248 [TGttt][tttgtttgtttg] indel/deletion 6 1 >rheMac2 280 hg18 chr22 16334120 16335613 panTro2 chr22 16368743 16370234 ponAbe2 chr22 14102033 14103528 rheMac2 chr10 62156889 62158396 calJac1 Contig9043 5235 6731 tetranucleotide [Gttt][TTTG] 27 1232 + 1248 [TGttt][tttgtttgtttg] indel/deletion 6 1 >calJac1 280 hg18 chr22 16334120 16335613 panTro2 chr22 16368743 16370234 ponAbe2 chr22 14102033 14103528 rheMac2 chr10 62156889 62158396 calJac1 Contig9043 5235 6731 tetranucleotide [Gttt][TTTG] 34 1232 + 1248 [TGttt][tttgtttgtttg] indel/deletion 6 1 ->calJac1 287 hg18 chr22 16337992 16338462 panTro2 chr22 16372603 16373074 ponAbe2 chr22 14106039 14106507 rheMac2 chr10 62162737 62163208 calJac1 Contig9043 9118 9579 mononucleotide T 1 56 + 65 tttttttttt ->hg18 289 hg18 chr22 16338674 16339485 panTro2 chr22 16373287 16374094 ponAbe2 chr22 14106724 14107536 rheMac2 chr10 62163740 62164545 calJac1 Contig9043 9776 10584 mononucleotide [T][T][T] 5 133 + 158 [T]C[ttt]c[tttttttttttttttttttt] indel/deletion,indel/deletion C,C 2,6 2 >panTro2 289 hg18 chr22 16338674 16339485 panTro2 chr22 16373287 16374094 ponAbe2 chr22 14106724 14107536 rheMac2 chr10 62163740 62164545 calJac1 Contig9043 9776 10584 mononucleotide [T][T][T][T] 5 133 + 155 [T]C[ttt]c[ttt]c[ttttttttttttt] indel/deletion,indel/deletion,indel/deletion C,C,C 2,6,10 3 >rheMac2 289 hg18 chr22 16338674 16339485 panTro2 chr22 16373287 16374094 ponAbe2 chr22 14106724 14107536 rheMac2 chr10 62163740 62164545 calJac1 Contig9043 9776 10584 mononucleotide [T][T] 5 133 + 147 [T]C[ttttttttttttt] indel/deletion C 2 1 >ponAbe2 289 hg18 chr22 16338674 16339485 panTro2 chr22 16373287 16374094 ponAbe2 chr22 14106724 14107536 rheMac2 chr10 62163740 62164545 calJac1 Contig9043 9776 10584 mononucleotide [t][T] 3 139 + 149 [t]c[ttttttttt] indel/deletion c 2 1 ->hg18 289 hg18 chr22 16338674 16339485 panTro2 chr22 16373287 16374094 ponAbe2 chr22 14106724 14107536 rheMac2 chr10 62163740 62164545 calJac1 Contig9043 9776 10584 dinucleotide AC 22 810 + 833 acacacacacacacacacacacac >panTro2 289 hg18 chr22 16338674 16339485 panTro2 chr22 16373287 16374094 ponAbe2 chr22 14106724 14107536 rheMac2 chr10 62163740 62164545 calJac1 Contig9043 9776 10584 dinucleotide AC 26 810 + 833 acacacacacacacacacacacac >ponAbe2 289 hg18 chr22 16338674 16339485 panTro2 chr22 16373287 16374094 ponAbe2 chr22 14106724 14107536 rheMac2 chr10 62163740 62164545 calJac1 Contig9043 9776 10584 dinucleotide AC 21 810 + 833 acacacacacacacacacacacac >rheMac2 289 hg18 chr22 16338674 16339485 panTro2 chr22 16373287 16374094 ponAbe2 chr22 14106724 14107536 rheMac2 chr10 62163740 62164545 calJac1 Contig9043 9776 10584 dinucleotide [ca][AC][ac] 28 817 + 833 [ca]t[acacacacaca]t[ac] indel/deletion,indel/deletion t,t 3,15 2 ->hg18 291 hg18 chr22 16342289 16342688 panTro2 chr22 16379642 16380042 ponAbe2 chr22 14109256 14109658 rheMac2 chr10 62166748 62167067 calJac1 Contig9043 12003 12441 mononucleotide [a][A][A][a] 19 356 + 383 [a]g[aaaa-------aaaaa]g[aaaaaaa]t[a] indel/deletion,insertion,indel/deletion g,g,t 2,12,20 3 >panTro2 291 hg18 chr22 16342289 16342688 panTro2 chr22 16379642 16380042 ponAbe2 chr22 14109256 14109658 rheMac2 chr10 62166748 62167067 calJac1 Contig9043 12003 12441 mononucleotide [a][A][A][a] 18 356 + 383 [a]g[aaaa-------aaaaa]g[aaaaaaa]t[a] indel/deletion,insertion,indel/deletion g,g,t 2,12,20 3 >rheMac2 291 hg18 chr22 16342289 16342688 panTro2 chr22 16379642 16380042 ponAbe2 chr22 14109256 14109658 rheMac2 chr10 62166748 62167067 calJac1 Contig9043 12003 12441 mononucleotide A 65 369 + 404 aaaaaaaaaaa--------------------aaaaa ->calJac1 292 hg18 chr22 16342688 16343025 panTro2 chr22 16380042 16380372 ponAbe2 chr22 14109658 14110009 rheMac2 chr10 62167067 62167393 calJac1 Contig9043 12564 12911 mononucleotide [A][A] 0 93 + 114 [aaaaaaaaaaa]-----c[aaaaa] insertion c 12 1 ->rheMac2 293 hg18 chr22 16343173 16344411 panTro2 chr22 16380520 16381757 ponAbe2 chr22 14110164 14111423 rheMac2 chr10 62167539 62168754 calJac1 Contig9043 12911 14123 tetranucleotide [gttt][TTTG] 12 367 + 400 [ttgttt]tt-c[tgtttgtttg-----ttt-----g] indel/deletion ttc 7 1 >ponAbe2 293 hg18 chr22 16343173 16344411 panTro2 chr22 16380520 16381757 ponAbe2 chr22 14110164 14111423 rheMac2 chr10 62167539 62168754 calJac1 Contig9043 12911 14123 mononucleotide T 7 388 + 398 ttttttttttt ->hg18 293 hg18 chr22 16343173 16344411 panTro2 chr22 16380520 16381757 ponAbe2 chr22 14110164 14111423 rheMac2 chr10 62167539 62168754 calJac1 Contig9043 12911 14123 tetranucleotide [gttt][GTTT][gttT] 10 446 + 474 [tgttt][tttgtttgtttgtttgttt][tgttt] indel/deletion,indel/deletion , 6,25 2 >panTro2 293 hg18 chr22 16343173 16344411 panTro2 chr22 16380520 16381757 ponAbe2 chr22 14110164 14111423 rheMac2 chr10 62167539 62168754 calJac1 Contig9043 12911 14123 tetranucleotide [GTTT][GTTT][GTTT] 9 446 + 474 [TGTTT][TTTGTTTGTTTGTTTGTTT][TGTTT] indel/deletion,indel/deletion , 6,25 2 >ponAbe2 293 hg18 chr22 16343173 16344411 panTro2 chr22 16380520 16381757 ponAbe2 chr22 14110164 14111423 rheMac2 chr10 62167539 62168754 calJac1 Contig9043 12911 14123 tetranucleotide [GTTT][gttT] 7 454 + 482 [tttgtttg---------tttgttt][tgttt] indel/deletion 16 1 >rheMac2 293 hg18 chr22 16343173 16344411 panTro2 chr22 16380520 16381757 ponAbe2 chr22 14110164 14111423 rheMac2 chr10 62167539 62168754 calJac1 Contig9043 12911 14123 tetranucleotide [GTTT][gttT] 26 454 + 482 [tttgtttg---------tttgttt][tgttt] indel/deletion 16 1 >calJac1 293 hg18 chr22 16343173 16344411 panTro2 chr22 16380520 16381757 ponAbe2 chr22 14110164 14111423 rheMac2 chr10 62167539 62168754 calJac1 Contig9043 12911 14123 mononucleotide A 61 483 + 491 aaaaaaaaa ->calJac1 293 hg18 chr22 16343173 16344411 panTro2 chr22 16380520 16381757 ponAbe2 chr22 14110164 14111423 rheMac2 chr10 62167539 62168754 calJac1 Contig9043 12911 14123 mononucleotide [A][a] 83 749 + 788 [AAA------------------Aaa---------aaa]c[aaa] indel/deletion c 10 1 ->calJac1 295 hg18 chr22 16346841 16348873 panTro2 chr22 16384178 16386214 ponAbe2 chr22 14113824 14115860 rheMac2 chr10 62171143 62173142 calJac1 Contig9043 16727 18527 mononucleotide T 2 29 + 52 ttttttt-----------tttttt ->rheMac2 295 hg18 chr22 16346841 16348873 panTro2 chr22 16384178 16386214 ponAbe2 chr22 14113824 14115860 rheMac2 chr10 62171143 62173142 calJac1 Contig9043 16727 18527 mononucleotide [T][T][t][T][T] 3 56 + 101 [TTTTT]C[TTTTTTT]C[tttt]c[ttttttttttt]g[ttttt-----ttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion C,C,c,g 6,14,19,31 4 >hg18 295 hg18 chr22 16346841 16348873 panTro2 chr22 16384178 16386214 ponAbe2 chr22 14113824 14115860 rheMac2 chr10 62171143 62173142 calJac1 Contig9043 16727 18527 tetranucleotide ATTT 3 65 + 101 tatttatttatttatttatttatt--------tattt >panTro2 295 hg18 chr22 16346841 16348873 panTro2 chr22 16384178 16386214 ponAbe2 chr22 14113824 14115860 rheMac2 chr10 62171143 62173142 calJac1 Contig9043 16727 18527 tetranucleotide [TATT][tatt] 3 65 + 101 [tatttatttatttatttatttatttatttat]g[tattt] indel/deletion g 32 1 >ponAbe2 295 hg18 chr22 16346841 16348873 panTro2 chr22 16384178 16386214 ponAbe2 chr22 14113824 14115860 rheMac2 chr10 62171143 62173142 calJac1 Contig9043 16727 18527 mononucleotide [t][T] 3 87 + 102 [t]c[ttttt---tttttt] indel/deletion c 2 1 ->calJac1 295 hg18 chr22 16346841 16348873 panTro2 chr22 16384178 16386214 ponAbe2 chr22 14113824 14115860 rheMac2 chr10 62171143 62173142 calJac1 Contig9043 16727 18527 mononucleotide [t][T][t][t] 210 1149 + 1197 [t-t]c[ttttt---ttttt]c[tt]c[ttttttt--------------------t] indel/deletion,indel/deletion,indel/deletion c,c,c 3,14,17 3 ->calJac1 295 hg18 chr22 16346841 16348873 panTro2 chr22 16384178 16386214 ponAbe2 chr22 14113824 14115860 rheMac2 chr10 62171143 62173142 calJac1 Contig9043 16727 18527 tetranucleotide.tetranucleotide.tetranucleotide TGTT.[ttta][ATTT].TTTG 303 1675 + 1709 [tgtttgtttgtttgtttatttaattTATTTATTTA] NA.indel/deletion.NA NA..NA NA.9.NA NA.1.NA 1372.1386.1372 1388.1406.1385 TGTTTGTTTGTTTGTTT.[tttattta][ATTTATTTATTTA].TGTTTGTTTGTTTG >rheMac2 295 hg18 chr22 16346841 16348873 panTro2 chr22 16384178 16386214 ponAbe2 chr22 14113824 14115860 rheMac2 chr10 62171143 62173142 calJac1 Contig9043 16727 18527 tetranucleotide [Ttta][TTTA] 58 1677 + 1711 [tttat]----------------[tttatttatttatt] indel/deletion 6 1 >ponAbe2 295 hg18 chr22 16346841 16348873 panTro2 chr22 16384178 16386214 ponAbe2 chr22 14113824 14115860 rheMac2 chr10 62171143 62173142 calJac1 Contig9043 16727 18527 tetranucleotide TATT 40 1682 + 1695 tttatttatttatt ->calJac1 295 hg18 chr22 16346841 16348873 panTro2 chr22 16384178 16386214 ponAbe2 chr22 14113824 14115860 rheMac2 chr10 62171143 62173142 calJac1 Contig9043 16727 18527 mononucleotide [t][T][T][T] 308 2076 + 2108 [tttt]a[ttt]c[ttt]c[tttttttttttttttttttt] indel/deletion,indel/deletion,indel/deletion a,C,C 5,9,13 3 ->hg18 296 hg18 chr22 16348873 16349128 panTro2 chr22 16386214 16386479 ponAbe2 chr22 14115860 14116133 rheMac2 chr10 62173142 62173417 calJac1 Contig9043 18816 19080 mononucleotide [t][T] 0 40 + 71 [t]c-----------------[ttttttttttttt] indel/deletion c 2 1 >panTro2 296 hg18 chr22 16348873 16349128 panTro2 chr22 16386214 16386479 ponAbe2 chr22 14115860 14116133 rheMac2 chr10 62173142 62173417 calJac1 Contig9043 18816 19080 mononucleotide [T][T][T] 0 40 + 71 [t]c[tt]c-------[tttttttttttttttttttt] indel/deletion,indel/deletion C,C 2,5 2 >ponAbe2 296 hg18 chr22 16348873 16349128 panTro2 chr22 16386214 16386479 ponAbe2 chr22 14115860 14116133 rheMac2 chr10 62173142 62173417 calJac1 Contig9043 18816 19080 mononucleotide [T][T][T] 0 40 + 71 [t]c[tt]c[ttttttttttttttttttttttttttt] indel/deletion,indel/deletion C,C 2,5 2 >rheMac2 296 hg18 chr22 16348873 16349128 panTro2 chr22 16386214 16386479 ponAbe2 chr22 14115860 14116133 rheMac2 chr10 62173142 62173417 calJac1 Contig9043 18816 19080 mononucleotide [t][T] 0 40 + 71 [t]c[tttttttttttttttttttttttttttttt] indel/deletion c 2 1 >calJac1 296 hg18 chr22 16348873 16349128 panTro2 chr22 16386214 16386479 ponAbe2 chr22 14115860 14116133 rheMac2 chr10 62173142 62173417 calJac1 Contig9043 18816 19080 mononucleotide [t][T] 0 40 + 71 [t------------------ttt]c[ttttttttt] indel/deletion c 5 1 ->panTro2 297 hg18 chr22 16349128 16349844 panTro2 chr22 16386479 16387214 ponAbe2 chr22 14116133 14116845 rheMac2 chr10 62173417 62174118 calJac1 Contig9043 19216 20196 dinucleotide.dinucleotide [Tg][TG][tg].[tg][GT][tg] 14 55 + 114 [tgttttgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtttggtgtgtgtgtgtttg] indel/deletion,indel/deletion.indel/deletion,indel/deletion tt,t.,t 4,43.3,15 2.2 41.84 85.100 [Tgt]tt[TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT]t[tg].[tg][GTGTGTGTGTGT]t[tg] >ponAbe2 297 hg18 chr22 16349128 16349844 panTro2 chr22 16386479 16387214 ponAbe2 chr22 14116133 14116845 rheMac2 chr10 62173417 62174118 calJac1 Contig9043 19216 20196 dinucleotide [Tg][TG][tg] 14 55 + 114 [tgt]tt[tgt-------------------------------------gtgtgtgtgtgt]t[tg] indel/deletion,indel/deletion tt,t 4,21 2 >hg18 297 hg18 chr22 16349128 16349844 panTro2 chr22 16386479 16387214 ponAbe2 chr22 14116133 14116845 rheMac2 chr10 62173417 62174118 calJac1 Contig9043 19216 20196 compound [T][GT] 14 57 + 111 [tttttttttt][gtgtgtgt-------------------------gtgtgtgtgtgt] ->rheMac2 297 hg18 chr22 16349128 16349844 panTro2 chr22 16386479 16387214 ponAbe2 chr22 14116133 14116845 rheMac2 chr10 62173417 62174118 calJac1 Contig9043 19216 20196 compound [TATT][TATC] 55 373 + 457 [TATTTATTTATT][TATCTAT-------------------------------------------------------------CTATC] >hg18 297 hg18 chr22 16349128 16349844 panTro2 chr22 16386479 16387214 ponAbe2 chr22 14116133 14116845 rheMac2 chr10 62173417 62174118 calJac1 Contig9043 19216 20196 tetranucleotide [tatt][TTTA] 42 377 + 459 [tatt]------[tttat-------------------------------------------------------------ttattta] indel/deletion 5 1 >panTro2 297 hg18 chr22 16349128 16349844 panTro2 chr22 16386479 16387214 ponAbe2 chr22 14116133 14116845 rheMac2 chr10 62173417 62174118 calJac1 Contig9043 19216 20196 tetranucleotide [tatt][TTTA] 17 377 + 459 [tatt]------[tttat-------------------------------------------------------------ttattta] indel/deletion 5 1 >ponAbe2 297 hg18 chr22 16349128 16349844 panTro2 chr22 16386479 16387214 ponAbe2 chr22 14116133 14116845 rheMac2 chr10 62173417 62174118 calJac1 Contig9043 19216 20196 tetranucleotide [tatt][TTTA] 53 377 + 459 [tatt]------[tttat-------------------------------------------------------------ttattta] indel/deletion 5 1 >calJac1 297 hg18 chr22 16349128 16349844 panTro2 chr22 16386479 16387214 ponAbe2 chr22 14116133 14116845 rheMac2 chr10 62173417 62174118 calJac1 Contig9043 19216 20196 mononucleotide T 43 456 + 465 tttttttttt ->hg18 297 hg18 chr22 16349128 16349844 panTro2 chr22 16386479 16387214 ponAbe2 chr22 14116133 14116845 rheMac2 chr10 62173417 62174118 calJac1 Contig9043 19216 20196 mononucleotide [T][T][T][T] 196 702 + 737 [tttttttttt]a[t-------tttt]a[tttttt]a[ttttt] insertion,insertion,insertion a,a,a 11,17,24 3 >panTro2 297 hg18 chr22 16349128 16349844 panTro2 chr22 16386479 16387214 ponAbe2 chr22 14116133 14116845 rheMac2 chr10 62173417 62174118 calJac1 Contig9043 19216 20196 mononucleotide [T][t] 171 702 + 740 [ttttt------t-------tttttttttttttttttt]g[t] indel/deletion g 25 1 >ponAbe2 297 hg18 chr22 16349128 16349844 panTro2 chr22 16386479 16387214 ponAbe2 chr22 14116133 14116845 rheMac2 chr10 62173417 62174118 calJac1 Contig9043 19216 20196 mononucleotide [T][T][T][T][T][T] 207 702 + 731 [tttttt]g[ttt]g[ttt]g[ttt]g[ttttttttt]g[t] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion G,G,G,G,g 7,11,15,19,29 5 >rheMac2 297 hg18 chr22 16349128 16349844 panTro2 chr22 16386479 16387214 ponAbe2 chr22 14116133 14116845 rheMac2 chr10 62173417 62174118 calJac1 Contig9043 19216 20196 mononucleotide [T][t][t] 203 702 + 731 [ttttt--------------tttttt]c[tt]g[t] indel/deletion,indel/deletion c,g 12,15 2 ->calJac1 297 hg18 chr22 16349128 16349844 panTro2 chr22 16386479 16387214 ponAbe2 chr22 14116133 14116845 rheMac2 chr10 62173417 62174118 calJac1 Contig9043 19216 20196 mononucleotide [t][T][T][T] 67 882 + 911 [ttt]c[ttttt]c[ttttttt]c[tttttttttttt] indel/deletion,insertion,insertion c,c,c 4,10,18 3 ->rheMac2 299 hg18 chr22 16350209 16350764 panTro2 chr22 16387580 16388142 ponAbe2 chr22 14117215 14117778 rheMac2 chr10 62174797 62175359 calJac1 Contig9043 20748 21298 mononucleotide T 5 360 + 368 TTTTTTTTT ->ponAbe2 299 hg18 chr22 16350209 16350764 panTro2 chr22 16387580 16388142 ponAbe2 chr22 14117215 14117778 rheMac2 chr10 62174797 62175359 calJac1 Contig9043 20748 21298 dinucleotide TG 12 405 + 441 tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg--tgt >hg18 299 hg18 chr22 16350209 16350764 panTro2 chr22 16387580 16388142 ponAbe2 chr22 14117215 14117778 rheMac2 chr10 62174797 62175359 calJac1 Contig9043 20748 21298 dinucleotide TG 16 407 + 422 TGTGTGTGTGTGTGTG >panTro2 299 hg18 chr22 16350209 16350764 panTro2 chr22 16387580 16388142 ponAbe2 chr22 14117215 14117778 rheMac2 chr10 62174797 62175359 calJac1 Contig9043 20748 21298 dinucleotide [TG][tg] 15 407 + 441 [tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt]c[tgt] indel/deletion c 32 1 >calJac1 299 hg18 chr22 16350209 16350764 panTro2 chr22 16387580 16388142 ponAbe2 chr22 14117215 14117778 rheMac2 chr10 62174797 62175359 calJac1 Contig9043 20748 21298 dinucleotide GT 10 407 + 440 gtgtgtgtgtgtgtgtgtgtgtgtg------tgt >rheMac2 299 hg18 chr22 16350209 16350764 panTro2 chr22 16387580 16388142 ponAbe2 chr22 14117215 14117778 rheMac2 chr10 62174797 62175359 calJac1 Contig9043 20748 21298 dinucleotide GT 6 410 + 439 gtgtgtgtgtgtgtgtgtgtgtg------t ->calJac1 304 hg18 chr22 16351578 16351662 panTro2 chr22 16388956 16389040 ponAbe2 chr22 14118596 14118680 rheMac2 chr10 62176585 62176712 calJac1 Contig9043 22828 22908 dinucleotide [Ct][CT][TC][ct] 0 1 + 30 [ctc]a[ctctctctctctctct]t[tctctc]c[ct] indel/deletion,indel/substitution,indel/deletion a,t,c 4,21,28 3 ->hg18 305 hg18 chr22 16351941 16352272 panTro2 chr22 16389319 16389650 ponAbe2 chr22 14118959 14119280 rheMac2 chr10 62176991 62177346 calJac1 Contig46949 3012 3293 trinucleotide CCT 25 169 + 180 cctcctcctcct >panTro2 305 hg18 chr22 16351941 16352272 panTro2 chr22 16389319 16389650 ponAbe2 chr22 14118959 14119280 rheMac2 chr10 62176991 62177346 calJac1 Contig46949 3012 3293 trinucleotide CCT 25 169 + 180 cctcctcctcct ->calJac1 305 hg18 chr22 16351941 16352272 panTro2 chr22 16389319 16389650 ponAbe2 chr22 14118959 14119280 rheMac2 chr10 62176991 62177346 calJac1 Contig46949 3012 3293 mononucleotide T 75 255 + 268 tttttttttttttt ->calJac1 308 hg18 chr22 16352922 16353147 panTro2 chr22 16390300 16390521 ponAbe2 chr22 14119897 14120118 rheMac2 chr10 62177997 62178218 calJac1 Contig9043 23736 23942 mononucleotide [T][T][T] 15 192 + 226 [ttttttttt-----ttt]g[ttttttt]g[ttttttttt] insertion,insertion g,g 13,21 2 >hg18 308 hg18 chr22 16352922 16353147 panTro2 chr22 16390300 16390521 ponAbe2 chr22 14119897 14120118 rheMac2 chr10 62177997 62178218 calJac1 Contig9043 23736 23942 tetranucleotide [TTTC][TTTC] 0 195 + 221 [TTTC]AT[tttc-tttctttctttctttc] indel/deletion AT 5 1 >panTro2 308 hg18 chr22 16352922 16353147 panTro2 chr22 16390300 16390521 ponAbe2 chr22 14119897 14120118 rheMac2 chr10 62177997 62178218 calJac1 Contig9043 23736 23942 tetranucleotide [tttc][TTTC] 0 195 + 221 [tttc]at-----[tttctttctttctttc] indel/deletion at 5 1 >ponAbe2 308 hg18 chr22 16352922 16353147 panTro2 chr22 16390300 16390521 ponAbe2 chr22 14119897 14120118 rheMac2 chr10 62177997 62178218 calJac1 Contig9043 23736 23942 tetranucleotide [TTTC][TTTC] 0 195 + 221 [TTTC]AT-----[TTtctttctttctttc] indel/deletion AT 5 1 >rheMac2 308 hg18 chr22 16352922 16353147 panTro2 chr22 16390300 16390521 ponAbe2 chr22 14119897 14120118 rheMac2 chr10 62177997 62178218 calJac1 Contig9043 23736 23942 mononucleotide [T][T] 5 200 + 226 [TTTT]C[TTTttttttttttttttttttt] indel/deletion C 5 1 ->calJac1 311 hg18 chr22 16354209 16354352 panTro2 chr22 16391580 16391723 ponAbe2 chr22 14121174 14121322 rheMac2 chr10 62178968 62179140 calJac1 Contig9043 25077 25224 mononucleotide T 5 74 + 82 TTTTTTTTT ->rheMac2 311 hg18 chr22 16354209 16354352 panTro2 chr22 16391580 16391723 ponAbe2 chr22 14121174 14121322 rheMac2 chr10 62178968 62179140 calJac1 Contig9043 25077 25224 tetranucleotide.tetranucleotide TAAN.NCAG 34 144 + 206 [TAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNcag] NA.NA NA.NA NA.NA NA.NA 110.113 169.172 TAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN.NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAG ->hg18 312 hg18 chr22 16354495 16355233 panTro2 chr22 16391865 16392606 ponAbe2 chr22 14121465 14122197 rheMac2 chr10 62179140 62179885 calJac1 Contig9043 25356 26077 mononucleotide A 1 106 + 121 aaaaaaaaaaaaaaaa >panTro2 312 hg18 chr22 16354495 16355233 panTro2 chr22 16391865 16392606 ponAbe2 chr22 14121465 14122197 rheMac2 chr10 62179140 62179885 calJac1 Contig9043 25356 26077 mononucleotide A 1 106 + 122 aaaaaaaaaaaaaaaaa >calJac1 312 hg18 chr22 16354495 16355233 panTro2 chr22 16391865 16392606 ponAbe2 chr22 14121465 14122197 rheMac2 chr10 62179140 62179885 calJac1 Contig9043 25356 26077 mononucleotide A 4 106 + 118 aaaaaaaaaaaaa >rheMac2 312 hg18 chr22 16354495 16355233 panTro2 chr22 16391865 16392606 ponAbe2 chr22 14121465 14122197 rheMac2 chr10 62179140 62179885 calJac1 Contig9043 25356 26077 mononucleotide A 0 107 + 126 aaaaaaaaaaaaaaaaaaaa ->hg18 312 hg18 chr22 16354495 16355233 panTro2 chr22 16391865 16392606 ponAbe2 chr22 14121465 14122197 rheMac2 chr10 62179140 62179885 calJac1 Contig9043 25356 26077 mononucleotide A 17 416 + 439 aaaaaaaaaaaaaaaaaaaaaaaa >ponAbe2 312 hg18 chr22 16354495 16355233 panTro2 chr22 16391865 16392606 ponAbe2 chr22 14121465 14122197 rheMac2 chr10 62179140 62179885 calJac1 Contig9043 25356 26077 mononucleotide A 17 416 + 432 aaaaaaaaaaaaaaaaa >rheMac2 312 hg18 chr22 16354495 16355233 panTro2 chr22 16391865 16392606 ponAbe2 chr22 14121465 14122197 rheMac2 chr10 62179140 62179885 calJac1 Contig9043 25356 26077 mononucleotide [A][A] 4 416 + 432 [aaaaaaaaaaaaaa]C[AA] indel/deletion C 15 1 >calJac1 312 hg18 chr22 16354495 16355233 panTro2 chr22 16391865 16392606 ponAbe2 chr22 14121465 14122197 rheMac2 chr10 62179140 62179885 calJac1 Contig9043 25356 26077 mononucleotide [A][A] 27 416 + 427 [aaaaaaaaaa]G[A] indel/deletion G 11 1 >panTro2 312 hg18 chr22 16354495 16355233 panTro2 chr22 16391865 16392606 ponAbe2 chr22 14121465 14122197 rheMac2 chr10 62179140 62179885 calJac1 Contig9043 25356 26077 mononucleotide A 16 417 + 441 aaaaaaaaaaaaaaaaaaaaaaaaa ->rheMac2 314 hg18 chr22 16355914 16356335 panTro2 chr22 16393283 16393704 ponAbe2 chr22 14122873 14123294 rheMac2 chr10 62180571 62181002 calJac1 Contig9043 26454 26877 tetranucleotide AAAC 1 412 + 427 aaacaaacaaacaaac ->calJac1 318 hg18 chr22 16357694 16357876 panTro2 chr22 16395074 16395259 ponAbe2 chr22 14124666 14124852 rheMac2 chr10 62182388 62182573 calJac1 Contig9043 27955 28138 trinucleotide [CAG][CAG] 1 118 + 137 [CAGCAGCAGCAGC]TCC[CAGC] indel/deletion TCC 14 1 ->hg18 321 hg18 chr22 16358631 16358781 panTro2 chr22 16396007 16396159 ponAbe2 chr22 14125948 14126098 rheMac2 chr10 62183323 62183479 calJac1 Contig9043 28560 28706 mononucleotide T 0 33 + 41 TTTTTTTTT >panTro2 321 hg18 chr22 16358631 16358781 panTro2 chr22 16396007 16396159 ponAbe2 chr22 14125948 14126098 rheMac2 chr10 62183323 62183479 calJac1 Contig9043 28560 28706 mononucleotide T 0 33 + 43 TTTTTTTTTTT >rheMac2 321 hg18 chr22 16358631 16358781 panTro2 chr22 16396007 16396159 ponAbe2 chr22 14125948 14126098 rheMac2 chr10 62183323 62183479 calJac1 Contig9043 28560 28706 mononucleotide T 0 33 + 45 TTTTTTTTTTTTT ->panTro2 328 hg18 chr22 16360931 16361697 panTro2 chr22 16398316 16399110 ponAbe2 chr22 14128246 14129010 rheMac2 chr10 62185091 62185845 calJac1 Contig9043 30569 31357 mononucleotide [A][A][A][A][A][A][A][A] 43 585 + 620 [A]T[AAAAAA]C[AA]G[AA]C[AAA]C[AAA]C[AAAAAAAAAAA]C[A] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion T,C,G,C,C,C,C 2,9,12,15,19,23,35 7 ->rheMac2 333 hg18 chr22 16362441 16362808 panTro2 chr22 16399855 16400223 ponAbe2 chr22 14129752 14130114 rheMac2 chr10 62187207 62187573 calJac1 Contig9043 32051 32429 mononucleotide T 15 294 + 304 TTTTTTTTTTT >hg18 333 hg18 chr22 16362441 16362808 panTro2 chr22 16399855 16400223 ponAbe2 chr22 14129752 14130114 rheMac2 chr10 62187207 62187573 calJac1 Contig9043 32051 32429 mononucleotide T 13 295 + 303 TTTTTTTTT >panTro2 333 hg18 chr22 16362441 16362808 panTro2 chr22 16399855 16400223 ponAbe2 chr22 14129752 14130114 rheMac2 chr10 62187207 62187573 calJac1 Contig9043 32051 32429 mononucleotide T 13 295 + 304 TTTTTTTTTT >ponAbe2 333 hg18 chr22 16362441 16362808 panTro2 chr22 16399855 16400223 ponAbe2 chr22 14129752 14130114 rheMac2 chr10 62187207 62187573 calJac1 Contig9043 32051 32429 mononucleotide T 18 295 + 303 TTTTTTTTT ->hg18 335 hg18 chr22 16362921 16363123 panTro2 chr22 16400336 16400534 ponAbe2 chr22 14130227 14130425 rheMac2 chr10 62187686 62187876 calJac1 Contig9043 32716 33051 tetranucleotide [TAAA][TAAA] 4 162 + 276 [taaataaataaataaataaataaat----------------------------------------------------------------------------aaataaa]ATT[TAAA] indel/deletion ATT 33 1 >panTro2 335 hg18 chr22 16362921 16363123 panTro2 chr22 16400336 16400534 ponAbe2 chr22 14130227 14130425 rheMac2 chr10 62187686 62187876 calJac1 Contig9043 32716 33051 tetranucleotide [TAAA][TAAA] 4 162 + 272 [taaataaataaataaataaat----------------------------------------------------------------------------aaataaa]ATT[TAAA] indel/deletion ATT 29 1 >ponAbe2 335 hg18 chr22 16362921 16363123 panTro2 chr22 16400336 16400534 ponAbe2 chr22 14130227 14130425 rheMac2 chr10 62187686 62187876 calJac1 Contig9043 32716 33051 tetranucleotide [TAAA][TAAA] 0 162 + 268 [taaataaataaataaat----------------------------------------------------------------------------aaataa]CATT[TAAA] indel/deletion CATT 24 1 >rheMac2 335 hg18 chr22 16362921 16363123 panTro2 chr22 16400336 16400534 ponAbe2 chr22 14130227 14130425 rheMac2 chr10 62187686 62187876 calJac1 Contig9043 32716 33051 tetranucleotide [TAAA][AAAT] 4 162 + 259 [taaataaataaat----------------------------------------------------------------------------aaaT]G[AAAT] indel/deletion G 18 1 >calJac1 335 hg18 chr22 16362921 16363123 panTro2 chr22 16400336 16400534 ponAbe2 chr22 14130227 14130425 rheMac2 chr10 62187686 62187876 calJac1 Contig9043 32716 33051 tetranucleotide TGGA 4 162 + 185 tggatggatggatggatggatgga >calJac1 335 hg18 chr22 16362921 16363123 panTro2 chr22 16400336 16400534 ponAbe2 chr22 14130227 14130425 rheMac2 chr10 62187686 62187876 calJac1 Contig9043 32716 33051 tetranucleotide CAGA 8 193 + 207 AGACAGACAGACAGA ->calJac1 335 hg18 chr22 16362921 16363123 panTro2 chr22 16400336 16400534 ponAbe2 chr22 14130227 14130425 rheMac2 chr10 62187686 62187876 calJac1 Contig9043 32716 33051 tetranucleotide GACA 8 320 + 333 gaCAGACAGACAGA ->panTro2 336 hg18 chr22 16363123 16363441 panTro2 chr22 16400534 16400869 ponAbe2 chr22 14130425 14130758 rheMac2 chr10 62187876 62188211 calJac1 Contig9043 33051 33373 mononucleotide A 0 284 + 299 aaaaaaaaaaaaaaaa >ponAbe2 336 hg18 chr22 16363123 16363441 panTro2 chr22 16400534 16400869 ponAbe2 chr22 14130425 14130758 rheMac2 chr10 62187876 62188211 calJac1 Contig9043 33051 33373 mononucleotide A 0 284 + 297 aaaaaaaaaaaaaa >rheMac2 336 hg18 chr22 16363123 16363441 panTro2 chr22 16400534 16400869 ponAbe2 chr22 14130425 14130758 rheMac2 chr10 62187876 62188211 calJac1 Contig9043 33051 33373 tetranucleotide [AATA][ataa] 5 290 + 315 [aaataaataaataaataaata]a[ataa] indel/deletion a 22 1 ->hg18 339 hg18 chr22 16364264 16364401 panTro2 chr22 16401635 16401772 ponAbe2 chr22 14131239 14131388 rheMac2 chr10 62188692 62188767 calJac1 Contig9043 33798 33929 mononucleotide A 0 109 + 135 AAAA-AAAAAAAAA------------A >panTro2 339 hg18 chr22 16364264 16364401 panTro2 chr22 16401635 16401772 ponAbe2 chr22 14131239 14131388 rheMac2 chr10 62188692 62188767 calJac1 Contig9043 33798 33929 mononucleotide A 0 109 + 135 AAAA-AAAAAAAAA------------A >ponAbe2 339 hg18 chr22 16364264 16364401 panTro2 chr22 16401635 16401772 ponAbe2 chr22 14131239 14131388 rheMac2 chr10 62188692 62188767 calJac1 Contig9043 33798 33929 mononucleotide [A][A][A][A] 0 109 + 135 [AAAA-AAAAAAAAAAAA]C[AAA]C[AAA]C[A] indel/deletion,indel/deletion,indel/deletion C,C,C 17,21,25 3 ->hg18 341 hg18 chr22 16364566 16364880 panTro2 chr22 16401937 16402248 ponAbe2 chr22 14131568 14131870 rheMac2 chr10 62188911 62189180 calJac1 Contig9043 34077 34390 mononucleotide T 0 1 + 23 ttttttttttttttttttttttt >panTro2 341 hg18 chr22 16364566 16364880 panTro2 chr22 16401937 16402248 ponAbe2 chr22 14131568 14131870 rheMac2 chr10 62188911 62189180 calJac1 Contig9043 34077 34390 mononucleotide T 0 1 + 19 ttttttttttttttttttt >ponAbe2 341 hg18 chr22 16364566 16364880 panTro2 chr22 16401937 16402248 ponAbe2 chr22 14131568 14131870 rheMac2 chr10 62188911 62189180 calJac1 Contig9043 34077 34390 mononucleotide T 0 1 + 23 ttttttttttttttttttttttt >rheMac2 341 hg18 chr22 16364566 16364880 panTro2 chr22 16401937 16402248 ponAbe2 chr22 14131568 14131870 rheMac2 chr10 62188911 62189180 calJac1 Contig9043 34077 34390 mononucleotide T 0 1 + 35 TTTTTTTTT-------------------------T ->calJac1 341 hg18 chr22 16364566 16364880 panTro2 chr22 16401937 16402248 ponAbe2 chr22 14131568 14131870 rheMac2 chr10 62188911 62189180 calJac1 Contig9043 34077 34390 trinucleotide [CAC][CCA][acc] 11 144 + 164 [cac][ccaccaccaccac]t[acca] indel/deletion,indel/deletion ,t 4,17 2 >hg18 341 hg18 chr22 16364566 16364880 panTro2 chr22 16401937 16402248 ponAbe2 chr22 14131568 14131870 rheMac2 chr10 62188911 62189180 calJac1 Contig9043 34077 34390 trinucleotide [CAC][cca] 0 148 + 170 [caccaccaccac]------gc[cca] indel/deletion gc 13 1 >panTro2 341 hg18 chr22 16364566 16364880 panTro2 chr22 16401937 16402248 ponAbe2 chr22 14131568 14131870 rheMac2 chr10 62188911 62189180 calJac1 Contig9043 34077 34390 trinucleotide [CAC][cca] 4 148 + 170 [caccaccaccac]------gc[cca] indel/deletion gc 13 1 >ponAbe2 341 hg18 chr22 16364566 16364880 panTro2 chr22 16401937 16402248 ponAbe2 chr22 14131568 14131870 rheMac2 chr10 62188911 62189180 calJac1 Contig9043 34077 34390 trinucleotide [CAC][cca] 0 148 + 170 [caccaccaccac]------gc[cca] indel/deletion gc 13 1 ->hg18 341 hg18 chr22 16364566 16364880 panTro2 chr22 16401937 16402248 ponAbe2 chr22 14131568 14131870 rheMac2 chr10 62188911 62189180 calJac1 Contig9043 34077 34390 mononucleotide T 24 326 + 338 ttttttttttttt >panTro2 341 hg18 chr22 16364566 16364880 panTro2 chr22 16401937 16402248 ponAbe2 chr22 14131568 14131870 rheMac2 chr10 62188911 62189180 calJac1 Contig9043 34077 34390 mononucleotide T 27 326 + 338 ttttttttttttt ->hg18 342 hg18 chr22 16370692 16370972 panTro2 chr22 16408071 16408336 ponAbe2 chr22 14137691 14137974 rheMac2 chr10 62195091 62195377 calJac1 Contig9043 41348 41611 trinucleotide [GCA][CAG] 3 78 + 102 [GCAGC---AGCAGCAGCAGCA]T[CAG] indel/deletion T 19 1 >ponAbe2 342 hg18 chr22 16370692 16370972 panTro2 chr22 16408071 16408336 ponAbe2 chr22 14137691 14137974 rheMac2 chr10 62195091 62195377 calJac1 Contig9043 41348 41611 trinucleotide [GCA][CAG] 0 78 + 102 [GCAGC---AGCAGCAGCAGCA]T[CAG] indel/deletion T 19 1 >panTro2 342 hg18 chr22 16370692 16370972 panTro2 chr22 16408071 16408336 ponAbe2 chr22 14137691 14137974 rheMac2 chr10 62195091 62195377 calJac1 Contig9043 41348 41611 trinucleotide [GCA][CAG] 18 81 + 102 [GC---AGCAGCAGCAGCA]T[CAG] indel/deletion T 16 1 ->rheMac2 343 hg18 chr22 16370972 16371260 panTro2 chr22 16408336 16408624 ponAbe2 chr22 14137974 14138259 rheMac2 chr10 62195377 62195653 calJac1 Contig9043 41611 41918 mononucleotide T 0 52 + 60 TTTTTTTTT ->rheMac2 344 hg18 chr22 16371469 16371843 panTro2 chr22 16408833 16409204 ponAbe2 chr22 14138468 14138833 rheMac2 chr10 62195836 62196191 calJac1 Contig9043 41934 42275 mononucleotide [A][A][A] 4 264 + 290 [aaaaaaaaaaaaaaaaaaa]g[aaa]g[aaa] indel/deletion,indel/deletion G,G 20,24 2 >hg18 344 hg18 chr22 16371469 16371843 panTro2 chr22 16408833 16409204 ponAbe2 chr22 14138468 14138833 rheMac2 chr10 62195836 62196191 calJac1 Contig9043 41934 42275 mononucleotide [A][A][A][A][A][A] 1 270 + 305 [a]g[aaaaaaaaaaaaaaaa]g[aaa]g[aaa]g[aaaA]G[AAAA] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion g,G,G,G,G 2,19,23,27,32 6 >ponAbe2 344 hg18 chr22 16371469 16371843 panTro2 chr22 16408833 16409204 ponAbe2 chr22 14138468 14138833 rheMac2 chr10 62195836 62196191 calJac1 Contig9043 41934 42275 mononucleotide [A][A][a] 4 270 + 299 [aaaaaaaaaaaaaaaaa]g[aaaaaaa]g[aaaa] insertion,indel/deletion g,g 18,26 2 >calJac1 344 hg18 chr22 16371469 16371843 panTro2 chr22 16408833 16409204 ponAbe2 chr22 14138468 14138833 rheMac2 chr10 62195836 62196191 calJac1 Contig9043 41934 42275 mononucleotide A 19 274 + 284 aaaaaaaaaaa >panTro2 344 hg18 chr22 16371469 16371843 panTro2 chr22 16408833 16409204 ponAbe2 chr22 14138468 14138833 rheMac2 chr10 62195836 62196191 calJac1 Contig9043 41934 42275 tetranucleotide [GAAA][GAAA] 4 281 + 304 [aaagaaagaaagaaagaaa][aGAAA] indel/deletion 20 1 ->ponAbe2 346 hg18 chr22 16372112 16372276 panTro2 chr22 16409473 16409637 ponAbe2 chr22 14139108 14139274 rheMac2 chr10 62196464 62196625 calJac1 Contig9043 42545 42720 mononucleotide A 24 130 + 138 aaaaaaaaa >calJac1 346 hg18 chr22 16372112 16372276 panTro2 chr22 16409473 16409637 ponAbe2 chr22 14139108 14139274 rheMac2 chr10 62196464 62196625 calJac1 Contig9043 42545 42720 mononucleotide A 2 130 + 146 aaaaaaaa--------a ->calJac1 352 hg18 chr22 16373709 16373775 panTro2 chr22 16411071 16411137 ponAbe2 chr22 14140711 14140777 rheMac2 chr10 62198885 62198952 calJac1 Contig9043 44560 44671 tetranucleotide.tetranucleotide CCNN.NNTT 3 85 + 98 [CCNNNNNNNNNNtt] NA.NA NA.NA NA.NA NA.NA 82.84 93.95 CCNNNNNNNNNN.NNNNNNNNNNTT ->hg18 353 hg18 chr22 16374086 16374714 panTro2 chr22 16411451 16412074 ponAbe2 chr22 14141084 14141727 rheMac2 chr10 62198961 62199622 calJac1 Contig9043 46367 46986 mononucleotide [T][T] 0 11 + 40 [TTTTTTTTT------------------T]C[T] indel/deletion C 11 1 >panTro2 353 hg18 chr22 16374086 16374714 panTro2 chr22 16411451 16412074 ponAbe2 chr22 14141084 14141727 rheMac2 chr10 62198961 62199622 calJac1 Contig9043 46367 46986 mononucleotide [T][T] 1 11 + 40 [TTTTTTTTT------------------T]C[T] indel/deletion C 11 1 >ponAbe2 353 hg18 chr22 16374086 16374714 panTro2 chr22 16411451 16412074 ponAbe2 chr22 14141084 14141727 rheMac2 chr10 62198961 62199622 calJac1 Contig9043 46367 46986 mononucleotide [T][T] 0 11 + 42 [TTTTTTTTTTT------------------T]C[T] indel/deletion C 13 1 >rheMac2 353 hg18 chr22 16374086 16374714 panTro2 chr22 16411451 16412074 ponAbe2 chr22 14141084 14141727 rheMac2 chr10 62198961 62199622 calJac1 Contig9043 46367 46986 mononucleotide T 0 12 + 37 tttttttttttttttttttttttttt ->calJac1 354 hg18 chr22 16375000 16375260 panTro2 chr22 16412360 16412619 ponAbe2 chr22 14142013 14142271 rheMac2 chr10 62199631 62199866 calJac1 Contig9043 46993 47246 dinucleotide AT 17 236 + 253 AT------ATATATATAT >hg18 354 hg18 chr22 16375000 16375260 panTro2 chr22 16412360 16412619 ponAbe2 chr22 14142013 14142271 rheMac2 chr10 62199631 62199866 calJac1 Contig9043 46993 47246 dinucleotide [AT][at] 6 242 + 268 [atatatatatat]-----gg[atatatat] indel/deletion gg 13 1 >panTro2 354 hg18 chr22 16375000 16375260 panTro2 chr22 16412360 16412619 ponAbe2 chr22 14142013 14142271 rheMac2 chr10 62199631 62199866 calJac1 Contig9043 46993 47246 dinucleotide [AT][at] 5 242 + 266 [atatatatat]-----gg[atatatat] indel/deletion gg 11 1 ->calJac1 355 hg18 chr22 16378662 16378834 panTro2 chr22 16416033 16416203 ponAbe2 chr22 14145388 14145541 rheMac2 chr10 62202309 62202474 calJac1 Contig9043 50553 50705 mononucleotide [T][T][T] 7 77 + 96 [TT]A[TT]G[TTTT-----TTTTT] indel/deletion,indel/deletion A,G 3,6 2 ->ponAbe2 357 hg18 chr22 16379292 16379425 panTro2 chr22 16416661 16416794 ponAbe2 chr22 14145999 14146134 rheMac2 chr10 62202934 62203069 calJac1 Contig9043 51180 51311 dinucleotide AT 0 36 + 48 ATATAT--ATATA >rheMac2 357 hg18 chr22 16379292 16379425 panTro2 chr22 16416661 16416794 ponAbe2 chr22 14145999 14146134 rheMac2 chr10 62202934 62203069 calJac1 Contig9043 51180 51311 dinucleotide TA 0 37 + 48 TATAT--ATATA ->ponAbe2 360 hg18 chr22 16381918 16382108 panTro2 chr22 16419291 16419481 ponAbe2 chr22 14148491 14148685 rheMac2 chr10 62205813 62205994 calJac1 Contig9043 51995 52160 mononucleotide N 0 1 + 10 nnnnnnnnnn ->hg18 360 hg18 chr22 16381918 16382108 panTro2 chr22 16419291 16419481 ponAbe2 chr22 14148491 14148685 rheMac2 chr10 62205813 62205994 calJac1 Contig9043 51995 52160 mononucleotide G 0 115 + 128 GGGGG----GGGGG >panTro2 360 hg18 chr22 16381918 16382108 panTro2 chr22 16419291 16419481 ponAbe2 chr22 14148491 14148685 rheMac2 chr10 62205813 62205994 calJac1 Contig9043 51995 52160 mononucleotide A 0 120 + 133 aaaaa---aaaaaa >ponAbe2 360 hg18 chr22 16381918 16382108 panTro2 chr22 16419291 16419481 ponAbe2 chr22 14148491 14148685 rheMac2 chr10 62205813 62205994 calJac1 Contig9043 51995 52160 mononucleotide A 0 120 + 137 aaaaaaaaa---aaaaaa ->hg18 361 hg18 chr22 16382193 16382490 panTro2 chr22 16419566 16419864 ponAbe2 chr22 14150628 14150928 rheMac2 chr10 62207086 62207366 calJac1 Contig9043 54752 55056 mononucleotide A 5 219 + 230 aaaaaaaaaaaa >panTro2 361 hg18 chr22 16382193 16382490 panTro2 chr22 16419566 16419864 ponAbe2 chr22 14150628 14150928 rheMac2 chr10 62207086 62207366 calJac1 Contig9043 54752 55056 mononucleotide A 5 219 + 231 aaaaaaaaaaaaa >ponAbe2 361 hg18 chr22 16382193 16382490 panTro2 chr22 16419566 16419864 ponAbe2 chr22 14150628 14150928 rheMac2 chr10 62207086 62207366 calJac1 Contig9043 54752 55056 mononucleotide A 6 219 + 234 aaaaaaaaaaaaaaaa >calJac1 361 hg18 chr22 16382193 16382490 panTro2 chr22 16419566 16419864 ponAbe2 chr22 14150628 14150928 rheMac2 chr10 62207086 62207366 calJac1 Contig9043 54752 55056 mononucleotide [A][A] 1 223 + 240 [aaaaaaaaaaaa]g[aaaaa] insertion g 13 1 >rheMac2 361 hg18 chr22 16382193 16382490 panTro2 chr22 16419566 16419864 ponAbe2 chr22 14150628 14150928 rheMac2 chr10 62207086 62207366 calJac1 Contig9043 54752 55056 mononucleotide A 16 230 + 240 aaaaaaaaaaa ->calJac1 363 hg18 chr22 16383138 16383316 panTro2 chr22 16420513 16420691 ponAbe2 chr22 14151593 14151771 rheMac2 chr10 62208222 62208400 calJac1 Contig9043 55409 55587 trinucleotide GAG 0 48 + 62 GAGGAGGAGGAGGAG ->hg18 365 hg18 chr22 16383923 16384403 panTro2 chr22 16421272 16421742 ponAbe2 chr22 14153069 14153530 rheMac2 chr10 62209038 62209496 calJac1 Contig9043 56548 56974 mononucleotide [T][T][T] 1 164 + 192 [T]C[ttttttttttttt]c[ttttttttttttt] indel/deletion,insertion C,c 2,16 2 >panTro2 365 hg18 chr22 16383923 16384403 panTro2 chr22 16421272 16421742 ponAbe2 chr22 14153069 14153530 rheMac2 chr10 62209038 62209496 calJac1 Contig9043 56548 56974 mononucleotide [T][T][t] 1 164 + 183 [T]C[ttttttttttttttt]g[tt] indel/deletion,indel/deletion C,g 2,18 2 >ponAbe2 365 hg18 chr22 16383923 16384403 panTro2 chr22 16421272 16421742 ponAbe2 chr22 14153069 14153530 rheMac2 chr10 62209038 62209496 calJac1 Contig9043 56548 56974 mononucleotide [T][T] 1 164 + 174 [T]C[ttttttttt] indel/deletion C 2 1 >rheMac2 365 hg18 chr22 16383923 16384403 panTro2 chr22 16421272 16421742 ponAbe2 chr22 14153069 14153530 rheMac2 chr10 62209038 62209496 calJac1 Contig9043 56548 56974 mononucleotide [T][T] 0 164 + 187 [T]C[tttttttttttttttttttttt] indel/deletion C 2 1 >calJac1 365 hg18 chr22 16383923 16384403 panTro2 chr22 16421272 16421742 ponAbe2 chr22 14153069 14153530 rheMac2 chr10 62209038 62209496 calJac1 Contig9043 56548 56974 compound [T][GA] 38 166 + 201 [ttttttttttttttt][gagagag------agagagag] ->ponAbe2 366 hg18 chr22 16385041 16385774 panTro2 chr22 16422717 16423450 ponAbe2 chr22 14154414 14155157 rheMac2 chr10 62209866 62210598 calJac1 Contig9043 56995 57802 mononucleotide [a][A][A] 1 262 + 276 [aa]t[aaaaaaaaa]C[AA] indel/deletion,indel/deletion t,C 3,13 2 ->hg18 367 hg18 chr22 16385774 16386225 panTro2 chr22 16423450 16423904 ponAbe2 chr22 14155157 14155619 rheMac2 chr10 62210598 62211053 calJac1 Contig9043 58042 58452 mononucleotide [a][A] 0 67 + 81 [a]g----[aaaaaaaaa] indel/deletion g 2 1 >panTro2 367 hg18 chr22 16385774 16386225 panTro2 chr22 16423450 16423904 ponAbe2 chr22 14155157 14155619 rheMac2 chr10 62210598 62211053 calJac1 Contig9043 58042 58452 mononucleotide [a][A] 0 67 + 81 [a]g[a---aaaaaaaaa] indel/deletion g 2 1 >ponAbe2 367 hg18 chr22 16385774 16386225 panTro2 chr22 16423450 16423904 ponAbe2 chr22 14155157 14155619 rheMac2 chr10 62210598 62211053 calJac1 Contig9043 58042 58452 mononucleotide [a][A] 0 67 + 81 [a]g[a---aaaaaaaaa] indel/deletion g 2 1 >calJac1 367 hg18 chr22 16385774 16386225 panTro2 chr22 16423450 16423904 ponAbe2 chr22 14155157 14155619 rheMac2 chr10 62210598 62211053 calJac1 Contig9043 58042 58452 mononucleotide [a][A] 0 67 + 81 [a]g[aa--aaaaaaaaa] indel/deletion g 2 1 ->hg18 369 hg18 chr22 16387257 16387926 panTro2 chr22 16425091 16425762 ponAbe2 chr22 14156664 14157340 rheMac2 chr10 62213095 62213752 calJac1 Contig9043 59176 59844 mononucleotide A 4 213 + 229 aaaaaaaaaaaaaaaaa >panTro2 369 hg18 chr22 16387257 16387926 panTro2 chr22 16425091 16425762 ponAbe2 chr22 14156664 14157340 rheMac2 chr10 62213095 62213752 calJac1 Contig9043 59176 59844 mononucleotide A 3 213 + 230 aaaaaaaaaaaaaaaaaa >rheMac2 369 hg18 chr22 16387257 16387926 panTro2 chr22 16425091 16425762 ponAbe2 chr22 14156664 14157340 rheMac2 chr10 62213095 62213752 calJac1 Contig9043 59176 59844 mononucleotide A 4 213 + 222 aaaaaaaaaa >ponAbe2 369 hg18 chr22 16387257 16387926 panTro2 chr22 16425091 16425762 ponAbe2 chr22 14156664 14157340 rheMac2 chr10 62213095 62213752 calJac1 Contig9043 59176 59844 mononucleotide [A][a][a] 3 217 + 242 [aaaaaaaaaaaaaaaaaaa]c[aaa]c[aa] indel/deletion,indel/deletion c,c 20,24 2 >calJac1 369 hg18 chr22 16387257 16387926 panTro2 chr22 16425091 16425762 ponAbe2 chr22 14156664 14157340 rheMac2 chr10 62213095 62213752 calJac1 Contig9043 59176 59844 mononucleotide [A][a] 9 222 + 234 [aaaaaaaaaaa]t[a] indel/deletion t 12 1 ->ponAbe2 370 hg18 chr22 16387962 16388935 panTro2 chr22 16425798 16426771 ponAbe2 chr22 14157381 14158368 rheMac2 chr10 62213784 62214750 calJac1 Contig9043 60456 61407 mononucleotide [a][A][a] 2 193 + 206 [a]c[aaaaaaaaaa]t[a] indel/deletion,indel/deletion c,t 2,13 2 ->hg18 370 hg18 chr22 16387962 16388935 panTro2 chr22 16425798 16426771 ponAbe2 chr22 14157381 14158368 rheMac2 chr10 62213784 62214750 calJac1 Contig9043 60456 61407 mononucleotide [T][t][t][t][t][t] 8 261 + 296 [TTTTTtttt]c[tttt]c[tttt]c[tttttt]g[tt]a-[ttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion c,c,c,g,a 10,15,20,27,30 5 >panTro2 370 hg18 chr22 16387962 16388935 panTro2 chr22 16425798 16426771 ponAbe2 chr22 14157381 14158368 rheMac2 chr10 62213784 62214750 calJac1 Contig9043 60456 61407 mononucleotide [T][t][t][t][t][t] 8 261 + 296 [TTTTTtttt]c[tttt]c[tttt]c[tttttt]g[tt]a-[ttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion c,c,c,g,a 10,15,20,27,30 5 >ponAbe2 370 hg18 chr22 16387962 16388935 panTro2 chr22 16425798 16426771 ponAbe2 chr22 14157381 14158368 rheMac2 chr10 62213784 62214750 calJac1 Contig9043 60456 61407 mononucleotide [T][t][t][t][t] 2 261 + 296 [TTttttt---tttt]c[tttt]c[tttt]c[tttt]c-[ttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion c,c,c,c 12,17,22,27 4 >rheMac2 370 hg18 chr22 16387962 16388935 panTro2 chr22 16425798 16426771 ponAbe2 chr22 14157381 14158368 rheMac2 chr10 62213784 62214750 calJac1 Contig9043 60456 61407 mononucleotide [T][T][T][t][t] 8 265 + 301 [TTTTTTTttttt]c[ttttttt]c[ttttt]c[ttt]g[tttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion c,c,c,g 13,21,27,31 4 >calJac1 370 hg18 chr22 16387962 16388935 panTro2 chr22 16425798 16426771 ponAbe2 chr22 14157381 14158368 rheMac2 chr10 62213784 62214750 calJac1 Contig9043 60456 61407 mononucleotide [t][T][t] 19 267 + 284 [tt]c[tttttttttttt]c[tt] indel/deletion,indel/deletion c,c 3,16 2 ->panTro2 371 hg18 chr22 16389406 16389625 panTro2 chr22 16427304 16427525 ponAbe2 chr22 14159051 14159270 rheMac2 chr10 62214954 62215171 calJac1 Contig9043 61509 61672 tetranucleotide [Gttt][TTTG] 1 65 + 82 [Gttt]tc[tttgtttgtttg] indel/deletion tc 5 1 >rheMac2 371 hg18 chr22 16389406 16389625 panTro2 chr22 16427304 16427525 ponAbe2 chr22 14159051 14159270 rheMac2 chr10 62214954 62215171 calJac1 Contig9043 61509 61672 tetranucleotide TTTG 7 67 + 82 TTTG----TTTGTTTG ->hg18 372 hg18 chr22 16390519 16391515 panTro2 chr22 16428416 16429411 ponAbe2 chr22 14160203 14161195 rheMac2 chr10 62215781 62216789 calJac1 Contig9043 62339 63235 mononucleotide [A][A][A] 6 379 + 394 [A]G[AAAA]C[AAAAAAAAA] indel/deletion,indel/deletion G,C 2,7 2 ->calJac1 373 hg18 chr22 16395013 16395281 panTro2 chr22 16433778 16434046 ponAbe2 chr22 14165009 14165277 rheMac2 chr10 62221728 62221992 calJac1 Contig9043 69242 69535 trinucleotide TAA 0 1 + 14 TAATAAT--AATAA ->hg18 374 hg18 chr22 16395281 16395451 panTro2 chr22 16434046 16434213 ponAbe2 chr22 14165277 14165449 rheMac2 chr10 62221992 62222163 calJac1 Contig9043 69535 69711 mononucleotide [A][A][A] 1 95 + 110 [A]G[AAAAAAAAAAAA]T[A] indel/deletion,indel/deletion G,T 2,15 2 >panTro2 374 hg18 chr22 16395281 16395451 panTro2 chr22 16434046 16434213 ponAbe2 chr22 14165277 14165449 rheMac2 chr10 62221992 62222163 calJac1 Contig9043 69535 69711 mononucleotide [A][A][A] 1 95 + 110 [A]G--[AAAAAAAAAA]T[A] indel/deletion,indel/deletion G,T 2,13 2 >ponAbe2 374 hg18 chr22 16395281 16395451 panTro2 chr22 16434046 16434213 ponAbe2 chr22 14165277 14165449 rheMac2 chr10 62221992 62222163 calJac1 Contig9043 69535 69711 mononucleotide [A][A] 1 95 + 110 [A]G--[AAAAAAAAAAAA] indel/deletion G 2 1 >rheMac2 374 hg18 chr22 16395281 16395451 panTro2 chr22 16434046 16434213 ponAbe2 chr22 14165277 14165449 rheMac2 chr10 62221992 62222163 calJac1 Contig9043 69535 69711 mononucleotide [A][A] 0 95 + 110 [A]G--[AAAAAAAAAAAA] indel/deletion G 2 1 >calJac1 374 hg18 chr22 16395281 16395451 panTro2 chr22 16434046 16434213 ponAbe2 chr22 14165277 14165449 rheMac2 chr10 62221992 62222163 calJac1 Contig9043 69535 69711 mononucleotide [A][A] 1 99 + 114 [AA--AAAAAAA]T[AAAA] indel/deletion T 10 1 ->hg18 374 hg18 chr22 16395281 16395451 panTro2 chr22 16434046 16434213 ponAbe2 chr22 14165277 14165449 rheMac2 chr10 62221992 62222163 calJac1 Contig9043 69535 69711 mononucleotide [A][a] 5 144 + 156 [aaaaaaaaaa]t[aa] indel/deletion t 11 1 ->ponAbe2 376 hg18 chr22 16395975 16396756 panTro2 chr22 16434737 16435518 ponAbe2 chr22 14165967 14166749 rheMac2 chr10 62222683 62223461 calJac1 Contig9043 70203 70934 dinucleotide TG 3 366 + 377 TGTGTGTGTGTG >rheMac2 376 hg18 chr22 16395975 16396756 panTro2 chr22 16434737 16435518 ponAbe2 chr22 14165967 14166749 rheMac2 chr10 62222683 62223461 calJac1 Contig9043 70203 70934 dinucleotide TG 3 366 + 377 TGTGTGTGTGTG ->ponAbe2 376 hg18 chr22 16395975 16396756 panTro2 chr22 16434737 16435518 ponAbe2 chr22 14165967 14166749 rheMac2 chr10 62222683 62223461 calJac1 Contig9043 70203 70934 tetranucleotide AGTT 3 618 + 629 AGTTAGTTAGTT ->hg18 379 hg18 chr22 16397412 16397956 panTro2 chr22 16436174 16436721 ponAbe2 chr22 14167529 14168076 rheMac2 chr10 62224135 62224688 calJac1 Contig9043 71534 72175 mononucleotide [A][A] 5 275 + 383 [aaaaaaaaaaaaaa-------------------------------------------------------------------------------------------aa]G[A] indel/deletion G 17 1 >panTro2 379 hg18 chr22 16397412 16397956 panTro2 chr22 16436174 16436721 ponAbe2 chr22 14167529 14168076 rheMac2 chr10 62224135 62224688 calJac1 Contig9043 71534 72175 mononucleotide [A][A] 1 275 + 382 [aaaaaaaaaaaaa-------------------------------------------------------------------------------------------aa]G[A] indel/deletion G 16 1 >rheMac2 379 hg18 chr22 16397412 16397956 panTro2 chr22 16436174 16436721 ponAbe2 chr22 14167529 14168076 rheMac2 chr10 62224135 62224688 calJac1 Contig9043 71534 72175 mononucleotide [A][A][A][A] 2 275 + 385 [aaaa]g[aa]g[aaaaaaaa-------------------------------------------------------------------------------------------aa]G[A] indel/deletion,indel/deletion,indel/deletion G,G,G 5,8,19 4 >calJac1 379 hg18 chr22 16397412 16397956 panTro2 chr22 16436174 16436721 ponAbe2 chr22 14167529 14168076 rheMac2 chr10 62224135 62224688 calJac1 Contig9043 71534 72175 mononucleotide [A][a] 9 278 + 294 [aaaaaaaaaaaaa]c[aaa] indel/deletion c 14 1 >ponAbe2 379 hg18 chr22 16397412 16397956 panTro2 chr22 16436174 16436721 ponAbe2 chr22 14167529 14168076 rheMac2 chr10 62224135 62224688 calJac1 Contig9043 71534 72175 mononucleotide [A][A] 7 281 + 385 [aaaaaaaaaa-------------------------------------------------------------------------------------------aa]G[A] indel/deletion G 13 1 ->ponAbe2 379 hg18 chr22 16397412 16397956 panTro2 chr22 16436174 16436721 ponAbe2 chr22 14167529 14168076 rheMac2 chr10 62224135 62224688 calJac1 Contig9043 71534 72175 tetranucleotide [AAat][TAAA] 99 594 + 617 [aaataa]g[taaa--taaat---aaa] indel/deletion g 7 1 ->ponAbe2 384 hg18 chr22 16399400 16399819 panTro2 chr22 16438175 16438594 ponAbe2 chr22 14169504 14169923 rheMac2 chr10 62225892 62226317 calJac1 Contig9043 73717 74152 mononucleotide [T][t][t] 1 116 + 150 [tttttttttt]c[ttt]a[t------------------t] indel/deletion,indel/deletion c,a 11,15 2 >rheMac2 384 hg18 chr22 16399400 16399819 panTro2 chr22 16438175 16438594 ponAbe2 chr22 14169504 14169923 rheMac2 chr10 62225892 62226317 calJac1 Contig9043 73717 74152 mononucleotide T 1 116 + 156 tttttttttttttttttttttt------------------t ->rheMac2 397 hg18 chr22 16404594 16404740 panTro2 chr22 16443402 16443548 ponAbe2 chr22 14174738 14174896 rheMac2 chr10 62231951 62232114 calJac1 Contig10103 3702 3788 mononucleotide [A][A][A] 0 65 + 82 [aaaaaa]g[aaaaaaaaa]T[A] insertion,indel/deletion g,T 7,17 2 ->hg18 398 hg18 chr22 16405251 16405545 panTro2 chr22 16444054 16444348 ponAbe2 chr22 14175392 14175686 rheMac2 chr10 62232305 62232603 calJac1 Contig10103 4284 4580 mononucleotide A 7 288 + 301 aaaaaaaaaaaaaa >panTro2 398 hg18 chr22 16405251 16405545 panTro2 chr22 16444054 16444348 ponAbe2 chr22 14175392 14175686 rheMac2 chr10 62232305 62232603 calJac1 Contig10103 4284 4580 mononucleotide A 7 288 + 301 aaaaaaaaaaaaaa >ponAbe2 398 hg18 chr22 16405251 16405545 panTro2 chr22 16444054 16444348 ponAbe2 chr22 14175392 14175686 rheMac2 chr10 62232305 62232603 calJac1 Contig10103 4284 4580 mononucleotide A 7 288 + 301 aaaaaaaaaaaaaa >rheMac2 398 hg18 chr22 16405251 16405545 panTro2 chr22 16444054 16444348 ponAbe2 chr22 14175392 14175686 rheMac2 chr10 62232305 62232603 calJac1 Contig10103 4284 4580 mononucleotide A 3 288 + 301 aaaaaaaaaaaaaa >calJac1 398 hg18 chr22 16405251 16405545 panTro2 chr22 16444054 16444348 ponAbe2 chr22 14175392 14175686 rheMac2 chr10 62232305 62232603 calJac1 Contig10103 4284 4580 tetranucleotide AAAT 5 288 + 301 aaataaataaataa ->hg18 400 hg18 chr22 16407821 16408558 panTro2 chr22 16446615 16447352 ponAbe2 chr22 14177198 14177954 rheMac2 chr10 62234546 62235283 calJac1 Contig10103 6282 7022 mononucleotide T 0 1 + 25 TTTTTTT-------------TTTTT >panTro2 400 hg18 chr22 16407821 16408558 panTro2 chr22 16446615 16447352 ponAbe2 chr22 14177198 14177954 rheMac2 chr10 62234546 62235283 calJac1 Contig10103 6282 7022 mononucleotide T 0 1 + 25 ttttttt-------------ttttt >rheMac2 400 hg18 chr22 16407821 16408558 panTro2 chr22 16446615 16447352 ponAbe2 chr22 14177198 14177954 rheMac2 chr10 62234546 62235283 calJac1 Contig10103 6282 7022 mononucleotide T 0 1 + 25 TTTTTTT-------------TTTTT >calJac1 400 hg18 chr22 16407821 16408558 panTro2 chr22 16446615 16447352 ponAbe2 chr22 14177198 14177954 rheMac2 chr10 62234546 62235283 calJac1 Contig10103 6282 7022 mononucleotide T 0 1 + 25 ttttttt-------------ttttt >ponAbe2 400 hg18 chr22 16407821 16408558 panTro2 chr22 16446615 16447352 ponAbe2 chr22 14177198 14177954 rheMac2 chr10 62234546 62235283 calJac1 Contig10103 6282 7022 trinucleotide GTT 0 6 + 25 ttgttgttgttgttgttgtt ->ponAbe2 401 hg18 chr22 16408558 16409204 panTro2 chr22 16447352 16448001 ponAbe2 chr22 14177954 14178603 rheMac2 chr10 62235283 62235932 calJac1 Contig10103 7022 7671 tetranucleotide AGCC 0 95 + 108 CCAGCCAGCCAGCC ->calJac1 402 hg18 chr22 16409301 16409625 panTro2 chr22 16448098 16448413 ponAbe2 chr22 14178700 14179033 rheMac2 chr10 62236030 62236357 calJac1 Contig10103 7768 8073 mononucleotide [t][T] 6 171 + 206 [t]c------------------[tttttt--tttttttt] indel/deletion c 2 1 >hg18 402 hg18 chr22 16409301 16409625 panTro2 chr22 16448098 16448413 ponAbe2 chr22 14178700 14179033 rheMac2 chr10 62236030 62236357 calJac1 Contig10103 7768 8073 mononucleotide [T][T] 8 175 + 206 [tt-------ttt]g[ttttttttt--tttttttt] insertion g 6 1 >panTro2 402 hg18 chr22 16409301 16409625 panTro2 chr22 16448098 16448413 ponAbe2 chr22 14178700 14179033 rheMac2 chr10 62236030 62236357 calJac1 Contig10103 7768 8073 mononucleotide [T][t] 8 175 + 193 [tttttt--ttttttttt]g[t] indel/deletion g 16 1 >ponAbe2 402 hg18 chr22 16409301 16409625 panTro2 chr22 16448098 16448413 ponAbe2 chr22 14178700 14179033 rheMac2 chr10 62236030 62236357 calJac1 Contig10103 7768 8073 mononucleotide [T][T][t][t] 2 175 + 209 [tt-------tttttttttttttt]a[tttttt]a[tt]g[t] insertion,indel/deletion,indel/deletion a,a,g 17,24,27 3 ->hg18 406 hg18 chr22 16411421 16411530 panTro2 chr22 16450582 16450691 ponAbe2 chr22 14180803 14180910 rheMac2 chr10 62238091 62238197 calJac1 Contig10103 10638 10748 mononucleotide [a][A][a] 2 64 + 81 [aaaa]g[aaaaaaaaaaa]t[a] indel/deletion,indel/deletion g,t 5,17 2 >panTro2 406 hg18 chr22 16411421 16411530 panTro2 chr22 16450582 16450691 ponAbe2 chr22 14180803 14180910 rheMac2 chr10 62238091 62238197 calJac1 Contig10103 10638 10748 mononucleotide [a][A][a] 2 64 + 81 [aaaa]g[aaaaaaaaaaa]t[a] indel/deletion,indel/deletion g,t 5,17 2 ->hg18 408 hg18 chr22 16411858 16412324 panTro2 chr22 16451019 16451485 ponAbe2 chr22 14181238 14181703 rheMac2 chr10 62238515 62238949 calJac1 Contig10103 11067 11457 trinucleotide CAT 6 432 + 443 CATCATCATCAT >panTro2 408 hg18 chr22 16411858 16412324 panTro2 chr22 16451019 16451485 ponAbe2 chr22 14181238 14181703 rheMac2 chr10 62238515 62238949 calJac1 Contig10103 11067 11457 trinucleotide CAT 6 432 + 443 CATCATCATCAT ->rheMac2 409 hg18 chr22 16412324 16412512 panTro2 chr22 16451485 16451668 ponAbe2 chr22 14181703 14181882 rheMac2 chr10 62238949 62239129 calJac1 Contig10103 11457 11642 mononucleotide T 1 133 + 164 t----------ttttttttttttttttttttt >hg18 409 hg18 chr22 16412324 16412512 panTro2 chr22 16451485 16451668 ponAbe2 chr22 14181703 14181882 rheMac2 chr10 62238949 62239129 calJac1 Contig10103 11457 11642 mononucleotide T 2 138 + 165 tttttttttttttttttttttttttttt >panTro2 409 hg18 chr22 16412324 16412512 panTro2 chr22 16451485 16451668 ponAbe2 chr22 14181703 14181882 rheMac2 chr10 62238949 62239129 calJac1 Contig10103 11457 11642 mononucleotide T 1 138 + 159 tttttttttttttttttttttt >ponAbe2 409 hg18 chr22 16412324 16412512 panTro2 chr22 16451485 16451668 ponAbe2 chr22 14181703 14181882 rheMac2 chr10 62238949 62239129 calJac1 Contig10103 11457 11642 mononucleotide [T][T] 11 151 + 165 [T]C[TTTTTTTTTTTTT] indel/deletion C 2 1 ->rheMac2 411 hg18 chr22 16413390 16415373 panTro2 chr22 16452554 16454536 ponAbe2 chr22 14182766 14184730 rheMac2 chr10 62240630 62242621 calJac1 Contig10103 12826 14792 dinucleotide TG 5 1184 + 1193 TGTGTGTGTG ->calJac1 411 hg18 chr22 16413390 16415373 panTro2 chr22 16452554 16454536 ponAbe2 chr22 14182766 14184730 rheMac2 chr10 62240630 62242621 calJac1 Contig10103 12826 14792 trinucleotide AGC 17 1665 + 1682 AG------CAGCAGCAGC >hg18 411 hg18 chr22 16413390 16415373 panTro2 chr22 16452554 16454536 ponAbe2 chr22 14182766 14184730 rheMac2 chr10 62240630 62242621 calJac1 Contig10103 12826 14792 trinucleotide CAG 12 1670 + 1681 CAGCAGCAGCAG >panTro2 411 hg18 chr22 16413390 16415373 panTro2 chr22 16452554 16454536 ponAbe2 chr22 14182766 14184730 rheMac2 chr10 62240630 62242621 calJac1 Contig10103 12826 14792 trinucleotide CAG 13 1670 + 1681 CAGCAGCAGCAG ->calJac1 412 hg18 chr22 16415373 16415737 panTro2 chr22 16454536 16454900 ponAbe2 chr22 14184730 14185098 rheMac2 chr10 62242621 62242989 calJac1 Contig10103 14792 15143 tetranucleotide CTGT 18 298 + 309 CTGTCTGTCTGT ->calJac1 415 hg18 chr22 16417151 16417376 panTro2 chr22 16456343 16456567 ponAbe2 chr22 14186497 14186721 rheMac2 chr10 62244716 62244939 calJac1 Contig10103 16769 17045 mononucleotide [T][T] 4 118 + 133 [T]G[TTTTTTTTTTTTTT] indel/deletion G 2 1 ->ponAbe2 417 hg18 chr22 16417574 16417885 panTro2 chr22 16456745 16457057 ponAbe2 chr22 14186909 14187220 rheMac2 chr10 62245122 62245436 calJac1 Contig10103 17152 17462 dinucleotide [TG][GT][TG] 1 286 + 311 [TGTGTGTGTG][GTGTG----TGT]C[TGT] indel/substitution,indel/deletion ,C 11,19 2 >hg18 417 hg18 chr22 16417574 16417885 panTro2 chr22 16456745 16457057 ponAbe2 chr22 14186909 14187220 rheMac2 chr10 62245122 62245436 calJac1 Contig10103 17152 17462 dinucleotide [TG][GT][TG] 1 288 + 311 [TGTGTGTGTG][GTG----TGT]C[TGT] indel/substitution,indel/deletion ,C 11,17 2 >panTro2 417 hg18 chr22 16417574 16417885 panTro2 chr22 16456745 16457057 ponAbe2 chr22 14186909 14187220 rheMac2 chr10 62245122 62245436 calJac1 Contig10103 17152 17462 dinucleotide [TG][GT][TG] 0 288 + 311 [TGTGTGTGTG][GTG----TGT]C[TGT] indel/substitution,indel/deletion ,C 11,17 2 ->rheMac2 420 hg18 chr22 16419164 16419416 panTro2 chr22 16458313 16458579 ponAbe2 chr22 14188497 14188735 rheMac2 chr10 62246707 62246961 calJac1 Contig10103 18193 18304 mononucleotide A 0 60 + 70 aaaaaa--aaa ->ponAbe2 432 hg18 chr22 16425398 16425602 panTro2 chr22 16464845 16465049 ponAbe2 chr22 14194507 14194711 rheMac2 chr10 62252531 62252735 calJac1 Contig10103 30384 30603 mononucleotide [A][a] 0 181 + 192 [aaaaaaaaaa]g[a] indel/deletion g 11 1 >calJac1 432 hg18 chr22 16425398 16425602 panTro2 chr22 16464845 16465049 ponAbe2 chr22 14194507 14194711 rheMac2 chr10 62252531 62252735 calJac1 Contig10103 30384 30603 mononucleotide A 0 181 + 200 aaaaaaaaaaaaaaaaaaaa ->hg18 434 hg18 chr22 16426122 16426378 panTro2 chr22 16465567 16465824 ponAbe2 chr22 14195242 14195495 rheMac2 chr10 32566045 32566294 calJac1 Contig10103 30962 31214 mononucleotide [t][T] 0 1 + 18 [tttt]c-[tttttttttttt] indel/deletion c 5 1 >panTro2 434 hg18 chr22 16426122 16426378 panTro2 chr22 16465567 16465824 ponAbe2 chr22 14195242 14195495 rheMac2 chr10 32566045 32566294 calJac1 Contig10103 30962 31214 mononucleotide [t][T] 0 1 + 18 [tttt]c[ttttttttttttt] indel/deletion c 5 1 >ponAbe2 434 hg18 chr22 16426122 16426378 panTro2 chr22 16465567 16465824 ponAbe2 chr22 14195242 14195495 rheMac2 chr10 32566045 32566294 calJac1 Contig10103 30962 31214 mononucleotide [t][T] 0 1 + 19 [tttt]c----[tttttttttt] indel/deletion c 5 1 >rheMac2 434 hg18 chr22 16426122 16426378 panTro2 chr22 16465567 16465824 ponAbe2 chr22 14195242 14195495 rheMac2 chr10 32566045 32566294 calJac1 Contig10103 30962 31214 mononucleotide T 0 1 + 10 tttttttttt ->rheMac2 436 hg18 chr22 16441818 16442135 panTro2 chr22 16479988 16480285 ponAbe2 chr22 14211465 14211766 rheMac2 chr10 62266946 62267228 calJac1 Contig1768 189978 190278 mononucleotide T 0 1 + 24 ttttttttttttttt--ttttttt >hg18 436 hg18 chr22 16441818 16442135 panTro2 chr22 16479988 16480285 ponAbe2 chr22 14211465 14211766 rheMac2 chr10 62266946 62267228 calJac1 Contig1768 189978 190278 tetranucleotide [gttt][TTTG][tttg] 0 16 + 59 [gttt][tttgtttgtttgtttgtttgtttgtttgtt--tg]tt[tttg] indel/deletion,indel/deletion ,tt 5,37 2 >panTro2 436 hg18 chr22 16441818 16442135 panTro2 chr22 16479988 16480285 ponAbe2 chr22 14211465 14211766 rheMac2 chr10 62266946 62267228 calJac1 Contig1768 189978 190278 tetranucleotide [Gttt][TTTG][tttg] 0 16 + 59 [Gttt]--------------------[tttgtttgtt--tg]tt[tttg] indel/deletion,indel/deletion ,tt 5,17 2 ->calJac1 442 hg18 chr22 16443501 16443586 panTro2 chr22 16481658 16481743 ponAbe2 chr22 14213129 14213214 rheMac2 chr10 62268891 62268976 calJac1 Contig10103 42676 42818 tetranucleotide.tetranucleotide AANN.NNCC 0 33 + 46 [AANNNNNNNNNNCC] NA.NA NA.NA NA.NA NA.NA 33.35 44.46 AANNNNNNNNNN.NNNNNNNNNNCC ->panTro2 445 hg18 chr22 16444400 16444627 panTro2 chr22 16482557 16482784 ponAbe2 chr22 14214017 14214242 rheMac2 chr10 62269783 62269988 calJac1 Contig10103 43592 43792 tetranucleotide [CCTG][CCTG] 0 19 + 42 [CCTGCCTGCC--TG]TCT[CTGCCTG] indel/deletion TCT 13 1 >panTro2 445 hg18 chr22 16444400 16444627 panTro2 chr22 16482557 16482784 ponAbe2 chr22 14214017 14214242 rheMac2 chr10 62269783 62269988 calJac1 Contig10103 43592 43792 dinucleotide [GA][AG] 2 52 + 63 [GA][AGAGAGAGAG] indel/deletion 3 1 >hg18 445 hg18 chr22 16444400 16444627 panTro2 chr22 16482557 16482784 ponAbe2 chr22 14214017 14214242 rheMac2 chr10 62269783 62269988 calJac1 Contig10103 43592 43792 dinucleotide [GA][AG] 2 52 + 63 [GA][AGAGAGAGAG] indel/deletion 3 1 >ponAbe2 445 hg18 chr22 16444400 16444627 panTro2 chr22 16482557 16482784 ponAbe2 chr22 14214017 14214242 rheMac2 chr10 62269783 62269988 calJac1 Contig10103 43592 43792 dinucleotide [GA][AG] 2 52 + 63 [GA][AGAGAGAGAG] indel/deletion 3 1 >rheMac2 445 hg18 chr22 16444400 16444627 panTro2 chr22 16482557 16482784 ponAbe2 chr22 14214017 14214242 rheMac2 chr10 62269783 62269988 calJac1 Contig10103 43592 43792 dinucleotide [GA][AG] 2 52 + 85 [GA][AGAGAGAGA----------------------G] indel/deletion 3 1 ->ponAbe2 446 hg18 chr22 16444857 16445196 panTro2 chr22 16483014 16483353 ponAbe2 chr22 14214472 14214829 rheMac2 chr10 62270394 62270738 calJac1 Contig10103 43980 44102 mononucleotide [a][A] 0 125 + 137 [a]c[aaaaaaaaaaa] indel/deletion c 2 1 ->hg18 446 hg18 chr22 16444857 16445196 panTro2 chr22 16483014 16483353 ponAbe2 chr22 14214472 14214829 rheMac2 chr10 62270394 62270738 calJac1 Contig10103 43980 44102 mononucleotide A 2 286 + 294 aaaaaaaaa >panTro2 446 hg18 chr22 16444857 16445196 panTro2 chr22 16483014 16483353 ponAbe2 chr22 14214472 14214829 rheMac2 chr10 62270394 62270738 calJac1 Contig10103 43980 44102 mononucleotide A 2 286 + 294 aaaaaaaaa >ponAbe2 446 hg18 chr22 16444857 16445196 panTro2 chr22 16483014 16483353 ponAbe2 chr22 14214472 14214829 rheMac2 chr10 62270394 62270738 calJac1 Contig10103 43980 44102 mononucleotide A 0 287 + 310 aaaaaaaaaaaaaaaaaaaaaaaa >rheMac2 446 hg18 chr22 16444857 16445196 panTro2 chr22 16483014 16483353 ponAbe2 chr22 14214472 14214829 rheMac2 chr10 62270394 62270738 calJac1 Contig10103 43980 44102 mononucleotide [A][A] 6 288 + 311 [aaaaaaa-------aaaaaaaa]g[a] indel/deletion G 16 1 ->hg18 453 hg18 chr22 16447557 16447873 panTro2 chr22 16485670 16485984 ponAbe2 chr22 14217089 14217402 rheMac2 chr10 62273152 62273505 calJac1 Contig10103 45820 46121 mononucleotide [A][a] 0 1 + 21 [aaaaaaaaaaaaaaaaa]g[aaA] indel/deletion g 18 1 >panTro2 453 hg18 chr22 16447557 16447873 panTro2 chr22 16485670 16485984 ponAbe2 chr22 14217089 14217402 rheMac2 chr10 62273152 62273505 calJac1 Contig10103 45820 46121 mononucleotide [A][a] 0 1 + 17 [aaaaaaaaaaaaa]g[aaa] indel/deletion g 14 1 >ponAbe2 453 hg18 chr22 16447557 16447873 panTro2 chr22 16485670 16485984 ponAbe2 chr22 14217089 14217402 rheMac2 chr10 62273152 62273505 calJac1 Contig10103 45820 46121 mononucleotide [A][a] 0 1 + 21 [aaaaaaaaaaaaaaaaa]g[aaa] indel/deletion g 18 1 >rheMac2 453 hg18 chr22 16447557 16447873 panTro2 chr22 16485670 16485984 ponAbe2 chr22 14217089 14217402 rheMac2 chr10 62273152 62273505 calJac1 Contig10103 45820 46121 mononucleotide [A][A] 0 1 + 13 [aaaaaaaaaaa]g[a] indel/deletion G 12 1 >calJac1 453 hg18 chr22 16447557 16447873 panTro2 chr22 16485670 16485984 ponAbe2 chr22 14217089 14217402 rheMac2 chr10 62273152 62273505 calJac1 Contig10103 45820 46121 mononucleotide [A][A] 3 5 + 22 [aaaaaaaaaaa]c[aaaaaa] insertion c 12 1 ->rheMac2 453 hg18 chr22 16447557 16447873 panTro2 chr22 16485670 16485984 ponAbe2 chr22 14217089 14217402 rheMac2 chr10 62273152 62273505 calJac1 Contig10103 45820 46121 mononucleotide A 6 347 + 361 aaaa--aaaaaaaaa >hg18 453 hg18 chr22 16447557 16447873 panTro2 chr22 16485670 16485984 ponAbe2 chr22 14217089 14217402 rheMac2 chr10 62273152 62273505 calJac1 Contig10103 45820 46121 mononucleotide A 45 351 + 360 aaaaaaaaaa >panTro2 453 hg18 chr22 16447557 16447873 panTro2 chr22 16485670 16485984 ponAbe2 chr22 14217089 14217402 rheMac2 chr10 62273152 62273505 calJac1 Contig10103 45820 46121 mononucleotide A 49 351 + 362 aaaaaaaaaaaa ->hg18 466 hg18 chr22 16456042 16456465 panTro2 chr22 16495513 16495936 ponAbe2 chr22 14225670 14226093 rheMac2 chr10 62284958 62285377 calJac1 Contig10103 52799 53208 mononucleotide [A][A][A] 0 1 + 18 [AAA]C[AAAA]C[AAAAAAAAA] indel/deletion,indel/deletion C,C 4,9 2 >panTro2 466 hg18 chr22 16456042 16456465 panTro2 chr22 16495513 16495936 ponAbe2 chr22 14225670 14226093 rheMac2 chr10 62284958 62285377 calJac1 Contig10103 52799 53208 mononucleotide A 0 1 + 18 aaaaaaaaaaaaaaaaaa >ponAbe2 466 hg18 chr22 16456042 16456465 panTro2 chr22 16495513 16495936 ponAbe2 chr22 14225670 14226093 rheMac2 chr10 62284958 62285377 calJac1 Contig10103 52799 53208 mononucleotide [A][A] 0 1 + 18 [AAAAAAAA]C[AAAAAAAAA] insertion C 9 1 >rheMac2 466 hg18 chr22 16456042 16456465 panTro2 chr22 16495513 16495936 ponAbe2 chr22 14225670 14226093 rheMac2 chr10 62284958 62285377 calJac1 Contig10103 52799 53208 mononucleotide A 0 1 + 13 AAAAAAAAAAAAA ->hg18 473 hg18 chr22 16458385 16458905 panTro2 chr22 16497858 16498375 ponAbe2 chr22 14228043 14228566 rheMac2 chr10 62287287 62287791 calJac1 Contig10103 60215 60734 trinucleotide [caa][AAC] 2 203 + 222 [caa]aat[acaacaacaacaac] indel/deletion aat 4 1 >panTro2 473 hg18 chr22 16458385 16458905 panTro2 chr22 16497858 16498375 ponAbe2 chr22 14228043 14228566 rheMac2 chr10 62287287 62287791 calJac1 Contig10103 60215 60734 trinucleotide [caa][CAA] 3 203 + 227 [caa]aa---[aacaacaacaacaacaa] indel/deletion aa 4 1 >ponAbe2 473 hg18 chr22 16458385 16458905 panTro2 chr22 16497858 16498375 ponAbe2 chr22 14228043 14228566 rheMac2 chr10 62287287 62287791 calJac1 Contig10103 60215 60734 mononucleotide [A][a][a][A] 1 204 + 231 [aaaaaaaaaaaa]c[aaaa]c[aaaaaaaa]G[A] indel/deletion,indel/deletion,indel/deletion c,c,G 13,18,27 3 >rheMac2 473 hg18 chr22 16458385 16458905 panTro2 chr22 16497858 16498375 ponAbe2 chr22 14228043 14228566 rheMac2 chr10 62287287 62287791 calJac1 Contig10103 60215 60734 mononucleotide [A][a] 4 204 + 242 [aaaa-------------aaaaaaaaa]g[a----------a] indel/deletion g 14 1 >calJac1 473 hg18 chr22 16458385 16458905 panTro2 chr22 16497858 16498375 ponAbe2 chr22 14228043 14228566 rheMac2 chr10 62287287 62287791 calJac1 Contig10103 60215 60734 mononucleotide [A][A] 0 204 + 231 [aaaa------------aaaaaaaaaa]G[A] indel/deletion G 15 1 ->ponAbe2 475 hg18 chr22 16460300 16460558 panTro2 chr22 16499774 16500032 ponAbe2 chr22 14229966 14230325 rheMac2 chr10 62288496 62288751 calJac1 Contig10103 62091 62351 tetranucleotide.tetranucleotide TGNN.NNAA 2 187 + 200 [tgnnnnnnnnnnaa] NA.NA NA.NA NA.NA NA.NA 185.187 196.198 TGNNNNNNNNNN.NNNNNNNNNNAA ->rheMac2 479 hg18 chr22 16463003 16463512 panTro2 chr22 16502471 16502980 ponAbe2 chr22 14233062 14233569 rheMac2 chr10 62292896 62293418 calJac1 Contig10103 67942 68441 tetranucleotide [AAAT][aaat] 0 34 + 55 [aaataaataaataaat]aa[aaat] indel/deletion aa 17 1 ->rheMac2 479 hg18 chr22 16463003 16463512 panTro2 chr22 16502471 16502980 ponAbe2 chr22 14233062 14233569 rheMac2 chr10 62292896 62293418 calJac1 Contig10103 67942 68441 tetranucleotide TAAA 3 219 + 243 aaataa--ataaataaataaataaa ->calJac1 480 hg18 chr22 16463512 16463711 panTro2 chr22 16502980 16503178 ponAbe2 chr22 14233569 14233768 rheMac2 chr10 62293418 62293616 calJac1 Contig10103 68441 68647 tetranucleotide CCAG 0 139 + 150 CCAGCCAGCCAG ->hg18 481 hg18 chr22 16463711 16463842 panTro2 chr22 16503178 16503309 ponAbe2 chr22 14233768 14233897 rheMac2 chr10 62293616 62293743 calJac1 Contig10103 68647 68775 mononucleotide [a][A] 0 11 + 25 [aaaa]g-[aaaaaaaaa] indel/deletion g 5 1 >panTro2 481 hg18 chr22 16463711 16463842 panTro2 chr22 16503178 16503309 ponAbe2 chr22 14233768 14233897 rheMac2 chr10 62293616 62293743 calJac1 Contig10103 68647 68775 mononucleotide [a][A] 0 11 + 25 [aaaa]g-[aaaaaaaaa] indel/deletion g 5 1 >ponAbe2 481 hg18 chr22 16463711 16463842 panTro2 chr22 16503178 16503309 ponAbe2 chr22 14233768 14233897 rheMac2 chr10 62293616 62293743 calJac1 Contig10103 68647 68775 mononucleotide [A][A] 0 11 + 25 [AAAA]G[AAAAAAAAAA] indel/deletion G 5 1 >rheMac2 481 hg18 chr22 16463711 16463842 panTro2 chr22 16503178 16503309 ponAbe2 chr22 14233768 14233897 rheMac2 chr10 62293616 62293743 calJac1 Contig10103 68647 68775 mononucleotide [A][A] 0 11 + 25 [AAAA]G[AAAAAAAAAA] indel/deletion G 5 1 ->calJac1 486 hg18 chr22 16469302 16469704 panTro2 chr22 16508811 16509213 ponAbe2 chr22 14242077 14242483 rheMac2 chr10 62297128 62297532 calJac1 Contig10103 74852 75243 mononucleotide [A][A][a][a] 0 5 + 40 [aaaa----------aaaaaa]g[aaaaa]g[aa-a]t[aaaa] insertion,indel/deletion,indel/deletion g,g,t 11,17,21 3 ->hg18 488 hg18 chr22 16469926 16470199 panTro2 chr22 16509435 16509705 ponAbe2 chr22 14242705 14243017 rheMac2 chr10 62297773 62298077 calJac1 Contig10103 75740 76075 mononucleotide [T][T] 0 1 + 54 [tttttttt--------------------------------------tt]a[ttttt] insertion a 11 1 >panTro2 488 hg18 chr22 16469926 16470199 panTro2 chr22 16509435 16509705 ponAbe2 chr22 14242705 14243017 rheMac2 chr10 62297773 62298077 calJac1 Contig10103 75740 76075 mononucleotide T 0 1 + 54 tttttttt-----------------------------------------ttttt >ponAbe2 488 hg18 chr22 16469926 16470199 panTro2 chr22 16509435 16509705 ponAbe2 chr22 14242705 14243017 rheMac2 chr10 62297773 62298077 calJac1 Contig10103 75740 76075 mononucleotide [t][T] 0 1 + 54 [tt]c[ttttt----------------------------------tttttttttttt] indel/deletion c 3 1 >rheMac2 488 hg18 chr22 16469926 16470199 panTro2 chr22 16509435 16509705 ponAbe2 chr22 14242705 14243017 rheMac2 chr10 62297773 62298077 calJac1 Contig10103 75740 76075 mononucleotide [T][T][T] 0 1 + 54 [tt]c[ttt]c[t-----------------------------------ttttttttttt] indel/deletion,indel/deletion C,C 3,7 2 >calJac1 488 hg18 chr22 16469926 16470199 panTro2 chr22 16509435 16509705 ponAbe2 chr22 14242705 14243017 rheMac2 chr10 62297773 62298077 calJac1 Contig10103 75740 76075 mononucleotide [T][T] 0 42 + 53 [T]C[tttttttttt] indel/deletion C 2 1 ->calJac1 490 hg18 chr22 16471173 16471466 panTro2 chr22 16512208 16512500 ponAbe2 chr22 14244118 14244416 rheMac2 chr10 62300280 62300577 calJac1 Contig10103 78345 78641 mononucleotide A 12 194 + 202 aaaaaaaaa ->hg18 491 hg18 chr22 16472757 16472947 panTro2 chr22 16512615 16512806 ponAbe2 chr22 14245721 14245926 rheMac2 chr10 62301347 62301543 calJac1 Contig10103 79782 79958 mononucleotide A 12 146 + 181 aaaaaa---------------------------aaa >ponAbe2 491 hg18 chr22 16472757 16472947 panTro2 chr22 16512615 16512806 ponAbe2 chr22 14245721 14245926 rheMac2 chr10 62301347 62301543 calJac1 Contig10103 79782 79958 mononucleotide A 1 146 + 181 aaaaaaa------------------------aaaaa >rheMac2 491 hg18 chr22 16472757 16472947 panTro2 chr22 16512615 16512806 ponAbe2 chr22 14245721 14245926 rheMac2 chr10 62301347 62301543 calJac1 Contig10103 79782 79958 mononucleotide A 13 147 + 186 aaaaaaaaaa------------------------aaaaaa ->ponAbe2 493 hg18 chr22 16473279 16473548 panTro2 chr22 16513139 16513408 ponAbe2 chr22 14246254 14246519 rheMac2 chr10 62302186 62302449 calJac1 Contig10103 81704 81957 mononucleotide [A][a] 0 1 + 15 [aaaaaaaaaa]t---[a] indel/deletion t 11 1 >rheMac2 493 hg18 chr22 16473279 16473548 panTro2 chr22 16513139 16513408 ponAbe2 chr22 14246254 14246519 rheMac2 chr10 62302186 62302449 calJac1 Contig10103 81704 81957 mononucleotide A 0 1 + 15 AAAAAAAAAA----A ->hg18 496 hg18 chr22 16474070 16474384 panTro2 chr22 16513932 16514246 ponAbe2 chr22 14247038 14247356 rheMac2 chr10 62304486 62304800 calJac1 Contig10103 82981 83289 tetranucleotide AACA 0 282 + 294 AAACAAACAAACA >panTro2 496 hg18 chr22 16474070 16474384 panTro2 chr22 16513932 16514246 ponAbe2 chr22 14247038 14247356 rheMac2 chr10 62304486 62304800 calJac1 Contig10103 82981 83289 tetranucleotide AACA 0 282 + 294 AAACAAACAAACA >ponAbe2 496 hg18 chr22 16474070 16474384 panTro2 chr22 16513932 16514246 ponAbe2 chr22 14247038 14247356 rheMac2 chr10 62304486 62304800 calJac1 Contig10103 82981 83289 tetranucleotide AACA 0 282 + 298 AAACAAACAAACAAACA >rheMac2 496 hg18 chr22 16474070 16474384 panTro2 chr22 16513932 16514246 ponAbe2 chr22 14247038 14247356 rheMac2 chr10 62304486 62304800 calJac1 Contig10103 82981 83289 tetranucleotide AACA 0 282 + 294 AAACAAACAAACA ->calJac1 497 hg18 chr22 16474384 16474761 panTro2 chr22 16514246 16514623 ponAbe2 chr22 14247356 14247772 rheMac2 chr10 62304983 62305524 calJac1 Contig10103 83289 83637 mononucleotide T 189 460 + 480 ttt------------tttttt ->rheMac2 503 hg18 chr22 16482482 16483094 panTro2 chr22 16522060 16522667 ponAbe2 chr22 14253904 14254509 rheMac2 chr10 62313304 62313912 calJac1 Contig15496 1654 2198 mononucleotide [t][T] 27 456 + 476 [t]c[tttt--ttttttttttttt] indel/deletion c 2 1 >hg18 503 hg18 chr22 16482482 16483094 panTro2 chr22 16522060 16522667 ponAbe2 chr22 14253904 14254509 rheMac2 chr10 62313304 62313912 calJac1 Contig15496 1654 2198 mononucleotide [t][T] 27 458 + 476 [ttt]g[ttttttttttttttt] indel/deletion g 4 1 >panTro2 503 hg18 chr22 16482482 16483094 panTro2 chr22 16522060 16522667 ponAbe2 chr22 14253904 14254509 rheMac2 chr10 62313304 62313912 calJac1 Contig15496 1654 2198 mononucleotide [t][T] 27 458 + 476 [ttt]g---[tttttttttttt] indel/deletion g 4 1 >ponAbe2 503 hg18 chr22 16482482 16483094 panTro2 chr22 16522060 16522667 ponAbe2 chr22 14253904 14254509 rheMac2 chr10 62313304 62313912 calJac1 Contig15496 1654 2198 mononucleotide T 25 458 + 467 tttttttttt ->calJac1 504 hg18 chr22 16483360 16483546 panTro2 chr22 16522909 16523095 ponAbe2 chr22 14254744 14254930 rheMac2 chr10 62314154 62314338 calJac1 Contig15496 2349 2531 tetranucleotide [TAAA][TAAA] 0 1 + 19 [TAAATAAATAAA]CC[TAAAT] indel/deletion CC 13 1 ->rheMac2 505 hg18 chr22 16485451 16485765 panTro2 chr22 16525000 16525316 ponAbe2 chr22 14256888 14257202 rheMac2 chr10 62317227 62317477 calJac1 Contig15496 3434 3763 mononucleotide A 68 292 + 334 AAAAA----------------------AAAAAAAAA---AAAA ->calJac1 507 hg18 chr22 16486411 16486752 panTro2 chr22 16525962 16526313 ponAbe2 chr22 14257847 14258194 rheMac2 chr10 62319654 62319993 calJac1 Contig15496 4390 4729 mononucleotide A 0 11 + 24 aaaaaaaaaaaaaa >hg18 507 hg18 chr22 16486411 16486752 panTro2 chr22 16525962 16526313 ponAbe2 chr22 14257847 14258194 rheMac2 chr10 62319654 62319993 calJac1 Contig15496 4390 4729 mononucleotide A 0 12 + 26 aaaaaaaaaaaaaaa >panTro2 507 hg18 chr22 16486411 16486752 panTro2 chr22 16525962 16526313 ponAbe2 chr22 14257847 14258194 rheMac2 chr10 62319654 62319993 calJac1 Contig15496 4390 4729 mononucleotide A 0 12 + 35 aaaaaaaaaaaaaaaaaaaaaaaa >ponAbe2 507 hg18 chr22 16486411 16486752 panTro2 chr22 16525962 16526313 ponAbe2 chr22 14257847 14258194 rheMac2 chr10 62319654 62319993 calJac1 Contig15496 4390 4729 mononucleotide A 0 12 + 32 aaaaaaaaaaaaaaaaaaaaa >rheMac2 507 hg18 chr22 16486411 16486752 panTro2 chr22 16525962 16526313 ponAbe2 chr22 14257847 14258194 rheMac2 chr10 62319654 62319993 calJac1 Contig15496 4390 4729 mononucleotide [A][A] 0 12 + 26 [aaaaa]g[aaaaaaaaa] insertion g 6 1 ->calJac1 509 hg18 chr22 16486960 16487598 panTro2 chr22 16526521 16527159 ponAbe2 chr22 14258402 14259066 rheMac2 chr10 62320202 62320864 calJac1 Contig15496 4936 5596 mononucleotide [A][A] 10 364 + 390 [aaaaaaaaaaaaaaaaaaaaaaaaa]T[A] indel/deletion T 26 1 ->hg18 509 hg18 chr22 16486960 16487598 panTro2 chr22 16526521 16527159 ponAbe2 chr22 14258402 14259066 rheMac2 chr10 62320202 62320864 calJac1 Contig15496 4936 5596 mononucleotide A 40 667 + 678 aaaaaaaaaaaa >panTro2 509 hg18 chr22 16486960 16487598 panTro2 chr22 16526521 16527159 ponAbe2 chr22 14258402 14259066 rheMac2 chr10 62320202 62320864 calJac1 Contig15496 4936 5596 mononucleotide A 40 667 + 678 aaaaaaaaaaaa ->hg18 510 hg18 chr22 16488039 16488357 panTro2 chr22 16527604 16527898 ponAbe2 chr22 14259515 14259809 rheMac2 chr10 62321631 62321929 calJac1 Contig15496 5773 6086 mononucleotide T 0 1 + 9 ttttttttt >panTro2 510 hg18 chr22 16488039 16488357 panTro2 chr22 16527604 16527898 ponAbe2 chr22 14259515 14259809 rheMac2 chr10 62321631 62321929 calJac1 Contig15496 5773 6086 mononucleotide T 0 1 + 9 ttttttttt >ponAbe2 510 hg18 chr22 16488039 16488357 panTro2 chr22 16527604 16527898 ponAbe2 chr22 14259515 14259809 rheMac2 chr10 62321631 62321929 calJac1 Contig15496 5773 6086 mononucleotide T 0 1 + 9 ttttttttt ->hg18 512 hg18 chr22 16488498 16489104 panTro2 chr22 16528038 16528648 ponAbe2 chr22 14259949 14260557 rheMac2 chr10 62322068 62322657 calJac1 Contig15496 6226 6860 mononucleotide A 26 161 + 186 AAAAAAAAAAAAA-----------AA >panTro2 512 hg18 chr22 16488498 16489104 panTro2 chr22 16528038 16528648 ponAbe2 chr22 14259949 14260557 rheMac2 chr10 62322068 62322657 calJac1 Contig15496 6226 6860 mononucleotide A 26 161 + 186 AAAAAAAAAAAAA-----------AA >ponAbe2 512 hg18 chr22 16488498 16489104 panTro2 chr22 16528038 16528648 ponAbe2 chr22 14259949 14260557 rheMac2 chr10 62322068 62322657 calJac1 Contig15496 6226 6860 mononucleotide A 26 161 + 186 AAAAAAAAAAAAA-----------AA >rheMac2 512 hg18 chr22 16488498 16489104 panTro2 chr22 16528038 16528648 ponAbe2 chr22 14259949 14260557 rheMac2 chr10 62322068 62322657 calJac1 Contig15496 6226 6860 mononucleotide A 28 161 + 187 aaaaaaaaaaaaa-----------aaa ->hg18 512 hg18 chr22 16488498 16489104 panTro2 chr22 16528038 16528648 ponAbe2 chr22 14259949 14260557 rheMac2 chr10 62322068 62322657 calJac1 Contig15496 6226 6860 mononucleotide [A][A][A] 43 619 + 651 [aaaaaaaaaaaa---aaaaaaaaa]g[aaa]g[aaaa] indel/deletion,indel/deletion G,G 22,26 3 >calJac1 512 hg18 chr22 16488498 16489104 panTro2 chr22 16528038 16528648 ponAbe2 chr22 14259949 14260557 rheMac2 chr10 62322068 62322657 calJac1 Contig15496 6226 6860 mononucleotide A 13 619 + 642 aaaaaaaaaaaa--aaaaaaaaaa >ponAbe2 512 hg18 chr22 16488498 16489104 panTro2 chr22 16528038 16528648 ponAbe2 chr22 14259949 14260557 rheMac2 chr10 62322068 62322657 calJac1 Contig15496 6226 6860 mononucleotide [A][A][A][A] 41 620 + 651 [aaaaaaaaaaa---aaaaa]g[aaa]g[aaa]g[aaaa] indel/deletion,indel/deletion,indel/deletion G,G,G 17,21,25 4 >panTro2 512 hg18 chr22 16488498 16489104 panTro2 chr22 16528038 16528648 ponAbe2 chr22 14259949 14260557 rheMac2 chr10 62322068 62322657 calJac1 Contig15496 6226 6860 tetranucleotide [agaa][GAAA] 42 630 + 650 [aaagaa][aaagaaagaaaGAAA] indel/deletion 7 1 ->calJac1 515 hg18 chr22 16491633 16492543 panTro2 chr22 16531150 16532057 ponAbe2 chr22 14261591 14262487 rheMac2 chr10 62325854 62326808 calJac1 Contig15496 9093 10048 mononucleotide T 0 43 + 52 TTTTTTTTTT ->hg18 515 hg18 chr22 16491633 16492543 panTro2 chr22 16531150 16532057 ponAbe2 chr22 14261591 14262487 rheMac2 chr10 62325854 62326808 calJac1 Contig15496 9093 10048 mononucleotide [a][A] 51 386 + 400 [aaaa]g[aaaaaaaaaa] indel/deletion g 5 1 >panTro2 515 hg18 chr22 16491633 16492543 panTro2 chr22 16531150 16532057 ponAbe2 chr22 14261591 14262487 rheMac2 chr10 62325854 62326808 calJac1 Contig15496 9093 10048 mononucleotide [a][A] 51 386 + 410 [aaaa]g[aaaaaaaaaa---------a] indel/deletion g 5 1 >ponAbe2 515 hg18 chr22 16491633 16492543 panTro2 chr22 16531150 16532057 ponAbe2 chr22 14261591 14262487 rheMac2 chr10 62325854 62326808 calJac1 Contig15496 9093 10048 mononucleotide [a][A] 62 386 + 400 [aaaa]g[aaaaaaaaaa] indel/deletion g 5 1 >rheMac2 515 hg18 chr22 16491633 16492543 panTro2 chr22 16531150 16532057 ponAbe2 chr22 14261591 14262487 rheMac2 chr10 62325854 62326808 calJac1 Contig15496 9093 10048 mononucleotide [A][a][a] 11 392 + 414 [aaaaaaaaa--aaaaaa]g[aaa]g[a] indel/deletion,indel/deletion g,g 16,20 2 ->calJac1 515 hg18 chr22 16491633 16492543 panTro2 chr22 16531150 16532057 ponAbe2 chr22 14261591 14262487 rheMac2 chr10 62325854 62326808 calJac1 Contig15496 9093 10048 mononucleotide [T][T] 89 752 + 762 [TTTTTTTTT]C[T] indel/deletion C 10 1 ->calJac1 515 hg18 chr22 16491633 16492543 panTro2 chr22 16531150 16532057 ponAbe2 chr22 14261591 14262487 rheMac2 chr10 62325854 62326808 calJac1 Contig15496 9093 10048 mononucleotide T 93 952 + 961 tttttttttt ->calJac1 516 hg18 chr22 16492711 16492848 panTro2 chr22 16532209 16532348 ponAbe2 chr22 14262661 14262800 rheMac2 chr10 62326962 62327101 calJac1 Contig15496 10302 10465 dinucleotide CA 0 138 + 153 caCACACACACACACA ->calJac1 517 hg18 chr22 16496949 16497250 panTro2 chr22 16536925 16537226 ponAbe2 chr22 14266663 14266961 rheMac2 chr10 62330722 62331008 calJac1 Contig15496 10684 10983 mononucleotide [T][T] 0 1 + 18 [ttttttt]c[tttttt-ttt] insertion c 8 1 ->hg18 518 hg18 chr22 16497320 16497678 panTro2 chr22 16537296 16537654 ponAbe2 chr22 14267031 14267387 rheMac2 chr10 62331098 62331389 calJac1 Contig15496 11218 11567 mononucleotide [a][A] 2 227 + 237 [a]c[aaaaaaaaa] indel/deletion c 2 1 >panTro2 518 hg18 chr22 16497320 16497678 panTro2 chr22 16537296 16537654 ponAbe2 chr22 14267031 14267387 rheMac2 chr10 62331098 62331389 calJac1 Contig15496 11218 11567 mononucleotide [a][A] 2 227 + 237 [a]c[aaaaaaaaa] indel/deletion c 2 1 >calJac1 518 hg18 chr22 16497320 16497678 panTro2 chr22 16537296 16537654 ponAbe2 chr22 14267031 14267387 rheMac2 chr10 62331098 62331389 calJac1 Contig15496 11218 11567 tetranucleotide AAAT 9 230 + 247 aaataaa--taaataaat ->hg18 519 hg18 chr22 16499053 16499858 panTro2 chr22 16539354 16540161 ponAbe2 chr22 14269078 14269874 rheMac2 chr10 62331389 62332111 calJac1 Contig15496 15915 16759 mononucleotide [A][A] 2 38 + 62 [aaaaaaaa]g[aaaaaaaaaaaaaaaa] insertion g 9 1 >panTro2 519 hg18 chr22 16499053 16499858 panTro2 chr22 16539354 16540161 ponAbe2 chr22 14269078 14269874 rheMac2 chr10 62331389 62332111 calJac1 Contig15496 15915 16759 mononucleotide [A][A] 2 38 + 62 [aaaaaaaa]g--[aaaaaaaaaaaaaa] insertion g 9 1 >ponAbe2 519 hg18 chr22 16499053 16499858 panTro2 chr22 16539354 16540161 ponAbe2 chr22 14269078 14269874 rheMac2 chr10 62331389 62332111 calJac1 Contig15496 15915 16759 mononucleotide [A][A][a] 2 38 + 62 [aaaaaaaaaa]g[aaaaaaaaaaa]g[aa] insertion,indel/deletion g,g 11,23 2 >rheMac2 519 hg18 chr22 16499053 16499858 panTro2 chr22 16539354 16540161 ponAbe2 chr22 14269078 14269874 rheMac2 chr10 62331389 62332111 calJac1 Contig15496 15915 16759 mononucleotide A 0 38 + 134 aaaaaaaaa--aaaaaaaaaa---------------------------------------------------------------------------a ->hg18 519 hg18 chr22 16499053 16499858 panTro2 chr22 16539354 16540161 ponAbe2 chr22 14269078 14269874 rheMac2 chr10 62331389 62332111 calJac1 Contig15496 15915 16759 mononucleotide [a][A][a] 9 355 + 368 [a]c[aaaaaaaaaa]t[a] indel/deletion,indel/deletion c,t 2,13 2 >panTro2 519 hg18 chr22 16499053 16499858 panTro2 chr22 16539354 16540161 ponAbe2 chr22 14269078 14269874 rheMac2 chr10 62331389 62332111 calJac1 Contig15496 15915 16759 mononucleotide [a][A][a] 7 355 + 368 [a]c[aaaaaaaaaa]t[a] indel/deletion,indel/deletion c,t 2,13 2 >ponAbe2 519 hg18 chr22 16499053 16499858 panTro2 chr22 16539354 16540161 ponAbe2 chr22 14269078 14269874 rheMac2 chr10 62331389 62332111 calJac1 Contig15496 15915 16759 mononucleotide [a][A] 5 355 + 368 [a]c[aaaaaaaaaaaa] indel/deletion c 2 1 >rheMac2 519 hg18 chr22 16499053 16499858 panTro2 chr22 16539354 16540161 ponAbe2 chr22 14269078 14269874 rheMac2 chr10 62331389 62332111 calJac1 Contig15496 15915 16759 mononucleotide [a][A] 82 355 + 368 [a]c[aaaaaaaa---a] indel/deletion c 2 1 >calJac1 519 hg18 chr22 16499053 16499858 panTro2 chr22 16539354 16540161 ponAbe2 chr22 14269078 14269874 rheMac2 chr10 62331389 62332111 calJac1 Contig15496 15915 16759 mononucleotide [a][A] 29 355 + 368 [a]c[aaaaaaaa---a] indel/deletion c 2 1 ->calJac1 519 hg18 chr22 16499053 16499858 panTro2 chr22 16539354 16540161 ponAbe2 chr22 14269078 14269874 rheMac2 chr10 62331389 62332111 calJac1 Contig15496 15915 16759 tetranucleotide [aaaT][AATA][ataa] 36 524 + 577 [aaaT]TAC[aataaataaataaataaataaataaataaataaataaataaa][ataaa] indel/deletion,indel/deletion TAC, 5,50 2 >ponAbe2 519 hg18 chr22 16499053 16499858 panTro2 chr22 16539354 16540161 ponAbe2 chr22 14269078 14269874 rheMac2 chr10 62331389 62332111 calJac1 Contig15496 15915 16759 trinucleotide [AAT][ata] 9 525 + 576 [aataataataa------------------------------taat-aa][ataa] indel/deletion 18 1 >hg18 519 hg18 chr22 16499053 16499858 panTro2 chr22 16539354 16540161 ponAbe2 chr22 14269078 14269874 rheMac2 chr10 62331389 62332111 calJac1 Contig15496 15915 16759 tetranucleotide [AATA][AAAT] 13 531 + 577 [aataaa]---------------------[aaataaataaat-aaataaa] indel/deletion 7 1 >panTro2 519 hg18 chr22 16499053 16499858 panTro2 chr22 16539354 16540161 ponAbe2 chr22 14269078 14269874 rheMac2 chr10 62331389 62332111 calJac1 Contig15496 15915 16759 tetranucleotide [AATA][AAAT] 11 531 + 577 [aataaa]---------------------[aaataaataaat-aaataaa] indel/deletion 7 1 ->ponAbe2 526 hg18 chr22 16502189 16502628 panTro2 chr22 16542499 16542940 ponAbe2 chr22 14272165 14272610 rheMac2 chr10 62335341 62335798 calJac1 Contig1262 2252 2692 trinucleotide TTG 4 288 + 307 TTG------TTGTTGTTGTT >hg18 526 hg18 chr22 16502189 16502628 panTro2 chr22 16542499 16542940 ponAbe2 chr22 14272165 14272610 rheMac2 chr10 62335341 62335798 calJac1 Contig1262 2252 2692 trinucleotide TTG 5 291 + 302 TTGTTGTTGTTG >rheMac2 526 hg18 chr22 16502189 16502628 panTro2 chr22 16542499 16542940 ponAbe2 chr22 14272165 14272610 rheMac2 chr10 62335341 62335798 calJac1 Contig1262 2252 2692 trinucleotide GTT 4 291 + 307 TTGTTGTTGTTGTTGTT ->calJac1 526 hg18 chr22 16502189 16502628 panTro2 chr22 16542499 16542940 ponAbe2 chr22 14272165 14272610 rheMac2 chr10 62335341 62335798 calJac1 Contig1262 2252 2692 mononucleotide A 14 312 + 325 AAAAAAAAAAAAAA ->panTro2 526 hg18 chr22 16502189 16502628 panTro2 chr22 16542499 16542940 ponAbe2 chr22 14272165 14272610 rheMac2 chr10 62335341 62335798 calJac1 Contig1262 2252 2692 tetranucleotide TTCT 22 449 + 467 ttctttctttc-----ttt >ponAbe2 526 hg18 chr22 16502189 16502628 panTro2 chr22 16542499 16542940 ponAbe2 chr22 14272165 14272610 rheMac2 chr10 62335341 62335798 calJac1 Contig1262 2252 2692 tetranucleotide TTCT 21 449 + 468 ttctttctttctt--tcttt ->hg18 527 hg18 chr22 16502628 16502923 panTro2 chr22 16542940 16543235 ponAbe2 chr22 14272610 14272903 rheMac2 chr10 62335798 62336094 calJac1 Contig1262 2692 3078 mononucleotide T 0 1 + 9 ttttttttt >panTro2 527 hg18 chr22 16502628 16502923 panTro2 chr22 16542940 16543235 ponAbe2 chr22 14272610 14272903 rheMac2 chr10 62335798 62336094 calJac1 Contig1262 2692 3078 mononucleotide T 0 1 + 9 ttttttttt >rheMac2 527 hg18 chr22 16502628 16502923 panTro2 chr22 16542940 16543235 ponAbe2 chr22 14272610 14272903 rheMac2 chr10 62335798 62336094 calJac1 Contig1262 2692 3078 mononucleotide T 0 1 + 9 ttttttttt ->calJac1 527 hg18 chr22 16502628 16502923 panTro2 chr22 16542940 16543235 ponAbe2 chr22 14272610 14272903 rheMac2 chr10 62335798 62336094 calJac1 Contig1262 2692 3078 mononucleotide [T][t] 0 162 + 176 [ttttttttttttt]g[t] indel/deletion g 14 1 >calJac1 527 hg18 chr22 16502628 16502923 panTro2 chr22 16542940 16543235 ponAbe2 chr22 14272610 14272903 rheMac2 chr10 62335798 62336094 calJac1 Contig1262 2692 3078 mononucleotide T 0 179 + 195 ttttttttttttttttt ->calJac1 528 hg18 chr22 16502923 16503094 panTro2 chr22 16543235 16543407 ponAbe2 chr22 14272903 14273073 rheMac2 chr10 62336094 62336258 calJac1 Contig1262 3663 3837 mononucleotide T 0 1 + 9 TTTTTTTTT ->rheMac2 528 hg18 chr22 16502923 16503094 panTro2 chr22 16543235 16543407 ponAbe2 chr22 14272903 14273073 rheMac2 chr10 62336094 62336258 calJac1 Contig1262 3663 3837 mononucleotide [T][T] 25 167 + 177 [T]A[TTTTTTTTT] indel/deletion A 2 1 ->hg18 529 hg18 chr22 16503094 16503480 panTro2 chr22 16543407 16543796 ponAbe2 chr22 14273073 14273459 rheMac2 chr10 62336258 62336655 calJac1 Contig1262 4149 4576 mononucleotide A 51 425 + 443 aaaaa------aaaaaaaa >panTro2 529 hg18 chr22 16503094 16503480 panTro2 chr22 16543407 16543796 ponAbe2 chr22 14273073 14273459 rheMac2 chr10 62336258 62336655 calJac1 Contig1262 4149 4576 mononucleotide A 51 425 + 446 aaaaaaaa------aaaaaaaa >ponAbe2 529 hg18 chr22 16503094 16503480 panTro2 chr22 16543407 16543796 ponAbe2 chr22 14273073 14273459 rheMac2 chr10 62336258 62336655 calJac1 Contig1262 4149 4576 mononucleotide A 53 425 + 445 aaaaaaa------aaaaaaaa ->rheMac2 531 hg18 chr22 16503955 16504097 panTro2 chr22 16544270 16544415 ponAbe2 chr22 14273935 14274080 rheMac2 chr10 62337106 62337257 calJac1 Contig1262 5037 5182 dinucleotide [ta][AT][ta][TA] 0 1 + 26 [ta]a[atatatatatat]g[tatat]TT[TAT] indel/deletion,indel/deletion,indel/deletion a,g,TT 3,16,22 3 >calJac1 531 hg18 chr22 16503955 16504097 panTro2 chr22 16544270 16544415 ponAbe2 chr22 14273935 14274080 rheMac2 chr10 62337106 62337257 calJac1 Contig1262 5037 5182 dinucleotide [TA][ta] 0 1 + 26 [tatatatata------tatat]tt[tat] indel/deletion tt 16 1 ->ponAbe2 532 hg18 chr22 16504097 16504832 panTro2 chr22 16544415 16545148 ponAbe2 chr22 14274080 14274812 rheMac2 chr10 62337257 62338048 calJac1 Contig1262 5182 5925 dinucleotide [TA][AT] 0 10 + 22 [TA][ATATATATATA] indel/deletion 3 1 ->hg18 532 hg18 chr22 16504097 16504832 panTro2 chr22 16544415 16545148 ponAbe2 chr22 14274080 14274812 rheMac2 chr10 62337257 62338048 calJac1 Contig1262 5182 5925 mononucleotide [T][T][T][T][T] 0 53 + 75 [TTT]A[TTTTTTTTT]C[T-T]G[TT]C[TT] indel/deletion,indel/deletion,indel/deletion,indel/deletion A,C,G,C 4,14,17,20 4 >panTro2 532 hg18 chr22 16504097 16504832 panTro2 chr22 16544415 16545148 ponAbe2 chr22 14274080 14274812 rheMac2 chr10 62337257 62338048 calJac1 Contig1262 5182 5925 mononucleotide [T][T][T][T][T] 0 53 + 75 [TTT]A[TTTTTTTTT]C[T-T]G[TT]C[TT] indel/deletion,indel/deletion,indel/deletion,indel/deletion A,C,G,C 4,14,17,20 4 >ponAbe2 532 hg18 chr22 16504097 16504832 panTro2 chr22 16544415 16545148 ponAbe2 chr22 14274080 14274812 rheMac2 chr10 62337257 62338048 calJac1 Contig1262 5182 5925 mononucleotide [T][T][T][T][T] 0 53 + 75 [TTT]A[TTTTTTTTT]C[T-T]G[TT]C[TT] indel/deletion,indel/deletion,indel/deletion,indel/deletion A,C,G,C 4,14,17,20 4 >rheMac2 532 hg18 chr22 16504097 16504832 panTro2 chr22 16544415 16545148 ponAbe2 chr22 14274080 14274812 rheMac2 chr10 62337257 62338048 calJac1 Contig1262 5182 5925 mononucleotide [T][T][T] 0 53 + 72 [TTT]A[TTTTTTTTT]A[T-TTTT] indel/deletion,indel/deletion A,A 4,14 2 >calJac1 532 hg18 chr22 16504097 16504832 panTro2 chr22 16544415 16545148 ponAbe2 chr22 14274080 14274812 rheMac2 chr10 62337257 62338048 calJac1 Contig1262 5182 5925 mononucleotide [T][T] 0 57 + 67 [TTTTTTTTT]C[T] indel/deletion C 10 1 ->ponAbe2 532 hg18 chr22 16504097 16504832 panTro2 chr22 16544415 16545148 ponAbe2 chr22 14274080 14274812 rheMac2 chr10 62337257 62338048 calJac1 Contig1262 5182 5925 mononucleotide T 4 203 + 211 TTTtttttt >rheMac2 532 hg18 chr22 16504097 16504832 panTro2 chr22 16544415 16545148 ponAbe2 chr22 14274080 14274812 rheMac2 chr10 62337257 62338048 calJac1 Contig1262 5182 5925 mononucleotide T 11 203 + 211 TTTtttttt ->hg18 532 hg18 chr22 16504097 16504832 panTro2 chr22 16544415 16545148 ponAbe2 chr22 14274080 14274812 rheMac2 chr10 62337257 62338048 calJac1 Contig1262 5182 5925 mononucleotide [t][T] 7 473 + 569 [t]g----------------------------------------------------------------------------[ttttttttttttttttttt] indel/deletion g 2 1 >panTro2 532 hg18 chr22 16504097 16504832 panTro2 chr22 16544415 16545148 ponAbe2 chr22 14274080 14274812 rheMac2 chr10 62337257 62338048 calJac1 Contig1262 5182 5925 mononucleotide [T][T][T] 7 473 + 569 [t]g------------------------------------------------------------------------------[tt]g[tttttttttttttt] indel/deletion,indel/deletion G,G 2,5 2 >ponAbe2 532 hg18 chr22 16504097 16504832 panTro2 chr22 16544415 16545148 ponAbe2 chr22 14274080 14274812 rheMac2 chr10 62337257 62338048 calJac1 Contig1262 5182 5925 mononucleotide [T][T][T] 7 473 + 569 [t]g------------------------------------------------------------------------------[ttt]g[ttttttttttttt] indel/deletion,indel/deletion G,G 2,6 2 >rheMac2 532 hg18 chr22 16504097 16504832 panTro2 chr22 16544415 16545148 ponAbe2 chr22 14274080 14274812 rheMac2 chr10 62337257 62338048 calJac1 Contig1262 5182 5925 mononucleotide [t][T][T][T] 14 473 + 490 [t]g[tttttttTTT]C[TTT]G[T] indel/deletion,indel/deletion,indel/deletion g,C,G 2,13,17 3 >rheMac2 532 hg18 chr22 16504097 16504832 panTro2 chr22 16544415 16545148 ponAbe2 chr22 14274080 14274812 rheMac2 chr10 62337257 62338048 calJac1 Contig1262 5182 5925 mononucleotide [T][T][T][t][T] 14 533 + 569 [TT]C[TT]C[Tttt]c[tttt]c[ttttttttttttttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion C,C,c,c 3,6,11,16 4 ->rheMac2 533 hg18 chr22 16505345 16505674 panTro2 chr22 16545661 16545991 ponAbe2 chr22 14275322 14275656 rheMac2 chr10 62340175 62340491 calJac1 Contig1262 6374 6702 mononucleotide T 0 1 + 18 tttttttttttttttttt >hg18 533 hg18 chr22 16505345 16505674 panTro2 chr22 16545661 16545991 ponAbe2 chr22 14275322 14275656 rheMac2 chr10 62340175 62340491 calJac1 Contig1262 6374 6702 mononucleotide T 0 19 + 31 ttttttttttttt >panTro2 533 hg18 chr22 16505345 16505674 panTro2 chr22 16545661 16545991 ponAbe2 chr22 14275322 14275656 rheMac2 chr10 62340175 62340491 calJac1 Contig1262 6374 6702 mononucleotide T 0 19 + 31 ttttttttttttt >ponAbe2 533 hg18 chr22 16505345 16505674 panTro2 chr22 16545661 16545991 ponAbe2 chr22 14275322 14275656 rheMac2 chr10 62340175 62340491 calJac1 Contig1262 6374 6702 mononucleotide T 0 19 + 36 tttttttttttttttttt ->panTro2 533 hg18 chr22 16505345 16505674 panTro2 chr22 16545661 16545991 ponAbe2 chr22 14275322 14275656 rheMac2 chr10 62340175 62340491 calJac1 Contig1262 6374 6702 mononucleotide [T][t] 5 187 + 197 [ttttttttt]g[t] indel/deletion g 10 1 ->calJac1 534 hg18 chr22 16505674 16506062 panTro2 chr22 16545991 16546379 ponAbe2 chr22 14275656 14276044 rheMac2 chr10 62340491 62340876 calJac1 Contig1262 6702 6876 mononucleotide T 0 1 + 27 tt-----ttt---------tttttttt ->hg18 534 hg18 chr22 16505674 16506062 panTro2 chr22 16545991 16546379 ponAbe2 chr22 14275656 14276044 rheMac2 chr10 62340491 62340876 calJac1 Contig1262 6702 6876 mononucleotide T 5 382 + 392 ttttttttttt >panTro2 534 hg18 chr22 16505674 16506062 panTro2 chr22 16545991 16546379 ponAbe2 chr22 14275656 14276044 rheMac2 chr10 62340491 62340876 calJac1 Contig1262 6702 6876 mononucleotide T 4 382 + 391 tttttttttt >ponAbe2 534 hg18 chr22 16505674 16506062 panTro2 chr22 16545991 16546379 ponAbe2 chr22 14275656 14276044 rheMac2 chr10 62340491 62340876 calJac1 Contig1262 6702 6876 mononucleotide T 4 382 + 391 tttttttttt >rheMac2 534 hg18 chr22 16505674 16506062 panTro2 chr22 16545991 16546379 ponAbe2 chr22 14275656 14276044 rheMac2 chr10 62340491 62340876 calJac1 Contig1262 6702 6876 mononucleotide T 6 382 + 390 ttttttttt ->calJac1 535 hg18 chr22 16506062 16506504 panTro2 chr22 16546379 16546825 ponAbe2 chr22 14276044 14276494 rheMac2 chr10 62340876 62341282 calJac1 Contig1262 6876 7301 mononucleotide T 13 118 + 126 TTTTTTTTT ->calJac1 535 hg18 chr22 16506062 16506504 panTro2 chr22 16546379 16546825 ponAbe2 chr22 14276044 14276494 rheMac2 chr10 62340876 62341282 calJac1 Contig1262 6876 7301 mononucleotide A 14 235 + 243 AAAAAAAAA ->hg18 535 hg18 chr22 16506062 16506504 panTro2 chr22 16546379 16546825 ponAbe2 chr22 14276044 14276494 rheMac2 chr10 62340876 62341282 calJac1 Contig1262 6876 7301 trinucleotide [TGT][TTG] 10 307 + 324 [TGTT][TTGTTGTTGTTGTT] indel/deletion 5 1 >panTro2 535 hg18 chr22 16506062 16506504 panTro2 chr22 16546379 16546825 ponAbe2 chr22 14276044 14276494 rheMac2 chr10 62340876 62341282 calJac1 Contig1262 6876 7301 trinucleotide [TGT][TTG] 6 307 + 324 [TGTT][TTGTTGTTGTTGTT] indel/deletion 5 1 >ponAbe2 535 hg18 chr22 16506062 16506504 panTro2 chr22 16546379 16546825 ponAbe2 chr22 14276044 14276494 rheMac2 chr10 62340876 62341282 calJac1 Contig1262 6876 7301 trinucleotide [TGT][TTG] 6 307 + 324 [TGTT][TTGTTGTTGTTGTT] indel/deletion 5 1 >rheMac2 535 hg18 chr22 16506062 16506504 panTro2 chr22 16546379 16546825 ponAbe2 chr22 14276044 14276494 rheMac2 chr10 62340876 62341282 calJac1 Contig1262 6876 7301 mononucleotide T 9 307 + 363 tttt-----------------------------------tttttttttttttttttt >hg18 535 hg18 chr22 16506062 16506504 panTro2 chr22 16546379 16546825 ponAbe2 chr22 14276044 14276494 rheMac2 chr10 62340876 62341282 calJac1 Contig1262 6876 7301 tetranucleotide [ttat][TTTA] 10 337 + 357 [tttat]----[tttatttattta] indel/deletion 6 1 >panTro2 535 hg18 chr22 16506062 16506504 panTro2 chr22 16546379 16546825 ponAbe2 chr22 14276044 14276494 rheMac2 chr10 62340876 62341282 calJac1 Contig1262 6876 7301 tetranucleotide [ttat][TTTA] 6 337 + 357 [tttat]----[tttatttattta] indel/deletion 6 1 >ponAbe2 535 hg18 chr22 16506062 16506504 panTro2 chr22 16546379 16546825 ponAbe2 chr22 14276044 14276494 rheMac2 chr10 62340876 62341282 calJac1 Contig1262 6876 7301 tetranucleotide [ttat][TTTA] 6 337 + 357 [tttat][tttatttatttattta] indel/deletion 6 1 >calJac1 535 hg18 chr22 16506062 16506504 panTro2 chr22 16546379 16546825 ponAbe2 chr22 14276044 14276494 rheMac2 chr10 62340876 62341282 calJac1 Contig1262 6876 7301 mononucleotide T 14 339 + 363 ttt----ttt---------tttttt ->rheMac2 536 hg18 chr22 16506504 16506848 panTro2 chr22 16546825 16547169 ponAbe2 chr22 14276494 14276835 rheMac2 chr10 62341302 62341711 calJac1 Contig1262 7320 7674 trinucleotide [GTT][GTT] 1 190 + 211 [TTGTTGTTGTTGTTGTT]AA[GTT] indel/deletion AA 18 1 ->rheMac2 536 hg18 chr22 16506504 16506848 panTro2 chr22 16546825 16547169 ponAbe2 chr22 14276494 14276835 rheMac2 chr10 62341302 62341711 calJac1 Contig1262 7320 7674 tetranucleotide [TTTA][TTTA] 1 228 + 249 [TTTA]At[tttatttatttattta] indel/deletion At 5 1 ->hg18 539 hg18 chr22 16517180 16517490 panTro2 chr22 16558889 16559199 ponAbe2 chr22 14287600 14287895 rheMac2 chr10 62352035 62352342 calJac1 Contig1262 9345 9642 mononucleotide.mononucleotide.mononucleotide [T][T][t][t].[t][T].[t][T] 0 1 + 26 [TCtttttttttcttctgttttttttt] indel/deletion,indel/deletion,indel/deletion.indel/deletion.indel/deletion C,c,c.g.g 2,12,15.2.2 3.1.1 1.16.16 16.26.26 [T]C[TTTTTTTTT]c[tt]c[t].[t]g[TTTTTTTTT].[t]g[TTTTTTTTT] >ponAbe2 539 hg18 chr22 16517180 16517490 panTro2 chr22 16558889 16559199 ponAbe2 chr22 14287600 14287895 rheMac2 chr10 62352035 62352342 calJac1 Contig1262 9345 9642 mononucleotide T 0 1 + 26 ttttt------------ttttttttt >rheMac2 539 hg18 chr22 16517180 16517490 panTro2 chr22 16558889 16559199 ponAbe2 chr22 14287600 14287895 rheMac2 chr10 62352035 62352342 calJac1 Contig1262 9345 9642 mononucleotide [T][T] 0 7 + 26 [T]C[tttttt---ttttttttt] indel/deletion C 2 1 >panTro2 539 hg18 chr22 16517180 16517490 panTro2 chr22 16558889 16559199 ponAbe2 chr22 14287600 14287895 rheMac2 chr10 62352035 62352342 calJac1 Contig1262 9345 9642 mononucleotide [t][T] 0 16 + 26 [t]g[ttttttttt] indel/deletion g 2 1 ->rheMac2 543 hg18 chr22 16518688 16519114 panTro2 chr22 16560397 16560794 ponAbe2 chr22 14289106 14289525 rheMac2 chr10 62353556 62353951 calJac1 Contig1262 10782 11185 tetranucleotide [caaa][AAAC] 4 322 + 341 [caaa][aaacaaacaaacaaac] indel/deletion 5 1 >hg18 543 hg18 chr22 16518688 16519114 panTro2 chr22 16560397 16560794 ponAbe2 chr22 14289106 14289525 rheMac2 chr10 62353556 62353951 calJac1 Contig1262 10782 11185 mononucleotide [A][a] 5 323 + 338 [aaaaaaaaa-aaaa]t[a] indel/deletion t 14 1 >panTro2 543 hg18 chr22 16518688 16519114 panTro2 chr22 16560397 16560794 ponAbe2 chr22 14289106 14289525 rheMac2 chr10 62353556 62353951 calJac1 Contig1262 10782 11185 mononucleotide A 5 323 + 331 aaaaaaaaa >calJac1 543 hg18 chr22 16518688 16519114 panTro2 chr22 16560397 16560794 ponAbe2 chr22 14289106 14289525 rheMac2 chr10 62353556 62353951 calJac1 Contig1262 10782 11185 mononucleotide [A][a][A] 6 323 + 355 [aaaaaaaaaaaaaa-------aaaaaa]g[aa]T[AA] indel/deletion,indel/deletion g,T 21,24 2 ->ponAbe2 543 hg18 chr22 16518688 16519114 panTro2 chr22 16560397 16560794 ponAbe2 chr22 14289106 14289525 rheMac2 chr10 62353556 62353951 calJac1 Contig1262 10782 11185 mononucleotide.mononucleotide A.[T][T] 4 388 + 412 [AAAAA--AAAAGTAttttttttttt] NA.indel/deletion NA.A NA.2 NA.1 384.394 392.406 AAAAAAAAA.[T]A[TTTTTTTTTTT] >rheMac2 543 hg18 chr22 16518688 16519114 panTro2 chr22 16560397 16560794 ponAbe2 chr22 14289106 14289525 rheMac2 chr10 62353556 62353951 calJac1 Contig1262 10782 11185 mononucleotide A 6 388 + 401 AAAAAAAAAAAAAA ->hg18 543 hg18 chr22 16518688 16519114 panTro2 chr22 16560397 16560794 ponAbe2 chr22 14289106 14289525 rheMac2 chr10 62353556 62353951 calJac1 Contig1262 10782 11185 mononucleotide [T][T][T] 15 421 + 441 [TTTT]A[TT]C[ttttttttttttt] indel/deletion,indel/deletion A,C 5,8 2 ->calJac1 546 hg18 chr22 16525581 16525872 panTro2 chr22 16567300 16567586 ponAbe2 chr22 14296352 14296641 rheMac2 chr10 62358193 62358315 calJac1 Contig1262 16877 17166 tetranucleotide AAAT 0 1 + 28 aaat--aaata-------aataaataaa ->hg18 549 hg18 chr22 16526330 16526629 panTro2 chr22 16568044 16568341 ponAbe2 chr22 14297096 14297411 rheMac2 chr10 62358769 62359056 calJac1 Contig1262 19185 19488 mononucleotide T 4 124 + 141 tttttttttttttttttt >panTro2 549 hg18 chr22 16526330 16526629 panTro2 chr22 16568044 16568341 ponAbe2 chr22 14297096 14297411 rheMac2 chr10 62358769 62359056 calJac1 Contig1262 19185 19488 mononucleotide T 4 124 + 138 ttttttttttttttt >ponAbe2 549 hg18 chr22 16526330 16526629 panTro2 chr22 16568044 16568341 ponAbe2 chr22 14297096 14297411 rheMac2 chr10 62358769 62359056 calJac1 Contig1262 19185 19488 mononucleotide T 4 124 + 146 ttttttttttttttttttttttt >calJac1 549 hg18 chr22 16526330 16526629 panTro2 chr22 16568044 16568341 ponAbe2 chr22 14297096 14297411 rheMac2 chr10 62358769 62359056 calJac1 Contig1262 19185 19488 mononucleotide [t][T] 2 124 + 138 [ttt]c[ttttttttttt] indel/deletion c 4 1 ->hg18 549 hg18 chr22 16526330 16526629 panTro2 chr22 16568044 16568341 ponAbe2 chr22 14297096 14297411 rheMac2 chr10 62358769 62359056 calJac1 Contig1262 19185 19488 mononucleotide T 19 309 + 318 tttttttttt >panTro2 549 hg18 chr22 16526330 16526629 panTro2 chr22 16568044 16568341 ponAbe2 chr22 14297096 14297411 rheMac2 chr10 62358769 62359056 calJac1 Contig1262 19185 19488 mononucleotide T 22 309 + 319 ttttttttttt >ponAbe2 549 hg18 chr22 16526330 16526629 panTro2 chr22 16568044 16568341 ponAbe2 chr22 14297096 14297411 rheMac2 chr10 62358769 62359056 calJac1 Contig1262 19185 19488 mononucleotide T 6 309 + 321 ttttttttttttt >rheMac2 549 hg18 chr22 16526330 16526629 panTro2 chr22 16568044 16568341 ponAbe2 chr22 14297096 14297411 rheMac2 chr10 62358769 62359056 calJac1 Contig1262 19185 19488 mononucleotide T 45 309 + 332 tttttttttttttttttttttttt ->rheMac2 551 hg18 chr22 16526901 16527003 panTro2 chr22 16568613 16568715 ponAbe2 chr22 14297682 14297786 rheMac2 chr10 62359326 62359428 calJac1 Contig1262 20223 20322 mononucleotide [T][T] 0 15 + 30 [tttttttttt]a[ttttt] insertion a 11 1 ->ponAbe2 552 hg18 chr22 16533507 16533842 panTro2 chr22 16575228 16575567 ponAbe2 chr22 14311893 14312230 rheMac2 chr10 62368969 62369303 calJac1 Contig1262 35562 35884 mononucleotide [A][a][A] 3 224 + 242 [AAAA]C[aaaa]c[aaaaaaaaa] indel/deletion,indel/deletion C,c 5,10 2 ->calJac1 554 hg18 chr22 16534577 16535384 panTro2 chr22 16576297 16577104 ponAbe2 chr22 14314037 14314845 rheMac2 chr10 62369752 62370561 calJac1 Contig1262 36303 37168 tetranucleotide [gttt][TTTG][ttgt] 0 215 + 244 [gttt]ct[tttgtttgtttgtttgttt][ttgtt] indel/deletion,indel/deletion ct, 5,26 2 ->hg18 561 hg18 chr22 16538112 16539510 panTro2 chr22 16579843 16581238 ponAbe2 chr22 14318650 14320069 rheMac2 chr10 62374666 62376068 calJac1 Contig1262 39909 41293 mononucleotide [A][A][a] 51 1005 + 1021 [aaaaa]c[aaaaaaaaa]t[a] insertion,indel/deletion c,t 6,16 2 ->panTro2 564 hg18 chr22 16540161 16540379 panTro2 chr22 16581888 16582107 ponAbe2 chr22 14320739 14320959 rheMac2 chr10 62376709 62376927 calJac1 Contig1262 44820 45017 mononucleotide [A][A] 5 180 + 194 [aaaaaaaaa]g[aaaaa] insertion g 10 1 >calJac1 564 hg18 chr22 16540161 16540379 panTro2 chr22 16581888 16582107 ponAbe2 chr22 14320739 14320959 rheMac2 chr10 62376709 62376927 calJac1 Contig1262 44820 45017 mononucleotide A 5 180 + 191 aaaaaaaaaaaa ->hg18 565 hg18 chr22 16540485 16540654 panTro2 chr22 16582213 16582386 ponAbe2 chr22 14321066 14321225 rheMac2 chr10 62377033 62377207 calJac1 Contig1262 45017 45188 mononucleotide [A][A] 4 153 + 174 [aaaaaaaaaa]----c[aaaaaaa] insertion c 11 1 >panTro2 565 hg18 chr22 16540485 16540654 panTro2 chr22 16582213 16582386 ponAbe2 chr22 14321066 14321225 rheMac2 chr10 62377033 62377207 calJac1 Contig1262 45017 45188 mononucleotide [A][A] 4 153 + 174 [aaaaaaaaaaaaa]c[aaaaaaaa] insertion c 14 1 >ponAbe2 565 hg18 chr22 16540485 16540654 panTro2 chr22 16582213 16582386 ponAbe2 chr22 14321066 14321225 rheMac2 chr10 62377033 62377207 calJac1 Contig1262 45017 45188 mononucleotide A 15 153 + 174 aaaaaaaaaaa---aaaaaaaa >rheMac2 565 hg18 chr22 16540485 16540654 panTro2 chr22 16582213 16582386 ponAbe2 chr22 14321066 14321225 rheMac2 chr10 62377033 62377207 calJac1 Contig1262 45017 45188 mononucleotide A 0 153 + 174 aaaaaaaaaaa---aaaaaaaa ->hg18 566 hg18 chr22 16541719 16542539 panTro2 chr22 16583451 16584266 ponAbe2 chr22 14322310 14323148 rheMac2 chr10 62377369 62378184 calJac1 Contig1262 46795 47594 mononucleotide [T][T] 12 322 + 347 [T]C[tttttttttttttttttttttttt] indel/deletion C 2 1 >panTro2 566 hg18 chr22 16541719 16542539 panTro2 chr22 16583451 16584266 ponAbe2 chr22 14322310 14323148 rheMac2 chr10 62377369 62378184 calJac1 Contig1262 46795 47594 mononucleotide [T][T] 12 322 + 347 [T]C-------[ttttttttttttttttt] indel/deletion C 2 1 >ponAbe2 566 hg18 chr22 16541719 16542539 panTro2 chr22 16583451 16584266 ponAbe2 chr22 14322310 14323148 rheMac2 chr10 62377369 62378184 calJac1 Contig1262 46795 47594 mononucleotide [T][T] 2 322 + 347 [T]C-----[ttttttttttttttttttt] indel/deletion C 2 1 >rheMac2 566 hg18 chr22 16541719 16542539 panTro2 chr22 16583451 16584266 ponAbe2 chr22 14322310 14323148 rheMac2 chr10 62377369 62378184 calJac1 Contig1262 46795 47594 mononucleotide T 24 337 + 347 ttttttttttt ->hg18 569 hg18 chr22 16550188 16550407 panTro2 chr22 16592110 16592355 ponAbe2 chr22 14328008 14328231 rheMac2 chr10 62386783 62386999 calJac1 Contig1262 52935 53143 trinucleotide TAT 4 87 + 131 tattattattattatta--------------------------tt >panTro2 569 hg18 chr22 16550188 16550407 panTro2 chr22 16592110 16592355 ponAbe2 chr22 14328008 14328231 rheMac2 chr10 62386783 62386999 calJac1 Contig1262 52935 53143 mononucleotide.trinucleotide [t][t][t][t][t][t][t][t][t][t][t][t][t][t][t][T].TAT 4 87 + 142 [tattattattattattattattattattattattattattattttctttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion.NA a,a,a,a,a,a,a,a,a,a,a,a,a,a,c.NA 2,5,8,11,14,17,20,23,26,29,32,35,38,41,46.NA 15.NA 83.83 138.125 [t]a[tt]a[tt]a[tt]a[tt]a[tt]a[tt]a[tt]a[tt]a[tt]a[tt]a[tt]a[tt]a[tt]a[tttt]c[TTTTTTTTTT].TATTATTATTATTATTATTATTATTATTATTATTATTATTATT >ponAbe2 569 hg18 chr22 16550188 16550407 panTro2 chr22 16592110 16592355 ponAbe2 chr22 14328008 14328231 rheMac2 chr10 62386783 62386999 calJac1 Contig1262 52935 53143 trinucleotide ATT 2 89 + 129 attattattatta--------------------------tt >rheMac2 569 hg18 chr22 16550188 16550407 panTro2 chr22 16592110 16592355 ponAbe2 chr22 14328008 14328231 rheMac2 chr10 62386783 62386999 calJac1 Contig1262 52935 53143 mononucleotide T 5 92 + 142 tttttttttt----------------------------ttttttttttttt ->hg18 571 hg18 chr22 16551199 16551635 panTro2 chr22 16593150 16593587 ponAbe2 chr22 14329048 14329492 rheMac2 chr10 62387777 62388223 calJac1 Contig1262 53591 54031 mononucleotide [T][T][T][T] 13 341 + 382 [T]A--------[TT]G[TT]G[tt-ttttt---------ttttttttt] indel/deletion,indel/deletion,indel/deletion A,G,G 2,5,8 3 >panTro2 571 hg18 chr22 16551199 16551635 panTro2 chr22 16593150 16593587 ponAbe2 chr22 14329048 14329492 rheMac2 chr10 62387777 62388223 calJac1 Contig1262 53591 54031 mononucleotide [T][T][T][T][T][T] 13 341 + 382 [T]A--------[TT]A[TT]A[TT]A[TT]A[tt---------ttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion A,A,A,A,A 2,5,8,11,14 5 >calJac1 571 hg18 chr22 16551199 16551635 panTro2 chr22 16593150 16593587 ponAbe2 chr22 14329048 14329492 rheMac2 chr10 62387777 62388223 calJac1 Contig1262 53591 54031 compound [ATTA][ATTT] 17 348 + 382 [aattaattaat-ta][att---------tatttattt] >rheMac2 571 hg18 chr22 16551199 16551635 panTro2 chr22 16593150 16593587 ponAbe2 chr22 14329048 14329492 rheMac2 chr10 62387777 62388223 calJac1 Contig1262 53591 54031 tetranucleotide [gttt][TTTG][tttg] 20 354 + 383 [ttgtt-t]t[tttgtttgtttgtttg]tt[tttg] indel/deletion,indel/deletion t,tt 7,24 2 >ponAbe2 571 hg18 chr22 16551199 16551635 panTro2 chr22 16593150 16593587 ponAbe2 chr22 14329048 14329492 rheMac2 chr10 62387777 62388223 calJac1 Contig1262 53591 54031 mononucleotide [T][T] 9 357 + 382 [T]C-----[t---------ttttttttt] indel/deletion C 2 1 ->rheMac2 577 hg18 chr22 16553329 16553545 panTro2 chr22 16595281 16595497 ponAbe2 chr22 14331248 14331480 rheMac2 chr10 62390274 62390488 calJac1 Contig1262 55994 56207 mononucleotide [A][a] 0 30 + 53 [aaa-aaaaaaaaaa---aa]g[aaaa] indel/deletion g 16 1 >ponAbe2 577 hg18 chr22 16553329 16553545 panTro2 chr22 16595281 16595497 ponAbe2 chr22 14331248 14331480 rheMac2 chr10 62390274 62390488 calJac1 Contig1262 55994 56207 mononucleotide [a][A] 0 32 + 42 [a]c[aaaaaaaaa] indel/deletion c 2 1 ->rheMac2 578 hg18 chr22 16553545 16553844 panTro2 chr22 16595497 16595792 ponAbe2 chr22 14331480 14331784 rheMac2 chr10 62390488 62390780 calJac1 Contig1262 56207 56504 tetranucleotide TTAT 8 240 + 265 TTA----TT----TATTTATTTAttt >hg18 578 hg18 chr22 16553545 16553844 panTro2 chr22 16595497 16595792 ponAbe2 chr22 14331480 14331784 rheMac2 chr10 62390488 62390780 calJac1 Contig1262 56207 56504 tetranucleotide [ATTT][attt] 5 243 + 272 [TTTATT----TATTTATTTAttt]taa[attt] indel/deletion taa 20 1 >panTro2 578 hg18 chr22 16553545 16553844 panTro2 chr22 16595497 16595792 ponAbe2 chr22 14331480 14331784 rheMac2 chr10 62390488 62390780 calJac1 Contig1262 56207 56504 tetranucleotide [ATTT][attt] 5 243 + 268 [TT----TATTTATTTAttt]taa[attt] indel/deletion taa 16 1 >ponAbe2 578 hg18 chr22 16553545 16553844 panTro2 chr22 16595497 16595792 ponAbe2 chr22 14331480 14331784 rheMac2 chr10 62390488 62390780 calJac1 Contig1262 56207 56504 tetranucleotide [TTTA][TATT][attt] 5 243 + 272 [TTTATTTAT]G[TATTTATTTAttt]taa[attt] indel/deletion,indel/deletion G,taa 10,24 2 >calJac1 578 hg18 chr22 16553545 16553844 panTro2 chr22 16595497 16595792 ponAbe2 chr22 14331480 14331784 rheMac2 chr10 62390488 62390780 calJac1 Contig1262 56207 56504 tetranucleotide [ATTT][attt] 7 246 + 272 [ATT----TATTTATTTAttt]taa[attt] indel/deletion taa 17 1 ->rheMac2 580 hg18 chr22 16554416 16554931 panTro2 chr22 16596362 16596876 ponAbe2 chr22 14332376 14332886 rheMac2 chr10 62391349 62391858 calJac1 Contig1262 56781 57286 mononucleotide [A][a][a] 0 1 + 18 [aaaaaaaaaaa]c[aaa]g[aa] indel/deletion,indel/deletion c,g 12,16 2 >hg18 580 hg18 chr22 16554416 16554931 panTro2 chr22 16596362 16596876 ponAbe2 chr22 14332376 14332886 rheMac2 chr10 62391349 62391858 calJac1 Contig1262 56781 57286 mononucleotide [A][a] 0 2 + 14 [aaaaaaaaaa]g[aa] indel/deletion g 11 1 >panTro2 580 hg18 chr22 16554416 16554931 panTro2 chr22 16596362 16596876 ponAbe2 chr22 14332376 14332886 rheMac2 chr10 62391349 62391858 calJac1 Contig1262 56781 57286 mononucleotide [A][a] 0 2 + 13 [aaaaaaaaa]g[aa] indel/deletion g 10 1 ->hg18 583 hg18 chr22 16556142 16556498 panTro2 chr22 16598074 16598427 ponAbe2 chr22 14334100 14334430 rheMac2 chr10 62392974 62393379 calJac1 Contig1262 58660 59052 mononucleotide T 0 1 + 20 tttttttttttttttttttt >panTro2 583 hg18 chr22 16556142 16556498 panTro2 chr22 16598074 16598427 ponAbe2 chr22 14334100 14334430 rheMac2 chr10 62392974 62393379 calJac1 Contig1262 58660 59052 mononucleotide T 0 1 + 17 ttttttttttttttttt >ponAbe2 583 hg18 chr22 16556142 16556498 panTro2 chr22 16598074 16598427 ponAbe2 chr22 14334100 14334430 rheMac2 chr10 62392974 62393379 calJac1 Contig1262 58660 59052 mononucleotide T 0 1 + 19 ttttttttttttttttttt >calJac1 583 hg18 chr22 16556142 16556498 panTro2 chr22 16598074 16598427 ponAbe2 chr22 14334100 14334430 rheMac2 chr10 62392974 62393379 calJac1 Contig1262 58660 59052 mononucleotide T 0 1 + 9 ttttttttt ->ponAbe2 584 hg18 chr22 16556498 16557328 panTro2 chr22 16598427 16599253 ponAbe2 chr22 14334430 14335274 rheMac2 chr10 62393379 62394211 calJac1 Contig1262 59292 60057 mononucleotide T 0 1 + 32 tt---------------------ttttttttt >calJac1 584 hg18 chr22 16556498 16557328 panTro2 chr22 16598427 16599253 ponAbe2 chr22 14334430 14335274 rheMac2 chr10 62393379 62394211 calJac1 Contig1262 59292 60057 tetranucleotide TCTT 0 1 + 16 TCtttctttctttctt >hg18 584 hg18 chr22 16556498 16557328 panTro2 chr22 16598427 16599253 ponAbe2 chr22 14334430 14335274 rheMac2 chr10 62393379 62394211 calJac1 Contig1262 59292 60057 mononucleotide [T][T] 0 2 + 32 [ttt----------------tt]c[ttttttttt] insertion c 6 1 >panTro2 584 hg18 chr22 16556498 16557328 panTro2 chr22 16598427 16599253 ponAbe2 chr22 14334430 14335274 rheMac2 chr10 62393379 62394211 calJac1 Contig1262 59292 60057 mononucleotide T 0 2 + 32 ttt-------------------ttttttttt ->hg18 584 hg18 chr22 16556498 16557328 panTro2 chr22 16598427 16599253 ponAbe2 chr22 14334430 14335274 rheMac2 chr10 62393379 62394211 calJac1 Contig1262 59292 60057 mononucleotide [t][T][t] 30 209 + 222 [t]a-[ttttttttt]c[t] indel/deletion,indel/deletion a,c 2,12 2 >panTro2 584 hg18 chr22 16556498 16557328 panTro2 chr22 16598427 16599253 ponAbe2 chr22 14334430 14335274 rheMac2 chr10 62393379 62394211 calJac1 Contig1262 59292 60057 mononucleotide [t][T][t] 33 209 + 222 [t]a[tttttttttt]c[t] indel/deletion,indel/deletion a,c 2,13 2 >ponAbe2 584 hg18 chr22 16556498 16557328 panTro2 chr22 16598427 16599253 ponAbe2 chr22 14334430 14335274 rheMac2 chr10 62393379 62394211 calJac1 Contig1262 59292 60057 mononucleotide [t][T][t] 25 209 + 222 [t]a[tttttttttt]c[t] indel/deletion,indel/deletion a,c 2,13 2 ->hg18 584 hg18 chr22 16556498 16557328 panTro2 chr22 16598427 16599253 ponAbe2 chr22 14334430 14335274 rheMac2 chr10 62393379 62394211 calJac1 Contig1262 59292 60057 compound [A][T] 71 846 + 868 [aaa---aaaaaaaa][TTTTTTTTT] >panTro2 584 hg18 chr22 16556498 16557328 panTro2 chr22 16598427 16599253 ponAbe2 chr22 14334430 14335274 rheMac2 chr10 62393379 62394211 calJac1 Contig1262 59292 60057 compound [A][T] 73 846 + 876 [aaaaa---aaaaaaaa][ttttttttttttttt] >rheMac2 584 hg18 chr22 16556498 16557328 panTro2 chr22 16598427 16599253 ponAbe2 chr22 14334430 14335274 rheMac2 chr10 62393379 62394211 calJac1 Contig1262 59292 60057 mononucleotide T 70 862 + 872 ttttttttttt ->ponAbe2 586 hg18 chr22 16558385 16558660 panTro2 chr22 16600310 16600585 ponAbe2 chr22 14336342 14336620 rheMac2 chr10 62394465 62394745 calJac1 Contig1262 60297 60572 mononucleotide A 0 1 + 9 aaaaaaaaa ->panTro2 593 hg18 chr22 16561310 16561630 panTro2 chr22 16603763 16604079 ponAbe2 chr22 14339540 14339852 rheMac2 chr10 62397392 62397701 calJac1 Contig1262 62911 63330 mononucleotide A 0 12 + 27 aaaaaaaaaaaaaaaa >ponAbe2 593 hg18 chr22 16561310 16561630 panTro2 chr22 16603763 16604079 ponAbe2 chr22 14339540 14339852 rheMac2 chr10 62397392 62397701 calJac1 Contig1262 62911 63330 mononucleotide [A][a] 0 12 + 28 [aaaaaaaaaaaaa]t[aaa] indel/deletion t 14 1 >calJac1 593 hg18 chr22 16561310 16561630 panTro2 chr22 16603763 16604079 ponAbe2 chr22 14339540 14339852 rheMac2 chr10 62397392 62397701 calJac1 Contig1262 62911 63330 mononucleotide A 1 12 + 20 aaaaaaaaa >hg18 593 hg18 chr22 16561310 16561630 panTro2 chr22 16603763 16604079 ponAbe2 chr22 14339540 14339852 rheMac2 chr10 62397392 62397701 calJac1 Contig1262 62911 63330 mononucleotide A 0 13 + 33 aaaaaaaaaaaaaaaaaaaaa >rheMac2 593 hg18 chr22 16561310 16561630 panTro2 chr22 16603763 16604079 ponAbe2 chr22 14339540 14339852 rheMac2 chr10 62397392 62397701 calJac1 Contig1262 62911 63330 mononucleotide A 10 23 + 33 aaaaaaaaaaa ->calJac1 593 hg18 chr22 16561310 16561630 panTro2 chr22 16603763 16604079 ponAbe2 chr22 14339540 14339852 rheMac2 chr10 62397392 62397701 calJac1 Contig1262 62911 63330 mononucleotide [a][A][a] 24 189 + 209 [a]g[aaaaaaaaaaaaaa]g[aaaa] indel/deletion,indel/deletion g,g 2,17 2 ->ponAbe2 596 hg18 chr22 16562001 16562778 panTro2 chr22 16604450 16605227 ponAbe2 chr22 14340220 14340997 rheMac2 chr10 62398384 62399158 calJac1 Contig1262 63910 64684 mononucleotide [a][A] 4 342 + 354 [aa]g-[aaaaaaaaa] indel/deletion g 3 1 >rheMac2 596 hg18 chr22 16562001 16562778 panTro2 chr22 16604450 16605227 ponAbe2 chr22 14340220 14340997 rheMac2 chr10 62398384 62399158 calJac1 Contig1262 63910 64684 mononucleotide [A][A] 8 342 + 354 [AA]G[AAAAAAAAAA] indel/deletion G 3 1 ->hg18 600 hg18 chr22 16563271 16563508 panTro2 chr22 16605721 16605959 ponAbe2 chr22 14341490 14341724 rheMac2 chr10 62399652 62399889 calJac1 Contig1262 65174 65403 tetranucleotide [GTTT][GTTT] 0 130 + 148 [GTTT][TTTGTTTGTTTGTTT] indel/deletion 5 1 >panTro2 600 hg18 chr22 16563271 16563508 panTro2 chr22 16605721 16605959 ponAbe2 chr22 14341490 14341724 rheMac2 chr10 62399652 62399889 calJac1 Contig1262 65174 65403 tetranucleotide [GTTT][GTTT] 0 130 + 148 [GTTT][TTTGTTTGTTTGTTT] indel/deletion 5 1 >ponAbe2 600 hg18 chr22 16563271 16563508 panTro2 chr22 16605721 16605959 ponAbe2 chr22 14341490 14341724 rheMac2 chr10 62399652 62399889 calJac1 Contig1262 65174 65403 tetranucleotide [GTTT][GTTT] 0 130 + 148 [GTTT][TTTGTTTGTTTGTTT] indel/deletion 5 1 >rheMac2 600 hg18 chr22 16563271 16563508 panTro2 chr22 16605721 16605959 ponAbe2 chr22 14341490 14341724 rheMac2 chr10 62399652 62399889 calJac1 Contig1262 65174 65403 tetranucleotide [GTTT][TTGT] 0 130 + 146 [GTTT][TTTGTTTGTTTGT] indel/deletion 5 1 ->hg18 603 hg18 chr22 16564401 16564715 panTro2 chr22 16606861 16607172 ponAbe2 chr22 14342150 14342459 rheMac2 chr10 62401093 62401394 calJac1 Contig1262 67121 67427 mononucleotide A 9 290 + 307 aaaaaaaaaaaaaaaaaa >panTro2 603 hg18 chr22 16564401 16564715 panTro2 chr22 16606861 16607172 ponAbe2 chr22 14342150 14342459 rheMac2 chr10 62401093 62401394 calJac1 Contig1262 67121 67427 mononucleotide A 9 290 + 304 aaaaaaaaaaaaaaa >ponAbe2 603 hg18 chr22 16564401 16564715 panTro2 chr22 16606861 16607172 ponAbe2 chr22 14342150 14342459 rheMac2 chr10 62401093 62401394 calJac1 Contig1262 67121 67427 mononucleotide [A][a] 8 290 + 305 [aaaaaaaaaaa]g[aaaa] indel/deletion g 12 1 >rheMac2 603 hg18 chr22 16564401 16564715 panTro2 chr22 16606861 16607172 ponAbe2 chr22 14342150 14342459 rheMac2 chr10 62401093 62401394 calJac1 Contig1262 67121 67427 mononucleotide [A][A][a] 9 290 + 313 [aaaaaaaaa]g[aaaaaa]g[a----aa] insertion,indel/deletion g,g 10,17 2 >calJac1 603 hg18 chr22 16564401 16564715 panTro2 chr22 16606861 16607172 ponAbe2 chr22 14342150 14342459 rheMac2 chr10 62401093 62401394 calJac1 Contig1262 67121 67427 trinucleotide TAA 11 304 + 321 aaTAATAATAATA----A ->rheMac2 605 hg18 chr22 16565196 16565942 panTro2 chr22 16607653 16608404 ponAbe2 chr22 14342939 14343692 rheMac2 chr10 62401875 62402627 calJac1 Contig1262 67882 68633 trinucleotide [GTT][TTG][ttg] 0 3 + 24 [GTT]CA[ttgttgttgttgtt][ttg] indel/deletion,indel/deletion CA, 4,20 2 >ponAbe2 605 hg18 chr22 16565196 16565942 panTro2 chr22 16607653 16608404 ponAbe2 chr22 14342939 14343692 rheMac2 chr10 62401875 62402627 calJac1 Contig1262 67882 68633 trinucleotide TTG 0 5 + 16 ttgttgttgttg ->hg18 605 hg18 chr22 16565196 16565942 panTro2 chr22 16607653 16608404 ponAbe2 chr22 14342939 14343692 rheMac2 chr10 62401875 62402627 calJac1 Contig1262 67882 68633 trinucleotide [tat][ATT] 14 220 + 240 [tat]gta[attattattattatt] indel/deletion gta 4 1 >panTro2 605 hg18 chr22 16565196 16565942 panTro2 chr22 16607653 16608404 ponAbe2 chr22 14342939 14343692 rheMac2 chr10 62401875 62402627 calJac1 Contig1262 67882 68633 trinucleotide [tat][ATT] 7 220 + 240 [tat]gta---[attattattatt] indel/deletion gta 4 1 >ponAbe2 605 hg18 chr22 16565196 16565942 panTro2 chr22 16607653 16608404 ponAbe2 chr22 14342939 14343692 rheMac2 chr10 62401875 62402627 calJac1 Contig1262 67882 68633 trinucleotide [tat][ATT] 8 220 + 238 [tat]gtg[attattattatta] indel/deletion gtg 4 1 >rheMac2 605 hg18 chr22 16565196 16565942 panTro2 chr22 16607653 16608404 ponAbe2 chr22 14342939 14343692 rheMac2 chr10 62401875 62402627 calJac1 Contig1262 67882 68633 trinucleotide [tat][ATT] 8 220 + 240 [tat]gta[attattattattatt] indel/deletion gta 4 1 ->hg18 605 hg18 chr22 16565196 16565942 panTro2 chr22 16607653 16608404 ponAbe2 chr22 14342939 14343692 rheMac2 chr10 62401875 62402627 calJac1 Contig1262 67882 68633 dinucleotide TA 14 443 + 454 atata-tatata >panTro2 605 hg18 chr22 16565196 16565942 panTro2 chr22 16607653 16608404 ponAbe2 chr22 14342939 14343692 rheMac2 chr10 62401875 62402627 calJac1 Contig1262 67882 68633 dinucleotide TA 10 443 + 454 atata-tatata >ponAbe2 605 hg18 chr22 16565196 16565942 panTro2 chr22 16607653 16608404 ponAbe2 chr22 14342939 14343692 rheMac2 chr10 62401875 62402627 calJac1 Contig1262 67882 68633 dinucleotide TA 8 443 + 454 atata-tatata >rheMac2 605 hg18 chr22 16565196 16565942 panTro2 chr22 16607653 16608404 ponAbe2 chr22 14342939 14343692 rheMac2 chr10 62401875 62402627 calJac1 Contig1262 67882 68633 dinucleotide AT 19 444 + 469 atatatatatatatatata-tatata ->ponAbe2 605 hg18 chr22 16565196 16565942 panTro2 chr22 16607653 16608404 ponAbe2 chr22 14342939 14343692 rheMac2 chr10 62401875 62402627 calJac1 Contig1262 67882 68633 trinucleotide [aca][CAA] 24 733 + 758 [caaca]gag[caaCAACAACAACAACAA] indel/deletion gag 6 1 >hg18 605 hg18 chr22 16565196 16565942 panTro2 chr22 16607653 16608404 ponAbe2 chr22 14342939 14343692 rheMac2 chr10 62401875 62402627 calJac1 Contig1262 67882 68633 compound [CAA][AT] 30 741 + 780 [caacaacaacaacaacaacaa]a[atata-------tatata] >panTro2 605 hg18 chr22 16565196 16565942 panTro2 chr22 16607653 16608404 ponAbe2 chr22 14342939 14343692 rheMac2 chr10 62401875 62402627 calJac1 Contig1262 67882 68633 compound [CAA][AT] 26 741 + 779 [caaCAACAACAACAACAA]-A[atatata-------tatat] >rheMac2 605 hg18 chr22 16565196 16565942 panTro2 chr22 16607653 16608404 ponAbe2 chr22 14342939 14343692 rheMac2 chr10 62401875 62402627 calJac1 Contig1262 67882 68633 compound [CAA][AT] 20 741 + 780 [caacaacaacaacaa][ata-tatatata-------tatata] >calJac1 605 hg18 chr22 16565196 16565942 panTro2 chr22 16607653 16608404 ponAbe2 chr22 14342939 14343692 rheMac2 chr10 62401875 62402627 calJac1 Contig1262 67882 68633 trinucleotide CAA 30 747 + 758 CAACAACAACAA ->hg18 606 hg18 chr22 16565942 16566238 panTro2 chr22 16609451 16609747 ponAbe2 chr22 14343692 14344001 rheMac2 chr10 62402627 62402898 calJac1 Contig1262 68639 69015 dinucleotide AC 0 1 + 38 acacacaca-------------------------caca >panTro2 606 hg18 chr22 16565942 16566238 panTro2 chr22 16609451 16609747 ponAbe2 chr22 14343692 14344001 rheMac2 chr10 62402627 62402898 calJac1 Contig1262 68639 69015 dinucleotide AC 0 1 + 38 acacacaca-------------------------caca >ponAbe2 606 hg18 chr22 16565942 16566238 panTro2 chr22 16609451 16609747 ponAbe2 chr22 14343692 14344001 rheMac2 chr10 62402627 62402898 calJac1 Contig1262 68639 69015 dinucleotide.dinucleotide.dinucleotide [AC][AC].TA.[CA][AC] 0 1 + 100 [acacacaca-------------------------aacacacacac--------------------------------------------gtatatatata] indel/substitution.NA.indel/substitution a.NA.a 10.NA.10 1.NA.1 1.22.1 20.31.20 [ACACACACA]a[ACACACACAC].TATATATATA.[ACACACACA]a[ACACACACAC] >calJac1 606 hg18 chr22 16565942 16566238 panTro2 chr22 16609451 16609747 ponAbe2 chr22 14343692 14344001 rheMac2 chr10 62402627 62402898 calJac1 Contig1262 68639 69015 dinucleotide [Ta][TA][AT][AT] 0 80 + 104 [tat]g[tatata][atatatatata]AC[AT] indel/deletion,indel/substitution,indel/deletion g,,AC 4,11,22 3 ->ponAbe2 607 hg18 chr22 16566238 16566992 panTro2 chr22 16609747 16610500 ponAbe2 chr22 14345322 14346076 rheMac2 chr10 62404563 62405302 calJac1 Contig1262 71605 72325 tetranucleotide CTTT 0 1 + 16 ctttctttctttcttt >hg18 607 hg18 chr22 16566238 16566992 panTro2 chr22 16609747 16610500 ponAbe2 chr22 14345322 14346076 rheMac2 chr10 62404563 62405302 calJac1 Contig1262 71605 72325 tetranucleotide CTTT 0 4 + 16 TCTTTCTTTCTTT >panTro2 607 hg18 chr22 16566238 16566992 panTro2 chr22 16609747 16610500 ponAbe2 chr22 14345322 14346076 rheMac2 chr10 62404563 62405302 calJac1 Contig1262 71605 72325 tetranucleotide CTTT 0 4 + 16 TCTTTCTTTCTTT ->hg18 607 hg18 chr22 16566238 16566992 panTro2 chr22 16609747 16610500 ponAbe2 chr22 14345322 14346076 rheMac2 chr10 62404563 62405302 calJac1 Contig1262 71605 72325 mononucleotide [t][T] 3 625 + 646 [tt]c---------[tttttttttt] indel/deletion c 3 1 >ponAbe2 607 hg18 chr22 16566238 16566992 panTro2 chr22 16609747 16610500 ponAbe2 chr22 14345322 14346076 rheMac2 chr10 62404563 62405302 calJac1 Contig1262 71605 72325 mononucleotide [t][T] 3 625 + 646 [tt]c---------[tttttttttt] indel/deletion c 3 1 >rheMac2 607 hg18 chr22 16566238 16566992 panTro2 chr22 16609747 16610500 ponAbe2 chr22 14345322 14346076 rheMac2 chr10 62404563 62405302 calJac1 Contig1262 71605 72325 mononucleotide [t][T] 28 625 + 646 [tt]c[ttttttttttttttttttt] indel/deletion c 3 1 ->hg18 608 hg18 chr22 16568240 16568498 panTro2 chr22 16611765 16612024 ponAbe2 chr22 14349636 14349897 rheMac2 chr10 62406066 62406325 calJac1 Contig1262 72911 73151 mononucleotide T 0 131 + 139 TTTTTTTTT >panTro2 608 hg18 chr22 16568240 16568498 panTro2 chr22 16611765 16612024 ponAbe2 chr22 14349636 14349897 rheMac2 chr10 62406066 62406325 calJac1 Contig1262 72911 73151 mononucleotide T 0 131 + 140 TTTTTTTTTT >ponAbe2 608 hg18 chr22 16568240 16568498 panTro2 chr22 16611765 16612024 ponAbe2 chr22 14349636 14349897 rheMac2 chr10 62406066 62406325 calJac1 Contig1262 72911 73151 mononucleotide T 0 131 + 139 TTTTTTTTT >rheMac2 608 hg18 chr22 16568240 16568498 panTro2 chr22 16611765 16612024 ponAbe2 chr22 14349636 14349897 rheMac2 chr10 62406066 62406325 calJac1 Contig1262 72911 73151 mononucleotide T 0 131 + 140 TTTTTTTTTT ->hg18 610 hg18 chr22 16568701 16570168 panTro2 chr22 16612225 16613669 ponAbe2 chr22 14350097 14351544 rheMac2 chr10 62406526 62407975 calJac1 Contig1262 73352 74833 mononucleotide [T][T] 2 394 + 411 [TT]G[TTTTTTTTTTTTTTT] indel/deletion G 3 1 >panTro2 610 hg18 chr22 16568701 16570168 panTro2 chr22 16612225 16613669 ponAbe2 chr22 14350097 14351544 rheMac2 chr10 62406526 62407975 calJac1 Contig1262 73352 74833 mononucleotide [T][T][T] 2 394 + 411 [TT]G--[TT]G[TTTTTTTTTT] indel/deletion,indel/deletion G,G 3,6 2 >rheMac2 610 hg18 chr22 16568701 16570168 panTro2 chr22 16612225 16613669 ponAbe2 chr22 14350097 14351544 rheMac2 chr10 62406526 62407975 calJac1 Contig1262 73352 74833 mononucleotide [T][T] 4 394 + 411 [TT]G----[TTTTTTTTTTT] indel/deletion G 3 1 >calJac1 610 hg18 chr22 16568701 16570168 panTro2 chr22 16612225 16613669 ponAbe2 chr22 14350097 14351544 rheMac2 chr10 62406526 62407975 calJac1 Contig1262 73352 74833 mononucleotide [T][T] 10 395 + 410 [T]G----[TTTTTTTTTT] indel/deletion G 2 1 ->hg18 611 hg18 chr22 16570234 16570445 panTro2 chr22 16613735 16613946 ponAbe2 chr22 14351893 14352104 rheMac2 chr10 62408065 62408276 calJac1 Contig1262 74883 75077 dinucleotide AT 0 187 + 197 ATATATATATA >panTro2 611 hg18 chr22 16570234 16570445 panTro2 chr22 16613735 16613946 ponAbe2 chr22 14351893 14352104 rheMac2 chr10 62408065 62408276 calJac1 Contig1262 74883 75077 dinucleotide AT 0 187 + 197 ATATATATATA >ponAbe2 611 hg18 chr22 16570234 16570445 panTro2 chr22 16613735 16613946 ponAbe2 chr22 14351893 14352104 rheMac2 chr10 62408065 62408276 calJac1 Contig1262 74883 75077 dinucleotide AT 0 187 + 197 ATATATATATA ->hg18 612 hg18 chr22 16570445 16570707 panTro2 chr22 16613946 16614208 ponAbe2 chr22 14352104 14352366 rheMac2 chr10 62408276 62408527 calJac1 Contig1262 75077 75339 mononucleotide A 2 214 + 222 AAAAAAAAA >panTro2 612 hg18 chr22 16570445 16570707 panTro2 chr22 16613946 16614208 ponAbe2 chr22 14352104 14352366 rheMac2 chr10 62408276 62408527 calJac1 Contig1262 75077 75339 mononucleotide A 2 214 + 222 AAAAAAAAA >ponAbe2 612 hg18 chr22 16570445 16570707 panTro2 chr22 16613946 16614208 ponAbe2 chr22 14352104 14352366 rheMac2 chr10 62408276 62408527 calJac1 Contig1262 75077 75339 mononucleotide A 2 214 + 222 AAAAAAAAA >rheMac2 612 hg18 chr22 16570445 16570707 panTro2 chr22 16613946 16614208 ponAbe2 chr22 14352104 14352366 rheMac2 chr10 62408276 62408527 calJac1 Contig1262 75077 75339 mononucleotide A 5 214 + 223 AAAAAAAAAA ->ponAbe2 613 hg18 chr22 16570707 16572020 panTro2 chr22 16614208 16615519 ponAbe2 chr22 14352366 14353672 rheMac2 chr10 62408527 62409749 calJac1 Contig1262 75339 76603 mononucleotide [A][A] 2 274 + 284 [AAAAAAAAA]C[A] indel/deletion C 10 1 ->calJac1 613 hg18 chr22 16570707 16572020 panTro2 chr22 16614208 16615519 ponAbe2 chr22 14352366 14353672 rheMac2 chr10 62408527 62409749 calJac1 Contig1262 75339 76603 trinucleotide [aat][AAT] 15 524 + 541 [aat]gga[aataataataat] indel/deletion gga 4 1 ->calJac1 613 hg18 chr22 16570707 16572020 panTro2 chr22 16614208 16615519 ponAbe2 chr22 14352366 14353672 rheMac2 chr10 62408527 62409749 calJac1 Contig1262 75339 76603 tetranucleotide.tetranucleotide TCNN.NNGG 33 932 + 945 [TCNNNNNNNNNNgg] NA.NA NA.NA NA.NA NA.NA 899.901 910.912 TCNNNNNNNNNN.NNNNNNNNNNGG ->rheMac2 618 hg18 chr22 16574585 16574622 panTro2 chr22 16618096 16618133 ponAbe2 chr22 14356271 14356308 rheMac2 chr10 62411989 62412217 calJac1 Contig1262 78270 78307 tetranucleotide AAAC 0 199 + 218 aaacaaacaaacaaacaaac ->hg18 620 hg18 chr22 16574790 16576226 panTro2 chr22 16618306 16619747 ponAbe2 chr22 14356479 14357920 rheMac2 chr10 62412387 62413850 calJac1 Contig1262 78965 80398 mononucleotide T 0 1 + 12 TTTTTTTTTTTT >panTro2 620 hg18 chr22 16574790 16576226 panTro2 chr22 16618306 16619747 ponAbe2 chr22 14356479 14357920 rheMac2 chr10 62412387 62413850 calJac1 Contig1262 78965 80398 mononucleotide T 0 1 + 12 TTTTTTTTTTTT >ponAbe2 620 hg18 chr22 16574790 16576226 panTro2 chr22 16618306 16619747 ponAbe2 chr22 14356479 14357920 rheMac2 chr10 62412387 62413850 calJac1 Contig1262 78965 80398 mononucleotide T 0 1 + 12 TTTTTTTTTTTT >rheMac2 620 hg18 chr22 16574790 16576226 panTro2 chr22 16618306 16619747 ponAbe2 chr22 14356479 14357920 rheMac2 chr10 62412387 62413850 calJac1 Contig1262 78965 80398 mononucleotide T 0 1 + 12 TTTTTTTTTTTT >calJac1 620 hg18 chr22 16574790 16576226 panTro2 chr22 16618306 16619747 ponAbe2 chr22 14356479 14357920 rheMac2 chr10 62412387 62413850 calJac1 Contig1262 78965 80398 dinucleotide TG 0 1 + 16 tgtgtgtgtgtgtgtg ->hg18 622 hg18 chr22 16577063 16577623 panTro2 chr22 16620843 16621411 ponAbe2 chr22 14359023 14359589 rheMac2 chr10 62414384 62415022 calJac1 Contig1262 80917 81488 mononucleotide A 1 156 + 166 aaaaaaaaaaa >panTro2 622 hg18 chr22 16577063 16577623 panTro2 chr22 16620843 16621411 ponAbe2 chr22 14359023 14359589 rheMac2 chr10 62414384 62415022 calJac1 Contig1262 80917 81488 mononucleotide A 1 156 + 174 aaaaaaaaaaaaaaaaaaa >rheMac2 622 hg18 chr22 16577063 16577623 panTro2 chr22 16620843 16621411 ponAbe2 chr22 14359023 14359589 rheMac2 chr10 62414384 62415022 calJac1 Contig1262 80917 81488 mononucleotide A 1 156 + 174 aaaaaaaaaaaaaaaaaaa >ponAbe2 622 hg18 chr22 16577063 16577623 panTro2 chr22 16620843 16621411 ponAbe2 chr22 14359023 14359589 rheMac2 chr10 62414384 62415022 calJac1 Contig1262 80917 81488 tetranucleotide AAAT 9 166 + 181 aaataaataaataaaT ->rheMac2 631 hg18 chr22 16581468 16581772 panTro2 chr22 16630318 16630622 ponAbe2 chr22 14363425 14363733 rheMac2 chr10 62419142 62419438 calJac1 Contig1262 86587 86889 tetranucleotide AAAT 16 300 + 311 aaataaataaaT ->rheMac2 633 hg18 chr22 16582611 16583193 panTro2 chr22 16631432 16631995 ponAbe2 chr22 14364311 14364881 rheMac2 chr10 62420106 62420665 calJac1 Contig1262 87429 88005 mononucleotide [A][a] 0 1 + 11 [aaaaaaaaa]g[a] indel/deletion g 10 1 ->hg18 633 hg18 chr22 16582611 16583193 panTro2 chr22 16631432 16631995 ponAbe2 chr22 14364311 14364881 rheMac2 chr10 62420106 62420665 calJac1 Contig1262 87429 88005 tetranucleotide [tttc][TTTC] 0 304 + 337 [tttc]at[tttctttctttctttctttctttctttc] indel/deletion at 5 1 >ponAbe2 633 hg18 chr22 16582611 16583193 panTro2 chr22 16631432 16631995 ponAbe2 chr22 14364311 14364881 rheMac2 chr10 62420106 62420665 calJac1 Contig1262 87429 88005 tetranucleotide [tttc][TTTC] 0 304 + 340 [tttc]at[tttctttctttctttct------------tt] indel/deletion at 5 1 >rheMac2 633 hg18 chr22 16582611 16583193 panTro2 chr22 16631432 16631995 ponAbe2 chr22 14364311 14364881 rheMac2 chr10 62420106 62420665 calJac1 Contig1262 87429 88005 tetranucleotide [TTTC][TTTC] 2 304 + 340 [TTTC]At[tttctttctttctttct------------tt] indel/deletion At 5 1 >panTro2 633 hg18 chr22 16582611 16583193 panTro2 chr22 16631432 16631995 ponAbe2 chr22 14364311 14364881 rheMac2 chr10 62420106 62420665 calJac1 Contig1262 87429 88005 tetranucleotide TTTA 3 310 + 341 tttatttatttat----------------tta >calJac1 633 hg18 chr22 16582611 16583193 panTro2 chr22 16631432 16631995 ponAbe2 chr22 14364311 14364881 rheMac2 chr10 62420106 62420665 calJac1 Contig1262 87429 88005 tetranucleotide TTTA 31 310 + 341 tttatttatttat----------------tta ->rheMac2 635 hg18 chr22 16584784 16585636 panTro2 chr22 16635419 16636275 ponAbe2 chr22 14367009 14367850 rheMac2 chr10 62420954 62421815 calJac1 Contig1262 88576 89485 dinucleotide [AT][ta] 0 83 + 97 [atatatatat]c[tata] indel/deletion c 11 1 >rheMac2 635 hg18 chr22 16584784 16585636 panTro2 chr22 16635419 16636275 ponAbe2 chr22 14367009 14367850 rheMac2 chr10 62420954 62421815 calJac1 Contig1262 88576 89485 dinucleotide [TA][AT] 0 103 + 130 [atatata]c[atatatatatatatatatat] indel/substitution c 8 1 >calJac1 635 hg18 chr22 16584784 16585636 panTro2 chr22 16635419 16636275 ponAbe2 chr22 14367009 14367850 rheMac2 chr10 62420954 62421815 calJac1 Contig1262 88576 89485 tetranucleotide TATG 36 116 + 132 tatgtatgtatgtatgt ->ponAbe2 635 hg18 chr22 16584784 16585636 panTro2 chr22 16635419 16636275 ponAbe2 chr22 14367009 14367850 rheMac2 chr10 62420954 62421815 calJac1 Contig1262 88576 89485 dinucleotide GT 42 401 + 436 gtgtgtgtgtgtgtgtgtgtgtgtgtgtg--tgtgt >hg18 635 hg18 chr22 16584784 16585636 panTro2 chr22 16635419 16636275 ponAbe2 chr22 14367009 14367850 rheMac2 chr10 62420954 62421815 calJac1 Contig1262 88576 89485 dinucleotide [GT][tg] 44 405 + 460 [g--------tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg--tgt]a[tgt] indel/deletion a 43 1 >panTro2 635 hg18 chr22 16584784 16585636 panTro2 chr22 16635419 16636275 ponAbe2 chr22 14367009 14367850 rheMac2 chr10 62420954 62421815 calJac1 Contig1262 88576 89485 dinucleotide [GT][GT][TG] 52 415 + 456 [gtg]c[gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt]a[tgt] indel/deletion,indel/deletion C,A 4,39 2 >rheMac2 635 hg18 chr22 16584784 16585636 panTro2 chr22 16635419 16636275 ponAbe2 chr22 14367009 14367850 rheMac2 chr10 62420954 62421815 calJac1 Contig1262 88576 89485 dinucleotide [gt][TG][tg] 12 422 + 449 [gt][tgtgtgtgtgtgtgtgtgtgtgt]a[tg] indel/deletion,indel/deletion ,a 3,26 2 ->hg18 635 hg18 chr22 16584784 16585636 panTro2 chr22 16635419 16636275 ponAbe2 chr22 14367009 14367850 rheMac2 chr10 62420954 62421815 calJac1 Contig1262 88576 89485 dinucleotide [at][AT] 131 939 + 951 [at]g[atatatatat] indel/deletion g 3 1 >panTro2 635 hg18 chr22 16584784 16585636 panTro2 chr22 16635419 16636275 ponAbe2 chr22 14367009 14367850 rheMac2 chr10 62420954 62421815 calJac1 Contig1262 88576 89485 dinucleotide [at][AT] 127 939 + 951 [at]g[atatatatat] indel/deletion g 3 1 >ponAbe2 635 hg18 chr22 16584784 16585636 panTro2 chr22 16635419 16636275 ponAbe2 chr22 14367009 14367850 rheMac2 chr10 62420954 62421815 calJac1 Contig1262 88576 89485 dinucleotide [at][AT] 142 939 + 951 [at]g[atatatatat] indel/deletion g 3 1 ->calJac1 637 hg18 chr22 16585709 16585968 panTro2 chr22 16636348 16636604 ponAbe2 chr22 14344375 14344600 rheMac2 chr10 62403264 62403519 calJac1 Contig1262 70899 71136 mononucleotide [T][T] 0 37 + 48 [T]A[TTTTTTTTTT] indel/deletion A 2 1 ->ponAbe2 637 hg18 chr22 16585709 16585968 panTro2 chr22 16636348 16636604 ponAbe2 chr22 14344375 14344600 rheMac2 chr10 62403264 62403519 calJac1 Contig1262 70899 71136 tetranucleotide.mononucleotide [TCCc][TCCC].[t][T][t][T] 40 206 + 265 [tccctccttccctccctccctccctccctcctCTTAttcttttttttttttttttttttt] indel/deletion.indel/deletion,indel/deletion,indel/deletion t.C,A,c 8.2,5,8 1.3 166.197 196.225 [TCCctcc]t[TCCCTCCCTCCCTCCCTCCCTCC].[t]C[TT]A[tt]c[TTTTTTTTTTTTTTTTTTTTT] >calJac1 637 hg18 chr22 16585709 16585968 panTro2 chr22 16636348 16636604 ponAbe2 chr22 14344375 14344600 rheMac2 chr10 62403264 62403519 calJac1 Contig1262 70899 71136 tetranucleotide [Tccc][CTCC][tccc] 3 206 + 233 [tccct]tt[ctccctccctcc]t[tccctc-c] indel/deletion,indel/deletion tt,t 6,20 2 >rheMac2 637 hg18 chr22 16585709 16585968 panTro2 chr22 16636348 16636604 ponAbe2 chr22 14344375 14344600 rheMac2 chr10 62403264 62403519 calJac1 Contig1262 70899 71136 mononucleotide [T][T][T] 10 237 + 265 [T]C[TT]A[tttttttttttttttttttttttt] indel/deletion,indel/deletion C,A 2,5 2 ->hg18 640 hg18 chr22 16586708 16588307 panTro2 chr22 16637357 16638957 ponAbe2 chr22 14369056 14370628 rheMac2 chr10 62423062 62424663 calJac1 Contig1262 90551 92095 mononucleotide [A][A][a] 0 1 + 35 [aaaaaaaaa]c[aaaa---------------aa]c[aaa] insertion,indel/deletion c,c 10,17 2 ->hg18 641 hg18 chr22 16588458 16588556 panTro2 chr22 16639108 16639206 ponAbe2 chr22 14370775 14370876 rheMac2 chr10 62424814 62424909 calJac1 Contig1262 92513 92608 mononucleotide T 0 71 + 83 ttttttttttttt >panTro2 641 hg18 chr22 16588458 16588556 panTro2 chr22 16639108 16639206 ponAbe2 chr22 14370775 14370876 rheMac2 chr10 62424814 62424909 calJac1 Contig1262 92513 92608 mononucleotide T 0 71 + 83 ttttttttttttt >ponAbe2 641 hg18 chr22 16588458 16588556 panTro2 chr22 16639108 16639206 ponAbe2 chr22 14370775 14370876 rheMac2 chr10 62424814 62424909 calJac1 Contig1262 92513 92608 mononucleotide T 0 71 + 85 ttttttttttttttt >rheMac2 641 hg18 chr22 16588458 16588556 panTro2 chr22 16639108 16639206 ponAbe2 chr22 14370775 14370876 rheMac2 chr10 62424814 62424909 calJac1 Contig1262 92513 92608 mononucleotide T 0 71 + 92 ttttttttttttt------ttt >calJac1 641 hg18 chr22 16588458 16588556 panTro2 chr22 16639108 16639206 ponAbe2 chr22 14370775 14370876 rheMac2 chr10 62424814 62424909 calJac1 Contig1262 92513 92608 mononucleotide [T][t] 0 71 + 92 [ttttttttttt]a[t------ttt] indel/deletion a 12 1 ->rheMac2 647 hg18 chr22 16591768 16591968 panTro2 chr22 16642487 16642687 ponAbe2 chr22 14374064 14374264 rheMac2 chr10 62427275 62427474 calJac1 Contig1262 95568 95783 trinucleotide [AAT][ATA] 0 98 + 114 [AAT]TT[ATAATAATAATA] indel/deletion TT 4 1 ->calJac1 647 hg18 chr22 16591768 16591968 panTro2 chr22 16642487 16642687 ponAbe2 chr22 14374064 14374264 rheMac2 chr10 62427275 62427474 calJac1 Contig1262 95568 95783 mononucleotide [t][t][t][t][T] 3 157 + 183 [tt]g[tttt]g[tttt]g[tttt]g[ttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion g,g,g,g 3,8,13,18 4 ->rheMac2 648 hg18 chr22 16591968 16592483 panTro2 chr22 16642687 16643202 ponAbe2 chr22 14374264 14374781 rheMac2 chr10 62427474 62427998 calJac1 Contig1262 95783 96304 mononucleotide [G][G][G] 1 156 + 170 [G]A[GG]T[GGG-GGGGGG] indel/deletion,indel/deletion A,T 2,5 2 ->ponAbe2 652 hg18 chr22 16593102 16593690 panTro2 chr22 16643821 16644378 ponAbe2 chr22 14375371 14375964 rheMac2 chr10 62428898 62429477 calJac1 Contig1262 97187 97770 mononucleotide A 4 583 + 592 AAAAAAAAAA ->ponAbe2 656 hg18 chr22 16594898 16595126 panTro2 chr22 16646788 16647016 ponAbe2 chr22 14377176 14377407 rheMac2 chr10 62430529 62430757 calJac1 Contig1262 98625 98843 dinucleotide TA 3 90 + 100 ATATATATATA ->hg18 670 hg18 chr22 16599238 16599807 panTro2 chr22 16651122 16651693 ponAbe2 chr22 14381820 14382383 rheMac2 chr10 62435177 62435715 calJac1 Contig1262 102835 103346 mononucleotide T 2 340 + 353 tttttttttttttt >panTro2 670 hg18 chr22 16599238 16599807 panTro2 chr22 16651122 16651693 ponAbe2 chr22 14381820 14382383 rheMac2 chr10 62435177 62435715 calJac1 Contig1262 102835 103346 mononucleotide T 0 340 + 353 tttttttttttttt >ponAbe2 670 hg18 chr22 16599238 16599807 panTro2 chr22 16651122 16651693 ponAbe2 chr22 14381820 14382383 rheMac2 chr10 62435177 62435715 calJac1 Contig1262 102835 103346 mononucleotide T 6 340 + 350 ttttttttttt >rheMac2 670 hg18 chr22 16599238 16599807 panTro2 chr22 16651122 16651693 ponAbe2 chr22 14381820 14382383 rheMac2 chr10 62435177 62435715 calJac1 Contig1262 102835 103346 mononucleotide [t][T][T] 32 340 + 360 [t]g[ttttttt]c[ttttttttttt] indel/deletion,insertion g,c 2,10 2 ->ponAbe2 670 hg18 chr22 16599238 16599807 panTro2 chr22 16651122 16651693 ponAbe2 chr22 14381820 14382383 rheMac2 chr10 62435177 62435715 calJac1 Contig1262 102835 103346 mononucleotide [T][t] 16 508 + 518 [ttttttttt]g[t] indel/deletion g 10 1 -UNDONE: 0 ->ponAbe2 15 hg18 chr22 14863634 14864685 panTro2 chr10 27714626 27715577 ponAbe2 chr22 13583948 13584992 rheMac2 chr9 37385642 37386689 mononucleotide [A][a][a][a] 5 457 + 575 [aaaaaaaaa]--------------t[aaa]-----------------------------------------------------------------------------------g[aaaa]g[aaa] indel/deletion,indel/deletion,indel/deletion t,g,g 10,14,19 3 >rheMac2 15 hg18 chr22 14863634 14864685 panTro2 chr10 27714626 27715577 ponAbe2 chr22 13583948 13584992 rheMac2 chr9 37385642 37386689 mononucleotide A 7 457 + 575 aaaaaaaaa----------------aa-----------------------------------------------------------------------------------aaaaaaaaa >hg18 15 hg18 chr22 14863634 14864685 panTro2 chr10 27714626 27715577 ponAbe2 chr22 13583948 13584992 rheMac2 chr9 37385642 37386689 tetranucleotide AAAT 7 460 + 484 aaataaa-------------taaat ->hg18 16 hg18 chr22 14864847 14865333 panTro2 chr10 27715577 27716025 ponAbe2 chr22 13585126 13585605 rheMac2 chr9 37386814 37387286 tetranucleotide [CATT][ATTC] 0 57 + 75 [CATTC]T[ATTCATTCATTCA] indel/deletion T 6 1 >ponAbe2 16 hg18 chr22 14864847 14865333 panTro2 chr10 27715577 27716025 ponAbe2 chr22 13585126 13585605 rheMac2 chr9 37386814 37387286 tetranucleotide [CATT][ATTC] 0 57 + 75 [CATTC]T[ATTCATTCATTca] indel/deletion T 6 1 ->hg18 20 hg18 chr22 14866655 14866936 panTro2 chr10 27718430 27718698 ponAbe2 chr22 13586925 13587206 rheMac2 chr9 37388637 37388906 tetranucleotide [AATT][TTAA][AATT] 10 106 + 138 [TAATT]TTTA[aattaattaa]c[taattaattaatt] indel/deletion,indel/substitution TTTA,c 6,20 2 >panTro2 20 hg18 chr22 14866655 14866936 panTro2 chr10 27718430 27718698 ponAbe2 chr22 13586925 13587206 rheMac2 chr9 37388637 37388906 tetranucleotide [ttaa][AATT] 14 111 + 138 [ttaa][aat--------taattaattaatt] indel/deletion 5 1 >ponAbe2 20 hg18 chr22 14866655 14866936 panTro2 chr10 27718430 27718698 ponAbe2 chr22 13586925 13587206 rheMac2 chr9 37388637 37388906 tetranucleotide [TTAA][TTAA] 10 112 + 138 [TTAAT][ttaattaattaattaattaatt] indel/deletion 6 1 ->hg18 23 hg18 chr22 14867544 14867676 panTro2 chr10 27719302 27719418 ponAbe2 chr22 13587814 13587956 rheMac2 chr9 37389517 37389670 dinucleotide [AC][ac] 0 4 + 61 [acacac---------------------acacacacacacacacacacacacaca]a[aca] indel/deletion a 34 1 >ponAbe2 23 hg18 chr22 14867544 14867676 panTro2 chr10 27719302 27719418 ponAbe2 chr22 13587814 13587956 rheMac2 chr9 37389517 37389670 dinucleotide.dinucleotide [AC][ca].[ca][AC][AC][ac] 0 4 + 61 [acacacacac-------acacacgcagacacacacacacaaacacacaca-caaaaca] indel/deletion.indel/deletion,indel/substitution,indel/deletion g.g,a,aa 17.3,17,29 1.3 4.21 22.53 [ACACACACACACACAC]g[ca].[ca]g[ACACACACACACA]a[ACACACACACA]aa[acA] >rheMac2 23 hg18 chr22 14867544 14867676 panTro2 chr10 27719302 27719418 ponAbe2 chr22 13587814 13587956 rheMac2 chr9 37389517 37389670 dinucleotide [CA][AC] 0 19 + 43 [ACA][acacacacacacacacacacac] indel/deletion 4 1 ->hg18 25 hg18 chr22 14867775 14868006 panTro2 chr10 27719513 27719743 ponAbe2 chr22 13588055 13588285 rheMac2 chr9 37389768 37389985 mononucleotide [T][T] 0 49 + 60 [T]G[TTTTTTTTTT] indel/deletion G 2 1 ->hg18 27 hg18 chr22 14868596 14868836 panTro2 chr10 27720111 27720273 ponAbe2 chr22 13588876 13589120 rheMac2 chr9 37390576 37390834 mononucleotide A 1 43 + 58 aaaaaaaaaaaaaaaa >ponAbe2 27 hg18 chr22 14868596 14868836 panTro2 chr10 27720111 27720273 ponAbe2 chr22 13588876 13589120 rheMac2 chr9 37390576 37390834 mononucleotide A 1 45 + 62 aaaaaaaaaaaaaaaaaa >rheMac2 27 hg18 chr22 14868596 14868836 panTro2 chr10 27720111 27720273 ponAbe2 chr22 13588876 13589120 rheMac2 chr9 37390576 37390834 mononucleotide [A][A] 0 45 + 63 [a-aaaa]g[aaaaaaaaaaaa] insertion g 6 1 ->panTro2 28 hg18 chr22 14868908 14869588 panTro2 chr10 27720273 27720957 ponAbe2 chr22 13589192 13589872 rheMac2 chr9 37390906 37391581 tetranucleotide TATC 1 637 + 648 TATCTATCTATC ->hg18 29 hg18 chr22 14869911 14870235 panTro2 chr10 28784976 28785305 ponAbe2 chr22 13590189 13590518 rheMac2 chr9 37391897 37392230 mononucleotide [T][T][T] 5 199 + 216 [TTTTTTT----TT]A[TT]G[T] indel/deletion,indel/deletion A,G 10,13 2 >rheMac2 29 hg18 chr22 14869911 14870235 panTro2 chr10 28784976 28785305 ponAbe2 chr22 13590189 13590518 rheMac2 chr9 37391897 37392230 mononucleotide T 0 199 + 208 TTTTTTTTTT ->ponAbe2 31 hg18 chr22 14870707 14870935 panTro2 chr10 28785465 28785716 ponAbe2 chr22 13590984 13591210 rheMac2 chr9 37392728 37392968 dinucleotide TA 0 157 + 195 TA--TATATATATA--------------------TATAT >rheMac2 31 hg18 chr22 14870707 14870935 panTro2 chr10 28785465 28785716 ponAbe2 chr22 13590984 13591210 rheMac2 chr9 37392728 37392968 dinucleotide AT 0 157 + 169 ta--tatatatat >hg18 31 hg18 chr22 14870707 14870935 panTro2 chr10 28785465 28785716 ponAbe2 chr22 13590984 13591210 rheMac2 chr9 37392728 37392968 dinucleotide [TA][AT] 0 161 + 195 [TA]A[ATATATA--------------------TATAT] indel/deletion A 3 1 >rheMac2 31 hg18 chr22 14870707 14870935 panTro2 chr10 28785465 28785716 ponAbe2 chr22 13590984 13591210 rheMac2 chr9 37392728 37392968 dinucleotide [AT][AT] 2 185 + 211 [ata---tatat---atatat]----C[AT] indel/deletion C 15 1 ->rheMac2 32 hg18 chr22 14870935 14872363 panTro2 chr10 28785716 28787118 ponAbe2 chr22 13591210 13592643 rheMac2 chr9 37392968 37394392 mononucleotide [T][T][T] 20 381 + 399 [TT]C[TTTTTTTTTTTTTT]C[T] indel/deletion,indel/deletion C,C 3,18 2 ->rheMac2 32 hg18 chr22 14870935 14872363 panTro2 chr10 28785716 28787118 ponAbe2 chr22 13591210 13592643 rheMac2 chr9 37392968 37394392 mononucleotide T 60 679 + 687 ttttttttt ->hg18 32 hg18 chr22 14870935 14872363 panTro2 chr10 28785716 28787118 ponAbe2 chr22 13591210 13592643 rheMac2 chr9 37392968 37394392 mononucleotide [t][T] 16 846 + 907 [tttt]c-----------------------------------------------[tttttttttt] indel/deletion c 5 1 >panTro2 32 hg18 chr22 14870935 14872363 panTro2 chr10 28785716 28787118 ponAbe2 chr22 13591210 13592643 rheMac2 chr9 37392968 37394392 mononucleotide T 41 846 + 907 ttttt-----------------------------------------------tttttttttt >rheMac2 32 hg18 chr22 14870935 14872363 panTro2 chr10 28785716 28787118 ponAbe2 chr22 13591210 13592643 rheMac2 chr9 37392968 37394392 mononucleotide [T][T][T][T][T][T][T][T][T][T][T][T][T] 60 846 + 909 [t]g[ttt]g[ttt]g[ttt]g[ttt]g[ttt]g[ttt]c[ttt]c[ttt]c[ttt]c[ttt]c[ttt]c[tttttttttttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion G,G,G,G,G,G,C,C,C,C,C,C 2,6,10,14,18,22,26,30,34,38,42,46 12 ->hg18 33 hg18 chr22 14872624 14873129 panTro2 chr10 28787379 28787740 ponAbe2 chr22 13594759 13595123 rheMac2 chr9 37394661 37395014 mononucleotide [A][A] 6 314 + 325 [aaaAAAAAAA]G[A] indel/deletion G 11 1 ->panTro2 34 hg18 chr22 14874002 14875966 panTro2 chr10 28787740 28789652 ponAbe2 chr22 13595997 13597921 rheMac2 chr9 37395871 37397838 dinucleotide [at][AT][at][ta] 0 215 + 280 [at]g------------------------------------c[atatatatat]--------g[atat][tat] indel/deletion,indel/deletion,indel/deletion gc,g, 3,15,20 3 >hg18 34 hg18 chr22 14874002 14875966 panTro2 chr10 28787740 28789652 ponAbe2 chr22 13595997 13597921 rheMac2 chr9 37395871 37397838 dinucleotide [AT][at] 8 221 + 275 [atatatatatatatat----------------atatatatatat--------a][at] indel/deletion 30 1 >rheMac2 34 hg18 chr22 14874002 14875966 panTro2 chr10 28787740 28789652 ponAbe2 chr22 13595997 13597921 rheMac2 chr9 37395871 37397838 compound [AT][CA][TA] 1 229 + 265 [atatatatata][cacacacacacacaca][tatatatata] ->ponAbe2 34 hg18 chr22 14874002 14875966 panTro2 chr10 28787740 28789652 ponAbe2 chr22 13595997 13597921 rheMac2 chr9 37395871 37397838 mononucleotide [t][T][t] 74 613 + 626 [t]c[ttttttttt]a[tt] indel/deletion,indel/deletion c,a 2,12 2 ->hg18 37 hg18 chr22 14876910 14878288 panTro2 chr10 28790281 28791672 ponAbe2 chr22 13598862 13600245 rheMac2 chr9 37398686 37400063 mononucleotide [A][a] 0 131 + 144 [aaaaaa-aaaa]c[aa] indel/deletion c 11 1 >ponAbe2 37 hg18 chr22 14876910 14878288 panTro2 chr10 28790281 28791672 ponAbe2 chr22 13598862 13600245 rheMac2 chr9 37398686 37400063 mononucleotide A 0 131 + 140 aaaaaaaaaa ->hg18 37 hg18 chr22 14876910 14878288 panTro2 chr10 28790281 28791672 ponAbe2 chr22 13598862 13600245 rheMac2 chr9 37398686 37400063 dinucleotide [ac][CA] 16 654 + 666 [ac]c[cacacacaca] indel/deletion c 3 1 ->hg18 40 hg18 chr22 14879494 14879601 panTro2 chr10 28793415 28793519 ponAbe2 chr22 13601453 13601555 rheMac2 chr9 37402533 37402661 dinucleotide [AC][ca] 0 61 + 99 [acacacacacacacacacacacacacacacaca]tg[caca] indel/deletion tg 34 1 >rheMac2 40 hg18 chr22 14879494 14879601 panTro2 chr10 28793415 28793519 ponAbe2 chr22 13601453 13601555 rheMac2 chr9 37402533 37402661 dinucleotide [AC][AC] 1 61 + 123 [acacacacacacacacacacacacacacacacacacacacacacacaca]t[acacacacacaca] indel/substitution t 50 1 >ponAbe2 40 hg18 chr22 14879494 14879601 panTro2 chr10 28793415 28793519 ponAbe2 chr22 13601453 13601555 rheMac2 chr9 37402533 37402661 dinucleotide [AC][CA] 27 87 + 123 [acacacacacacacacacacacacacacac]g[cacaca] indel/substitution g 31 1 >panTro2 40 hg18 chr22 14879494 14879601 panTro2 chr10 28793415 28793519 ponAbe2 chr22 13601453 13601555 rheMac2 chr9 37402533 37402661 dinucleotide [ac][ac][AC][AC] 25 91 + 119 [aca]t[acacac]ga[acacacacacaca]a[aca] indel/deletion,indel/deletion,indel/deletion t,ga,A 4,11,26 3 ->rheMac2 41 hg18 chr22 14879962 14881439 panTro2 chr10 28793576 28795027 ponAbe2 chr22 13601917 13603430 rheMac2 chr9 37403033 37404485 dinucleotide [AT][TA] 4 210 + 222 [ATATATATAT]T[TA] indel/deletion T 11 1 ->hg18 41 hg18 chr22 14879962 14881439 panTro2 chr10 28793576 28795027 ponAbe2 chr22 13601917 13603430 rheMac2 chr9 37403033 37404485 mononucleotide [A][A][A][A][A][A] 4 941 + 1003 [aaaaa------------------------aaaa]g[aaaaaaaaa]g[aaaaaaa]g[aaA]G[AAAAA]T[A] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion g,g,G,G,T 10,20,28,32,38 6 >panTro2 41 hg18 chr22 14879962 14881439 panTro2 chr10 28793576 28795027 ponAbe2 chr22 13601917 13603430 rheMac2 chr9 37403033 37404485 mononucleotide [A][A][A][a] 41 941 + 1003 [aaaaa-----------------------------aaaaaaaaaaa]g[aaaaaaaaa]g[aaaaa]t[a] insertion,insertion,indel/deletion g,g,t 17,27,33 3 >ponAbe2 41 hg18 chr22 14879962 14881439 panTro2 chr10 28793576 28795027 ponAbe2 chr22 13601917 13603430 rheMac2 chr9 37403033 37404485 mononucleotide [A][A] 7 941 + 960 [aaaaaaaaaaaa]g[aaaaaaa] insertion g 13 1 >rheMac2 41 hg18 chr22 14879962 14881439 panTro2 chr10 28793576 28795027 ponAbe2 chr22 13601917 13603430 rheMac2 chr9 37403033 37404485 tetranucleotide [gaaa][GAAA] 71 977 + 999 [aaagaaa]a[aaagaaagaaagaaa] indel/deletion a 8 1 ->hg18 42 hg18 chr22 14882246 14884933 panTro2 chr10 28795027 28797601 ponAbe2 chr22 13604234 13606808 rheMac2 chr9 37405303 37407982 dinucleotide [CA][CA][ac][CA] 16 632 + 654 [ca]tg[cacacacaca]t[acaca]t[CA] indel/deletion,indel/deletion,indel/deletion TG,t,t 3,15,21 3 >rheMac2 42 hg18 chr22 14882246 14884933 panTro2 chr10 28795027 28797601 ponAbe2 chr22 13604234 13606808 rheMac2 chr9 37405303 37407982 dinucleotide [CA][CA][ac][CA] 12 632 + 654 [ca]tg[cacacacaca]t[acaca]t[CA] indel/deletion,indel/deletion,indel/deletion TG,t,t 3,15,21 3 ->hg18 42 hg18 chr22 14882246 14884933 panTro2 chr10 28795027 28797601 ponAbe2 chr22 13604234 13606808 rheMac2 chr9 37405303 37407982 tetranucleotide TAAA 16 713 + 725 TAAATAAATAAAT >panTro2 42 hg18 chr22 14882246 14884933 panTro2 chr10 28795027 28797601 ponAbe2 chr22 13604234 13606808 rheMac2 chr9 37405303 37407982 tetranucleotide TAAA 49 713 + 725 TAAATAAATAAAT >ponAbe2 42 hg18 chr22 14882246 14884933 panTro2 chr10 28795027 28797601 ponAbe2 chr22 13604234 13606808 rheMac2 chr9 37405303 37407982 tetranucleotide TAAA 23 713 + 725 TAAATAAATAAAT ->panTro2 42 hg18 chr22 14882246 14884933 panTro2 chr10 28795027 28797601 ponAbe2 chr22 13604234 13606808 rheMac2 chr9 37405303 37407982 mononucleotide [A][A] 54 981 + 992 [AA]T[AAAAAAAAA] indel/deletion T 3 1 ->hg18 42 hg18 chr22 14882246 14884933 panTro2 chr10 28795027 28797601 ponAbe2 chr22 13604234 13606808 rheMac2 chr9 37405303 37407982 mononucleotide [A][a][A] 20 1739 + 1757 [aaaaaaaaa--aaa]g[aa]T[A] indel/deletion,indel/deletion g,T 13,16 2 >ponAbe2 42 hg18 chr22 14882246 14884933 panTro2 chr10 28795027 28797601 ponAbe2 chr22 13604234 13606808 rheMac2 chr9 37405303 37407982 mononucleotide A 38 1739 + 1751 aaaaaaaaa--aa ->panTro2 42 hg18 chr22 14882246 14884933 panTro2 chr10 28795027 28797601 ponAbe2 chr22 13604234 13606808 rheMac2 chr9 37405303 37407982 mononucleotide [A][A] 62 2115 + 2135 [AAAA]G-------[AAAAAAAAA] indel/deletion G 5 1 >hg18 42 hg18 chr22 14882246 14884933 panTro2 chr10 28795027 28797601 ponAbe2 chr22 13604234 13606808 rheMac2 chr9 37405303 37407982 mononucleotide A 40 2121 + 2135 AAAAAAAAAAAAAAA ->hg18 42 hg18 chr22 14882246 14884933 panTro2 chr10 28795027 28797601 ponAbe2 chr22 13604234 13606808 rheMac2 chr9 37405303 37407982 dinucleotide [TA][at] 40 2196 + 2214 [tatatatatatata]c[atat] indel/deletion c 15 1 ->hg18 42 hg18 chr22 14882246 14884933 panTro2 chr10 28795027 28797601 ponAbe2 chr22 13604234 13606808 rheMac2 chr9 37405303 37407982 compound [TA][ATGT][TA] 40 2244 + 2277 [tatatatata]c[atgtatgtatgt]g[tatatatata] >ponAbe2 42 hg18 chr22 14882246 14884933 panTro2 chr10 28795027 28797601 ponAbe2 chr22 13604234 13606808 rheMac2 chr9 37405303 37407982 dinucleotide [GT][gT] 141 2254 + 2290 [tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt]a[tgt] indel/deletion a 34 1 >rheMac2 42 hg18 chr22 14882246 14884933 panTro2 chr10 28795027 28797601 ponAbe2 chr22 13604234 13606808 rheMac2 chr9 37405303 37407982 dinucleotide TA 100 2266 + 2281 tatatatatatatata ->hg18 42 hg18 chr22 14882246 14884933 panTro2 chr10 28795027 28797601 ponAbe2 chr22 13604234 13606808 rheMac2 chr9 37405303 37407982 dinucleotide CA 40 2293 + 2317 acacacacacacacacacacacaca ->panTro2 43 hg18 chr22 14885589 14886844 panTro2 chr10 28797633 28798896 ponAbe2 chr22 13607104 13608331 rheMac2 chr9 37408631 37409877 dinucleotide [Gt][GT][TG][tg] 0 195 + 265 [gtgtg]---------[gtgtgtg--------tgtgtgt]c[tgtgtgtgtgtgtgtgtgtgtgtgtgtgtg]ac[tg] indel/deletion,indel/substitution,indel/deletion ,c,ac 6,20,51 3 >rheMac2 43 hg18 chr22 14885589 14886844 panTro2 chr10 28797633 28798896 ponAbe2 chr22 13607104 13608331 rheMac2 chr9 37408631 37409877 dinucleotide [TG][TG][tg] 0 198 + 231 [TG]CT[tgtgtgtgtgtgtg--tgtg]ca[tgtgtgtg] indel/deletion,indel/deletion CT,ca 3,23 2 >rheMac2 43 hg18 chr22 14885589 14886844 panTro2 chr10 28797633 28798896 ponAbe2 chr22 13607104 13608331 rheMac2 chr9 37408631 37409877 dinucleotide [GT][tg] 2 235 + 264 [gtgtgtgtgtgtgtgtgtgtgtgtgtg]a[tg] indel/deletion a 28 1 >hg18 43 hg18 chr22 14885589 14886844 panTro2 chr10 28797633 28798896 ponAbe2 chr22 13607104 13608331 rheMac2 chr9 37408631 37409877 dinucleotide [TG][tg][tg] 0 204 + 261 [tgtgtgtgtgtgt]a[tgtg]ct[tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg] indel/deletion,indel/deletion a,ct 14,19 2 >ponAbe2 43 hg18 chr22 14885589 14886844 panTro2 chr10 28797633 28798896 ponAbe2 chr22 13607104 13608331 rheMac2 chr9 37408631 37409877 dinucleotide [TG][TG] 0 204 + 259 [t----gtgtgtg----------------------tgtgtgtgt]c[tgtgtgtgtgtg] indel/substitution c 18 1 ->ponAbe2 44 hg18 chr22 15242475 15244125 panTro2 chrUn 186703 188379 ponAbe2 chr22 13679996 13681638 rheMac2 chr3 73205302 73206980 mononucleotide T 0 50 + 58 ttttttttt ->panTro2 44 hg18 chr22 15242475 15244125 panTro2 chrUn 186703 188379 ponAbe2 chr22 13679996 13681638 rheMac2 chr3 73205302 73206980 mononucleotide A 4 659 + 673 aaaaaaaaaaaa--a ->ponAbe2 44 hg18 chr22 15242475 15244125 panTro2 chrUn 186703 188379 ponAbe2 chr22 13679996 13681638 rheMac2 chr3 73205302 73206980 mononucleotide [g][G] 16 730 + 744 [g]t[g---ggggggggg] indel/deletion t 2 1 >panTro2 44 hg18 chr22 15242475 15244125 panTro2 chrUn 186703 188379 ponAbe2 chr22 13679996 13681638 rheMac2 chr3 73205302 73206980 mononucleotide G 6 733 + 744 gggggggggggg ->panTro2 46 hg18 chr22 15244247 15246957 panTro2 chrUn 188809 191531 ponAbe2 chr22 13681760 13684468 rheMac2 chr3 73207102 73209816 mononucleotide [T][T] 7 1024 + 1034 [T]A[TTTTTTTTT] indel/deletion A 2 1 >ponAbe2 46 hg18 chr22 15244247 15246957 panTro2 chrUn 188809 191531 ponAbe2 chr22 13681760 13684468 rheMac2 chr3 73207102 73209816 mononucleotide [T][T] 12 1024 + 1034 [T]A[TTTTTTTTT] indel/deletion A 2 1 ->ponAbe2 46 hg18 chr22 15244247 15246957 panTro2 chrUrn 188809 191531 ponAbe2 chr22 13681760 13684468 rheMac2 chr3 73207102 73209816 mononucleotide [A][A] 18 1705 + 1715 [AAAAAAAAA]G[A] indel/deletion G 10 1 ->rheMac2 48 hg18 chr22 15247122 15247394 panTro2 chrUn 191692 191964 ponAbe2 chr22 13684627 13684898 rheMac2 chr3 73210321 73210576 mononucleotide [T][T][T] 0 156 + 175 [T]C[TTTTTTTTTTTTTTTT]G[T] indel/deletion,indel/deletion C,G 2,19 2 ->hg18 51 hg18 chr22 15567555 15569229 panTro2 chr3 126042915 126044595 ponAbe2 chr22 13719223 13720916 rheMac2 chr2 189384558 189386230 mononucleotide [t][T] 20 780 + 790 [t]a[ttttttttt] indel/deletion a 2 1 ->panTro2 51 hg18 chr22 15567555 15569229 panTro2 chr3 126042915 126044595 ponAbe2 chr22 13719223 13720916 rheMac2 chr2 189384558 189386230 dinucleotide AC 17 1526 + 1535 ACACACACAC >ponAbe2 51 hg18 chr22 15567555 15569229 panTro2 chr3 126042915 126044595 ponAbe2 chr22 13719223 13720916 rheMac2 chr2 189384558 189386230 dinucleotide AC 7 1526 + 1535 ACACACACAC ->panTro2 53 hg18 chr22 15573056 15574108 panTro2 chr3 126050687 126051750 ponAbe2 chr22 13725470 13726534 rheMac2 chr2 189390087 189391091 compound [TG][AT] 8 611 + 638 [tgtgtgtgtgtgt][atatatatatatata] >rheMac2 53 hg18 chr22 15573056 15574108 panTro2 chr3 126050687 126051750 ponAbe2 chr22 13725470 13726534 rheMac2 chr2 189390087 189391091 dinucleotide AT 14 616 + 641 atata------tatatatatata-ta >ponAbe2 53 hg18 chr22 15573056 15574108 panTro2 chr3 126050687 126051750 ponAbe2 chr22 13725470 13726534 rheMac2 chr2 189390087 189391091 dinucleotide AT 2 619 + 637 ta------tatatatatat ->hg18 54 hg18 chr22 15574108 15574898 panTro2 chr3 126051750 126052596 ponAbe2 chr22 13726534 13727373 rheMac2 chr2 189391091 189391938 tetranucleotide [aaat][AAAT] 0 188 + 210 [aaat][aataaataaataaataaat] indel/deletion 5 1 >ponAbe2 54 hg18 chr22 15574108 15574898 panTro2 chr3 126051750 126052596 ponAbe2 chr22 13726534 13727373 rheMac2 chr2 189391091 189391938 tetranucleotide [AAAT][AAAT] 0 188 + 210 [AAAT]----[AATAAATAAATAAAT] indel/deletion 5 1 >rheMac2 54 hg18 chr22 15574108 15574898 panTro2 chr3 126051750 126052596 ponAbe2 chr22 13726534 13727373 rheMac2 chr2 189391091 189391938 tetranucleotide AATA 1 192 + 206 AATAAATAAATAAAT ->hg18 58 hg18 chr22 16060813 16061911 panTro2 chr22 16069281 16070379 ponAbe2 chr22 13762720 13763847 rheMac2 chr10 61845366 61846480 tetranucleotide [aaac][AACA] 2 270 + 294 [aaac]-[aacaaacaaaca----aaca] indel/deletion 5 1 >panTro2 58 hg18 chr22 16060813 16061911 panTro2 chr22 16069281 16070379 ponAbe2 chr22 13762720 13763847 rheMac2 chr10 61845366 61846480 tetranucleotide AACA 2 270 + 294 a----aacaaacaaaca----aaca >ponAbe2 58 hg18 chr22 16060813 16061911 panTro2 chr22 16069281 16070379 ponAbe2 chr22 13762720 13763847 rheMac2 chr10 61845366 61846480 tetranucleotide [AACA][acaa] 2 270 + 292 [aaacaaacaaacaaaca]a[ac-aa] indel/deletion a 18 1 >rheMac2 58 hg18 chr22 16060813 16061911 panTro2 chr22 16069281 16070379 ponAbe2 chr22 13762720 13763847 rheMac2 chr10 61845366 61846480 tetranucleotide AACA 0 270 + 294 aaacaaacaaacaaacaaacaaaca ->ponAbe2 58 hg18 chr22 16060813 16061911 panTro2 chr22 16069281 16070379 ponAbe2 chr22 13762720 13763847 rheMac2 chr10 61845366 61846480 tetranucleotide [caaa][AAAC][aaac] 11 974 + 1015 [c---aaa][aaacaaacaaacaaacaaacaaacaaac]aaa[aaac] indel/deletion,indel/deletion ,aaa 5,33 2 >hg18 58 hg18 chr22 16060813 16061911 panTro2 chr22 16069281 16070379 ponAbe2 chr22 13762720 13763847 rheMac2 chr10 61845366 61846480 mononucleotide [A][A] 15 975 + 990 [aaaaaaaaaaaaaa]C[A] indel/deletion C 15 1 >panTro2 58 hg18 chr22 16060813 16061911 panTro2 chr22 16069281 16070379 ponAbe2 chr22 13762720 13763847 rheMac2 chr10 61845366 61846480 mononucleotide [A][A] 18 975 + 993 [aaaaaaaaaaaaaaaaa]C[A] indel/deletion C 18 1 >rheMac2 58 hg18 chr22 16060813 16061911 panTro2 chr22 16069281 16070379 ponAbe2 chr22 13762720 13763847 rheMac2 chr10 61845366 61846480 tetranucleotide [AAAT][aaaT] 8 981 + 1021 [aaataaataaataaat]aa[a-------------------aaT] indel/deletion aa 17 1 ->ponAbe2 59 hg18 chr22 16060822 16061104 panTro2 chr22 16069290 16069569 ponAbe2 chr22 13761875 13762161 rheMac2 chr10 61843907 61844186 mononucleotide A 2 265 + 289 aaa---aaaaaaaaaaaaaaaaaaa >rheMac2 59 hg18 chr22 16060822 16061104 panTro2 chr22 16069290 16069569 ponAbe2 chr22 13761875 13762161 rheMac2 chr10 61843907 61844186 mononucleotide A 2 265 + 284 aaa---aaaaaaaaaaaaaa >hg18 59 hg18 chr22 16060822 16061104 panTro2 chr22 16069290 16069569 ponAbe2 chr22 13761875 13762161 rheMac2 chr10 61843907 61844186 tetranucleotide [aaac][AACA] 8 267 + 286 [aaac][aacaaacaaacaaaca] indel/deletion 5 1 >panTro2 59 hg18 chr22 16060822 16061104 panTro2 chr22 16069290 16069569 ponAbe2 chr22 13761875 13762161 rheMac2 chr10 61843907 61844186 tetranucleotide AACA 8 267 + 286 a---aacaaacaaacaaaca ->hg18 63 hg18 chr22 16064792 16065225 panTro2 chr22 16073297 16073729 ponAbe2 chr22 13765330 13765764 rheMac2 chr10 61849990 61850374 dinucleotide TC 2 207 + 221 CTCTCTCTCTCTCTC >panTro2 63 hg18 chr22 16064792 16065225 panTro2 chr22 16073297 16073729 ponAbe2 chr22 13765330 13765764 rheMac2 chr10 61849990 61850374 dinucleotide TC 3 207 + 221 CTCTCTCTCTCTCTC >ponAbe2 63 hg18 chr22 16064792 16065225 panTro2 chr22 16073297 16073729 ponAbe2 chr22 13765330 13765764 rheMac2 chr10 61849990 61850374 compound [TC][T] 1 207 + 228 [CTCTCTCTCTCTC][TTTTTTTTT] >rheMac2 63 hg18 chr22 16064792 16065225 panTro2 chr22 16073297 16073729 ponAbe2 chr22 13765330 13765764 rheMac2 chr10 61849990 61850374 compound [TC][T] 1 207 + 231 [CTCTCTCTCTCTC][TTTTTTTTT-TT] ->hg18 65 hg18 chr22 16067249 16067383 panTro2 chr22 16076066 16076179 ponAbe2 chr22 13768228 13768341 rheMac2 chr10 61852904 61853017 trinucleotide AAT 0 120 + 134 aataataataataat >panTro2 65 hg18 chr22 16067249 16067383 panTro2 chr22 16076066 16076179 ponAbe2 chr22 13768228 13768341 rheMac2 chr10 61852904 61853017 trinucleotide AAT 21 120 + 134 aataataataataat >rheMac2 65 hg18 chr22 16067249 16067383 panTro2 chr22 16076066 16076179 ponAbe2 chr22 13768228 13768341 rheMac2 chr10 61852904 61853017 trinucleotide AAT 21 120 + 134 aataataataataat >ponAbe2 65 hg18 chr22 16067249 16067383 panTro2 chr22 16076066 16076179 ponAbe2 chr22 13768228 13768341 rheMac2 chr10 61852904 61853017 trinucleotide AAT 21 123 + 134 aataataataat ->panTro2 66 hg18 chr22 16067383 16067912 panTro2 chr22 16076179 16076703 ponAbe2 chr22 13768341 13768861 rheMac2 chr10 61853314 61853841 trinucleotide TAA 0 2 + 24 aat---------aataataataa >ponAbe2 66 hg18 chr22 16067383 16067912 panTro2 chr22 16076179 16076703 ponAbe2 chr22 13768341 13768861 rheMac2 chr10 61853314 61853841 trinucleotide TAA 0 2 + 24 aataataataataataataataa >rheMac2 66 hg18 chr22 16067383 16067912 panTro2 chr22 16076179 16076703 ponAbe2 chr22 13768341 13768861 rheMac2 chr10 61853314 61853841 trinucleotide AAT 0 5 + 16 aataataaTAAT ->hg18 66 hg18 chr22 16067383 16067912 panTro2 chr22 16076179 16076703 ponAbe2 chr22 13768341 13768861 rheMac2 chr10 61853314 61853841 mononucleotide T 6 162 + 170 ttttttttt >panTro2 66 hg18 chr22 16067383 16067912 panTro2 chr22 16076179 16076703 ponAbe2 chr22 13768341 13768861 rheMac2 chr10 61853314 61853841 mononucleotide T 10 162 + 187 tttttttttttttttttttttttttt >ponAbe2 66 hg18 chr22 16067383 16067912 panTro2 chr22 16076179 16076703 ponAbe2 chr22 13768341 13768861 rheMac2 chr10 61853314 61853841 mononucleotide T 1 162 + 176 ttttttttttttttt ->rheMac2 72 hg18 chr22 16094969 16095324 panTro2 chr22 16105978 16106333 ponAbe2 chr22 13802979 13803302 rheMac2 chr10 61893496 61893856 trinucleotide CAC 6 216 + 230 CACCACCACCACCAC ->hg18 73 hg18 chr22 16104191 16104501 panTro2 chr22 16115194 16115505 ponAbe2 chr22 13812355 13812669 rheMac2 chr10 61902739 61903042 mononucleotide A 1 286 + 305 aaaaaaaaaaaaaaaaaaaa >panTro2 73 hg18 chr22 16104191 16104501 panTro2 chr22 16115194 16115505 ponAbe2 chr22 13812355 13812669 rheMac2 chr10 61902739 61903042 mononucleotide A 1 286 + 306 aaaaaaaaaaaaaaaaaaaaa >ponAbe2 73 hg18 chr22 16104191 16104501 panTro2 chr22 16115194 16115505 ponAbe2 chr22 13812355 13812669 rheMac2 chr10 61902739 61903042 mononucleotide A 0 286 + 308 aaaaaaaaaaaaaaaaaaaaaaa >rheMac2 73 hg18 chr22 16104191 16104501 panTro2 chr22 16115194 16115505 ponAbe2 chr22 13812355 13812669 rheMac2 chr10 61902739 61903042 mononucleotide A 1 286 + 298 aaaaaaaaaaaaa ->hg18 74 hg18 chr22 16107131 16108471 panTro2 chr22 16118678 16120001 ponAbe2 chr22 13815039 13816359 rheMac2 chr10 61905927 61907245 mononucleotide [a][A] 0 420 + 430 [a]g[aaaaaaaaa] indel/deletion g 2 1 >panTro2 74 hg18 chr22 16107131 16108471 panTro2 chr22 16118678 16120001 ponAbe2 chr22 13815039 13816359 rheMac2 chr10 61905927 61907245 mononucleotide [a][A] 0 420 + 430 [a]g[aaaaaaaaa] indel/deletion g 2 1 >ponAbe2 74 hg18 chr22 16107131 16108471 panTro2 chr22 16118678 16120001 ponAbe2 chr22 13815039 13816359 rheMac2 chr10 61905927 61907245 mononucleotide [a][A] 0 420 + 430 [a]g[aaaaaaaaa] indel/deletion g 2 1 >rheMac2 74 hg18 chr22 16107131 16108471 panTro2 chr22 16118678 16120001 ponAbe2 chr22 13815039 13816359 rheMac2 chr10 61905927 61907245 mononucleotide [a][A] 3 420 + 430 [a]g[aaaaaaaaa] indel/deletion g 2 1 ->hg18 74 hg18 chr22 16107131 16108471 panTro2 chr22 16118678 16120001 ponAbe2 chr22 13815039 13816359 rheMac2 chr10 61905927 61907245 mononucleotide [A][A][a][a][A][A] 1 942 + 988 [aaaaaaaaaaaaaaa]g[aaaaa]g[aaaa]g[aaaAAAAA]G[AAAAA]G[AAAAA] insertion,indel/deletion,indel/deletion,indel/deletion,indel/deletion g,g,g,G,G 16,22,27,36,42 5 >ponAbe2 74 hg18 chr22 16107131 16108471 panTro2 chr22 16118678 16120001 ponAbe2 chr22 13815039 13816359 rheMac2 chr10 61905927 61907245 mononucleotide [A][A][A] 3 942 + 994 [aaaaaaaa--------aaaaaaaaaa]g[aaaaa]g[aa---------------aaa] insertion,insertion g,g 19,25 2 >rheMac2 74 hg18 chr22 16107131 16108471 panTro2 chr22 16118678 16120001 ponAbe2 chr22 13815039 13816359 rheMac2 chr10 61905927 61907245 mononucleotide [A][a] 4 942 + 972 [aaaaaaaa--------aaaaaaaaaa]g[aaaa] indel/deletion g 19 1 ->hg18 74 hg18 chr22 16107131 16108471 panTro2 chr22 16118678 16120001 ponAbe2 chr22 13815039 13816359 rheMac2 chr10 61905927 61907245 mononucleotide A 2 1287 + 1298 aaaaaaaaaaaa >panTro2 74 hg18 chr22 16107131 16108471 panTro2 chr22 16118678 16120001 ponAbe2 chr22 13815039 13816359 rheMac2 chr10 61905927 61907245 mononucleotide A 23 1287 + 1302 aaaaaaaaaaaaaaaa >ponAbe2 74 hg18 chr22 16107131 16108471 panTro2 chr22 16118678 16120001 ponAbe2 chr22 13815039 13816359 rheMac2 chr10 61905927 61907245 mononucleotide A 26 1288 + 1302 aaaaaaaaaaaaaaa >rheMac2 74 hg18 chr22 16107131 16108471 panTro2 chr22 16118678 16120001 ponAbe2 chr22 13815039 13816359 rheMac2 chr10 61905927 61907245 mononucleotide A 34 1288 + 1302 aa-aaaaaaaaaaaa ->hg18 75 hg18 chr22 16116290 16116687 panTro2 chr22 16132717 16133117 ponAbe2 chr22 13835535 13835935 rheMac2 chr10 61916292 61916704 mononucleotide [A][A] 1 36 + 52 [aaaaaaaaaaaaaaa]C[A] indel/deletion C 16 1 >panTro2 75 hg18 chr22 16116290 16116687 panTro2 chr22 16132717 16133117 ponAbe2 chr22 13835535 13835935 rheMac2 chr10 61916292 61916704 mononucleotide A 1 36 + 53 aaaaaaaaaaaaaaaaaa >ponAbe2 75 hg18 chr22 16116290 16116687 panTro2 chr22 16132717 16133117 ponAbe2 chr22 13835535 13835935 rheMac2 chr10 61916292 61916704 mononucleotide [a][A] 0 36 + 50 [a]t[aaaaaaaaaaaaa] indel/deletion t 2 1 ->hg18 75 hg18 chr22 16116290 16116687 panTro2 chr22 16132717 16133117 ponAbe2 chr22 13835535 13835935 rheMac2 chr10 61916292 61916704 mononucleotide T 17 401 + 413 ttttttttttttt >panTro2 75 hg18 chr22 16116290 16116687 panTro2 chr22 16132717 16133117 ponAbe2 chr22 13835535 13835935 rheMac2 chr10 61916292 61916704 mononucleotide T 15 401 + 414 tttttttttttttt >ponAbe2 75 hg18 chr22 16116290 16116687 panTro2 chr22 16132717 16133117 ponAbe2 chr22 13835535 13835935 rheMac2 chr10 61916292 61916704 mononucleotide T 15 401 + 414 tttttttttttttt >rheMac2 75 hg18 chr22 16116290 16116687 panTro2 chr22 16132717 16133117 ponAbe2 chr22 13835535 13835935 rheMac2 chr10 61916292 61916704 mononucleotide T 2 401 + 414 tttttttttttttt ->ponAbe2 77 hg18 chr22 16117347 16117704 panTro2 chr22 16133777 16134130 ponAbe2 chr22 13836768 13837113 rheMac2 chr10 61917653 61917998 mononucleotide T 4 77 + 101 ttttt--------tttttttttttt >rheMac2 77 hg18 chr22 16117347 16117704 panTro2 chr22 16133777 16134130 ponAbe2 chr22 13836768 13837113 rheMac2 chr10 61917653 61917998 mononucleotide T 4 77 + 101 ttttt--------tttttttttttt >panTro2 77 hg18 chr22 16117347 16117704 panTro2 chr22 16133777 16134130 ponAbe2 chr22 13836768 13837113 rheMac2 chr10 61917653 61917998 trinucleotide [TTG][gTT] 4 81 + 100 [ttgttgttgttg]ttt[ttgtt] indel/deletion ttt 13 1 ->hg18 82 hg18 chr22 16129047 16130298 panTro2 chr22 16145849 16147084 ponAbe2 chr22 13849124 13850363 rheMac2 chr10 61930726 61931954 mononucleotide [A][A] 2 391 + 412 [AAAAAAA]G[AAAAAAAAAAAAAA] insertion G 8 1 >panTro2 82 hg18 chr22 16129047 16130298 panTro2 chr22 16145849 16147084 ponAbe2 chr22 13849124 13850363 rheMac2 chr10 61930726 61931954 mononucleotide [A][A] 2 391 + 412 [AAAAAAA]G---[AAAAAAAAAAA] insertion G 8 1 >ponAbe2 82 hg18 chr22 16129047 16130298 panTro2 chr22 16145849 16147084 ponAbe2 chr22 13849124 13850363 rheMac2 chr10 61930726 61931954 mononucleotide A 13 391 + 412 AAAAAAA----AAAAAAAAAAA ->hg18 82 hg18 chr22 16129047 16130298 panTro2 chr22 16145849 16147084 ponAbe2 chr22 13849124 13850363 rheMac2 chr10 61930726 61931954 tetranucleotide AAGG 3 939 + 950 AAGGAAGGAAGG >panTro2 82 hg18 chr22 16129047 16130298 panTro2 chr22 16145849 16147084 ponAbe2 chr22 13849124 13850363 rheMac2 chr10 61930726 61931954 tetranucleotide AAGG 6 939 + 950 AAGGAAGGAAGG >ponAbe2 82 hg18 chr22 16129047 16130298 panTro2 chr22 16145849 16147084 ponAbe2 chr22 13849124 13850363 rheMac2 chr10 61930726 61931954 tetranucleotide AAGG 18 939 + 950 AAGGAAGGAAGG >rheMac2 82 hg18 chr22 16129047 16130298 panTro2 chr22 16145849 16147084 ponAbe2 chr22 13849124 13850363 rheMac2 chr10 61930726 61931954 tetranucleotide AAGG 22 939 + 950 AAGGAAGGAAGG ->ponAbe2 83 hg18 chr22 16131190 16131832 panTro2 chr22 16147976 16148613 ponAbe2 chr22 13852894 13853533 rheMac2 chr10 61934057 61934680 tetranucleotide CATG 1 522 + 533 CATGCATGCATG ->hg18 83 hg18 chr22 16131190 16131832 panTro2 chr22 16147976 16148613 ponAbe2 chr22 13852894 13853533 rheMac2 chr10 61934057 61934680 mononucleotide [t][t][t][T] 1 563 + 592 [ttt]a[ttttt]c[tttt]c[ttttttttttttttt] indel/deletion,indel/deletion,indel/deletion a,c,c 4,10,15 3 >panTro2 83 hg18 chr22 16131190 16131832 panTro2 chr22 16147976 16148613 ponAbe2 chr22 13852894 13853533 rheMac2 chr10 61934057 61934680 mononucleotide [t][T][T][T] 1 563 + 592 [ttt]c[ttttt]c[tt---ttttttttt]c[ttttt] indel/deletion,insertion,insertion c,c,c 4,10,22 3 >ponAbe2 83 hg18 chr22 16131190 16131832 panTro2 chr22 16147976 16148613 ponAbe2 chr22 13852894 13853533 rheMac2 chr10 61934057 61934680 mononucleotide [t][t][t][T] 1 563 + 592 [ttt]c[tttt]c[ttt---t]c[ttttttttttttt] indel/deletion,indel/deletion,indel/deletion c,c,c 4,9,14 3 >rheMac2 83 hg18 chr22 16131190 16131832 panTro2 chr22 16147976 16148613 ponAbe2 chr22 13852894 13853533 rheMac2 chr10 61934057 61934680 mononucleotide [T][T][T] 1 564 + 592 [TT]C[TT]C--------[TTTTTTTTTTTTTTT] indel/deletion,indel/deletion C,C 3,6 2 ->hg18 84 hg18 chr22 16137705 16138405 panTro2 chr22 16154263 16154962 ponAbe2 chr22 13860046 13860739 rheMac2 chr10 61941762 61942469 mononucleotide T 0 34 + 77 ttt--------------------------ttttttttttttttt >panTro2 84 hg18 chr22 16137705 16138405 panTro2 chr22 16154263 16154962 ponAbe2 chr22 13860046 13860739 rheMac2 chr10 61941762 61942469 mononucleotide T 0 34 + 76 tt--------------------------ttttttttttttttt >ponAbe2 84 hg18 chr22 16137705 16138405 panTro2 chr22 16154263 16154962 ponAbe2 chr22 13860046 13860739 rheMac2 chr10 61941762 61942469 mononucleotide T 1 34 + 48 ttttttttttttttt >rheMac2 84 hg18 chr22 16137705 16138405 panTro2 chr22 16154263 16154962 ponAbe2 chr22 13860046 13860739 rheMac2 chr10 61941762 61942469 mononucleotide [T][T] 0 34 + 46 [TTT]A[TTTtttttt] indel/deletion A 4 1 ->hg18 84 hg18 chr22 16137705 16138405 panTro2 chr22 16154263 16154962 ponAbe2 chr22 13860046 13860739 rheMac2 chr10 61941762 61942469 mononucleotide [T][T][T] 26 227 + 253 [tttttt]c[ttttt]c[tttttttttttttt] insertion,insertion c,c 7,13 2 >panTro2 84 hg18 chr22 16137705 16138405 panTro2 chr22 16154263 16154962 ponAbe2 chr22 13860046 13860739 rheMac2 chr10 61941762 61942469 mononucleotide [T][T][T] 27 227 + 253 [tttttt]c[ttttt]c[tttttttttttttt] insertion,insertion c,c 7,13 2 >ponAbe2 84 hg18 chr22 16137705 16138405 panTro2 chr22 16154263 16154962 ponAbe2 chr22 13860046 13860739 rheMac2 chr10 61941762 61942469 mononucleotide [T][T][T] 30 227 + 253 [tttttt]c[ttttt]c---[ttttttttttt] insertion,insertion c,c 7,13 2 >rheMac2 84 hg18 chr22 16137705 16138405 panTro2 chr22 16154263 16154962 ponAbe2 chr22 13860046 13860739 rheMac2 chr10 61941762 61942469 mononucleotide T 0 228 + 253 tt-------------ttttttttttt ->panTro2 85 hg18 chr22 16138070 16138593 panTro2 chr22 34008160 34008614 ponAbe2 chr22 32672693 32673135 rheMac2 chr10 32911352 32911798 mononucleotide [T][T] 0 143 + 172 [tttt------tttttt]a[t--tttttttttt] insertion a 11 1 >ponAbe2 85 hg18 chr22 16138070 16138593 panTro2 chr22 34008160 34008614 ponAbe2 chr22 32672693 32673135 rheMac2 chr10 32911352 32911798 mononucleotide T 2 143 + 158 tttt------tttttt >ponAbe2 85 hg18 chr22 16138070 16138593 panTro2 chr22 34008160 34008614 ponAbe2 chr22 32672693 32673135 rheMac2 chr10 32911352 32911798 mononucleotide T 8 162 + 172 ttttttttttt >rheMac2 85 hg18 chr22 16138070 16138593 panTro2 chr22 34008160 34008614 ponAbe2 chr22 32672693 32673135 rheMac2 chr10 32911352 32911798 mononucleotide T 0 143 + 160 tttt------tttttttt ->hg18 88 hg18 chr22 16139028 16139315 panTro2 chr22 16155881 16156173 ponAbe2 chr22 13861549 13861841 rheMac2 chr10 61943159 61943448 mononucleotide [T][T][t] 0 12 + 29 [T]C[ttttttttttttt]c[tt] indel/deletion,indel/deletion C,c 2,16 2 >ponAbe2 88 hg18 chr22 16139028 16139315 panTro2 chr22 16155881 16156173 ponAbe2 chr22 13861549 13861841 rheMac2 chr10 61943159 61943448 mononucleotide [T][T] 0 12 + 32 [T]C[ttttttttttttttttttt] indel/deletion C 2 1 >rheMac2 88 hg18 chr22 16139028 16139315 panTro2 chr22 16155881 16156173 ponAbe2 chr22 13861549 13861841 rheMac2 chr10 61943159 61943448 mononucleotide [t][T] 0 12 + 36 [t]c[ttttttttttttttttttttttt] indel/deletion c 2 1 >panTro2 88 hg18 chr22 16139028 16139315 panTro2 chr22 16155881 16156173 ponAbe2 chr22 13861549 13861841 rheMac2 chr10 61943159 61943448 tetranucleotide TGTC 0 17 + 32 TGTCTGTCTGTCTGTC ->hg18 88 hg18 chr22 16139028 16139315 panTro2 chr22 16155881 16156173 ponAbe2 chr22 13861549 13861841 rheMac2 chr10 61943159 61943448 mononucleotide T 8 187 + 201 tttttttt--ttttt >ponAbe2 88 hg18 chr22 16139028 16139315 panTro2 chr22 16155881 16156173 ponAbe2 chr22 13861549 13861841 rheMac2 chr10 61943159 61943448 mononucleotide T 5 187 + 201 ttttttttttttttt ->hg18 89 hg18 chr22 16139377 16139692 panTro2 chr22 16159787 16160102 ponAbe2 chr22 13865240 13865552 rheMac2 chr10 61946542 61946865 mononucleotide [T][T][T][T] 1 290 + 322 [ttt]c[ttt]c[ttt]c-------[tttttttttttttt] indel/deletion,indel/deletion,indel/deletion C,C,C 4,8,12 3 >panTro2 89 hg18 chr22 16139377 16139692 panTro2 chr22 16159787 16160102 ponAbe2 chr22 13865240 13865552 rheMac2 chr10 61946542 61946865 mononucleotide [T][T][T][T] 0 290 + 322 [ttt]c[ttt]c[ttt]c--------[ttttttttttttt] indel/deletion,indel/deletion,indel/deletion C,C,C 4,8,12 3 >ponAbe2 89 hg18 chr22 16139377 16139692 panTro2 chr22 16159787 16160102 ponAbe2 chr22 13865240 13865552 rheMac2 chr10 61946542 61946865 mononucleotide [T][T][t] 1 290 + 322 [ttt]c[tttttt----------tttttttt]a[tttt] indel/deletion,indel/deletion C,a 4,19 2 ->hg18 100 hg18 chr22 16152355 16152746 panTro2 chr22 16173078 16173465 ponAbe2 chr22 13878876 13879267 rheMac2 chr10 61961383 61961771 dinucleotide [TA][AT][AT][AT][TA] 0 341 + 367 [TA]A[ATATATATAT]GA[ATAT]GG[ATAT][TA] indel/deletion,indel/deletion,indel/deletion,indel/deletion A,GA,GG, 3,14,20,26 4 >panTro2 100 hg18 chr22 16152355 16152746 panTro2 chr22 16173078 16173465 ponAbe2 chr22 13878876 13879267 rheMac2 chr10 61961383 61961771 dinucleotide [TA][AT][AT][AT][TA][TA][AT] 0 341 + 377 [TA]A[ATATATATAT]GA[ATAT]GG[ATAT][TATA]CT[TATA][AT] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion A,GA,GG,,CT, 3,14,20,26,30,36 6 >ponAbe2 100 hg18 chr22 16152355 16152746 panTro2 chr22 16173078 16173465 ponAbe2 chr22 13878876 13879267 rheMac2 chr10 61961383 61961771 dinucleotide [TA][AT][AT][AT][TA][TA][AT] 0 341 + 377 [TA]A[ATATATATAT]GA[ATAT]GG[ATAT][TATAT]T[TATA][AT] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion A,GA,GG,,T, 3,14,20,26,31,36 6 >rheMac2 100 hg18 chr22 16152355 16152746 panTro2 chr22 16173078 16173465 ponAbe2 chr22 13878876 13879267 rheMac2 chr10 61961383 61961771 dinucleotide [TA][AT][AT] 3 341 + 358 [TA]A[ATATATATAT]GA[ATA] indel/deletion,indel/deletion A,GA 3,14 2 ->hg18 104 hg18 chr22 16153783 16154051 panTro2 chr22 16174841 16175099 ponAbe2 chr22 13880942 13881208 rheMac2 chr10 61962546 61962830 mononucleotide A 2 109 + 121 aaaaaaaaaaaaa >panTro2 104 hg18 chr22 16153783 16154051 panTro2 chr22 16174841 16175099 ponAbe2 chr22 13880942 13881208 rheMac2 chr10 61962546 61962830 mononucleotide A 15 109 + 124 aaaaaaaaaaaaaaaa >ponAbe2 104 hg18 chr22 16153783 16154051 panTro2 chr22 16174841 16175099 ponAbe2 chr22 13880942 13881208 rheMac2 chr10 61962546 61962830 mononucleotide A 2 109 + 119 aaaaaaaaaaa >rheMac2 104 hg18 chr22 16153783 16154051 panTro2 chr22 16174841 16175099 ponAbe2 chr22 13880942 13881208 rheMac2 chr10 61962546 61962830 mononucleotide A 0 109 + 135 aaaaaaaaaaaaaaaaaaaaaaaaaaa ->hg18 106 hg18 chr22 16168384 16169226 panTro2 chr22 16189805 16190649 ponAbe2 chr22 13897079 13897917 rheMac2 chr10 61978430 61979279 tetranucleotide AGAA 0 1 + 13 aagaaagaaagaa >panTro2 106 hg18 chr22 16168384 16169226 panTro2 chr22 16189805 16190649 ponAbe2 chr22 13897079 13897917 rheMac2 chr10 61978430 61979279 tetranucleotide AAGA 0 1 + 14 aagaaagaaagaaa >ponAbe2 106 hg18 chr22 16168384 16169226 panTro2 chr22 16189805 16190649 ponAbe2 chr22 13897079 13897917 rheMac2 chr10 61978430 61979279 tetranucleotide AAGA 0 1 + 14 aagaaagaaagaaa >rheMac2 106 hg18 chr22 16168384 16169226 panTro2 chr22 16189805 16190649 ponAbe2 chr22 13897079 13897917 rheMac2 chr10 61978430 61979279 tetranucleotide AAGA 0 1 + 14 aagaaagaaagaaa ->rheMac2 106 hg18 chr22 16168384 16169226 panTro2 chr22 16189805 16190649 ponAbe2 chr22 13897079 13897917 rheMac2 chr10 61978430 61979279 mononucleotide [A][A][A][a][a] 22 395 + 427 [aaaaaaaaaaaaaa]g[aaaaa]g[aaaaa]g[aaaa]c[a] insertion,insertion,indel/deletion,indel/deletion g,g,g,c 15,21,27,32 4 ->hg18 106 hg18 chr22 16168384 16169226 panTro2 chr22 16189805 16190649 ponAbe2 chr22 13897079 13897917 rheMac2 chr10 61978430 61979279 mononucleotide [t][T] 37 724 + 738 [t]c--[ttttttttttt] indel/deletion c 2 1 >panTro2 106 hg18 chr22 16168384 16169226 panTro2 chr22 16189805 16190649 ponAbe2 chr22 13897079 13897917 rheMac2 chr10 61978430 61979279 mononucleotide [t][T] 38 724 + 738 [t]c[ttttttttttttt] indel/deletion c 2 1 >ponAbe2 106 hg18 chr22 16168384 16169226 panTro2 chr22 16189805 16190649 ponAbe2 chr22 13897079 13897917 rheMac2 chr10 61978430 61979279 mononucleotide [t][T] 41 724 + 738 [t]c---[tttttttttt] indel/deletion c 2 1 >rheMac2 106 hg18 chr22 16168384 16169226 panTro2 chr22 16189805 16190649 ponAbe2 chr22 13897079 13897917 rheMac2 chr10 61978430 61979279 mononucleotide [t][T] 27 724 + 738 [t]c[ttttttttttttt] indel/deletion c 2 1 ->panTro2 106 hg18 chr22 16168384 16169226 panTro2 chr22 16189805 16190649 ponAbe2 chr22 13897079 13897917 rheMac2 chr10 61978430 61979279 compound [TA][ATCT] 40 852 + 884 [tatatatata]g[atctatctatctatctatctat] >ponAbe2 106 hg18 chr22 16168384 16169226 panTro2 chr22 16189805 16190649 ponAbe2 chr22 13897079 13897917 rheMac2 chr10 61978430 61979279 compound [TA][ATCT] 46 852 + 884 [tatatatata]g[atctatctatctatctatctat] >rheMac2 106 hg18 chr22 16168384 16169226 panTro2 chr22 16189805 16190649 ponAbe2 chr22 13897079 13897917 rheMac2 chr10 61978430 61979279 compound [TA][ATCT] 35 852 + 884 [TATATATATA]G[atctatctatctatctatctat] ->rheMac2 107 hg18 chr22 16169260 16169890 panTro2 chr22 16190654 16191272 ponAbe2 chr22 13898138 13898766 rheMac2 chr10 61979358 61979989 dinucleotide.mononucleotide [TA][TA].[t][T][T][t] 0 1 + 27 [tatatatatATTATTTTTTttttttgt] indel/deletion.indel/deletion,indel/deletion,indel/deletion .A,A,g 12.2,5,18 1.3 1.9 14.27 [TATATATATAT][TAT].[t]A[TT]A[TTTTTTTTTTTT]g[t] >hg18 107 hg18 chr22 16169260 16169890 panTro2 chr22 16190654 16191272 ponAbe2 chr22 13898138 13898766 rheMac2 chr10 61979358 61979989 mononucleotide [T][T][t] 0 11 + 27 [ttttttttt]c[ttttt]g[t] insertion,indel/deletion c,g 10,16 2 >ponAbe2 107 hg18 chr22 16169260 16169890 panTro2 chr22 16190654 16191272 ponAbe2 chr22 13898138 13898766 rheMac2 chr10 61979358 61979989 mononucleotide [T][t] 0 12 + 27 [tttttttttttttt]g[t] indel/deletion g 15 1 ->hg18 107 hg18 chr22 16169260 16169890 panTro2 chr22 16190654 16191272 ponAbe2 chr22 13898138 13898766 rheMac2 chr10 61979358 61979989 mononucleotide A 0 620 + 629 aaaaaaaaaa >panTro2 107 hg18 chr22 16169260 16169890 panTro2 chr22 16190654 16191272 ponAbe2 chr22 13898138 13898766 rheMac2 chr10 61979358 61979989 mononucleotide A 11 620 + 628 aaaaaaaaa >ponAbe2 107 hg18 chr22 16169260 16169890 panTro2 chr22 16190654 16191272 ponAbe2 chr22 13898138 13898766 rheMac2 chr10 61979358 61979989 mononucleotide A 0 620 + 628 aaaaaaaaa ->rheMac2 109 hg18 chr22 16171713 16171947 panTro2 chr22 16194113 16194359 ponAbe2 chr22 13902608 13902842 rheMac2 chr10 61982200 61982434 tetranucleotide AAAT 1 218 + 246 aaa-----------taaataaataaataa >hg18 109 hg18 chr22 16171713 16171947 panTro2 chr22 16194113 16194359 ponAbe2 chr22 13902608 13902842 rheMac2 chr10 61982200 61982434 tetranucleotide ATAA 0 221 + 234 aaataaataaataa >panTro2 109 hg18 chr22 16171713 16171947 panTro2 chr22 16194113 16194359 ponAbe2 chr22 13902608 13902842 rheMac2 chr10 61982200 61982434 tetranucleotide ATAA 0 221 + 246 aaataaataaataaataaataaataa >ponAbe2 109 hg18 chr22 16171713 16171947 panTro2 chr22 16194113 16194359 ponAbe2 chr22 13902608 13902842 rheMac2 chr10 61982200 61982434 tetranucleotide ATAA 0 221 + 234 aaataaataaataa ->hg18 110 hg18 chr22 16172029 16172345 panTro2 chr22 16194441 16194757 ponAbe2 chr22 13902924 13903238 rheMac2 chr10 61982516 61982838 mononucleotide [A][A] 0 300 + 321 [aaaa------a]g[aaaaaaaaaa] insertion g 6 1 >panTro2 110 hg18 chr22 16172029 16172345 panTro2 chr22 16194441 16194757 ponAbe2 chr22 13902924 13903238 rheMac2 chr10 61982516 61982838 mononucleotide [A][A] 0 300 + 321 [aaaa------a]g[aaaaaaaaaa] insertion g 6 1 >ponAbe2 110 hg18 chr22 16172029 16172345 panTro2 chr22 16194441 16194757 ponAbe2 chr22 13902924 13903238 rheMac2 chr10 61982516 61982838 mononucleotide A 0 300 + 321 aaaa--------aaaaaaaaaa >rheMac2 110 hg18 chr22 16172029 16172345 panTro2 chr22 16194441 16194757 ponAbe2 chr22 13902924 13903238 rheMac2 chr10 61982516 61982838 mononucleotide [a][A][A] 0 300 + 320 [aa]g[aaaaaa]g[aaaaaaaaaaa] indel/deletion,insertion g,g 3,10 2 ->hg18 113 hg18 chr22 16179408 16180368 panTro2 chr22 16202766 16203726 ponAbe2 chr22 13910895 13911919 rheMac2 chr10 61989155 61990120 dinucleotide [GA][ga] 8 419 + 432 [gagagagaga]cg[ga] indel/deletion cg 11 1 >panTro2 113 hg18 chr22 16179408 16180368 panTro2 chr22 16202766 16203726 ponAbe2 chr22 13910895 13911919 rheMac2 chr10 61989155 61990120 dinucleotide [GA][ga] 8 419 + 432 [gagagagaga]cg[ga] indel/deletion cg 11 1 >ponAbe2 113 hg18 chr22 16179408 16180368 panTro2 chr22 16202766 16203726 ponAbe2 chr22 13910895 13911919 rheMac2 chr10 61989155 61990120 dinucleotide [GA][ga] 7 419 + 436 [gagagagagagaga]cg[ga] indel/deletion cg 15 1 ->hg18 114 hg18 chr22 16181507 16182279 panTro2 chr22 16204865 16205652 ponAbe2 chr22 13912842 13913643 rheMac2 chr10 61991251 61992115 mononucleotide [T][T] 25 424 + 471 [TTT------------------------------TTTTTTTTTTTTT]G[T] indel/deletion G 17 1 >panTro2 114 hg18 chr22 16181507 16182279 panTro2 chr22 16204865 16205652 ponAbe2 chr22 13912842 13913643 rheMac2 chr10 61991251 61992115 mononucleotide [T][T][t][t] 24 424 + 468 [ttt-------ttttttttt]a[ttttt]a[tt]----a[tttttttttttt] insertion,indel/deletion,indel/deletion a,a,a 13,19,22 3 ->rheMac2 114 hg18 chr22 16181507 16182279 panTro2 chr22 16204865 16205652 ponAbe2 chr22 13912842 13913643 rheMac2 chr10 61991251 61992115 mononucleotide [T][T][t][t] 25 498 + 528 [tttttttt---tt]c[ttttt]c[ttt]g[ttttttt] insertion,indel/deletion,indel/deletion c,c,g 11,17,21 3 >hg18 114 hg18 chr22 16181507 16182279 panTro2 chr22 16204865 16205652 ponAbe2 chr22 13912842 13913643 rheMac2 chr10 61991251 61992115 mononucleotide T 55 506 + 528 ttttttttttttttttttttttt >panTro2 114 hg18 chr22 16181507 16182279 panTro2 chr22 16204865 16205652 ponAbe2 chr22 13912842 13913643 rheMac2 chr10 61991251 61992115 mononucleotide T 40 512 + 528 ttttttttttttttttt >ponAbe2 114 hg18 chr22 16181507 16182279 panTro2 chr22 16204865 16205652 ponAbe2 chr22 13912842 13913643 rheMac2 chr10 61991251 61992115 mononucleotide T 25 512 + 528 ttttttttttttttttt ->rheMac2 114 hg18 chr22 16181507 16182279 panTro2 chr22 16204865 16205652 ponAbe2 chr22 13912842 13913643 rheMac2 chr10 61991251 61992115 mononucleotide T 30 834 + 845 tttttttttttt ->hg18 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide A 4 535 + 550 aaaaaaaaaaaaaaaa >panTro2 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide A 4 535 + 554 aaaaaaaaaaaaaaaaaaaa >ponAbe2 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide A 4 535 + 554 aaaaaaaaaaaaaaaaaaaa >rheMac2 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide A 0 535 + 548 aaaaaaaaaaaaaa ->rheMac2 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide [a][A] 7 759 + 780 [a]c[a---------aaaaaaaaaa] indel/deletion c 2 1 >hg18 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide A 8 762 + 778 aaaaaaaaaaaaaaaaa >panTro2 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide A 4 762 + 780 aaaaaaaaaaaaaaaaaaa >ponAbe2 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide A 4 762 + 776 aaaaaaaaaaaaaaa ->hg18 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide [A][A][a][a][a] 10 1137 + 1177 [aaaaaaaaaaaaaaaaaaaa]g[aaaaa]g[aaaa]g[aaaaaa]t[aa] insertion,indel/deletion,indel/deletion,indel/deletion g,g,g,t 21,27,32,39 4 >panTro2 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide [A][a][a][a][a][a] 4 1137 + 1173 [aaaaaaaaaaaa]t[aaa]g[aaaaa]g[aaaa]g[aaaaaa]t[aa] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion t,g,g,g,t 13,17,23,28,35 5 >ponAbe2 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide [A][A][A][A][a][a][a] 9 1137 + 1178 [aaaaaaaaaaaaa]g[aaa]g[aaa]g[aaaaa]g[aaaa]g[aaaaaa]t[aa] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion G,G,G,g,g,t 14,18,22,28,33,40 7 >rheMac2 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide [A][a] 17 1137 + 1150 [aaaaaaaaaaa]c[aa] indel/deletion c 12 1 ->rheMac2 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide A 24 1399 + 1429 a--------------aaaaaaaaaaaaaaaa >hg18 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide A 11 1400 + 1428 aaaaaaaaaaaaaaaaaaaaaaaaaaaaa >panTro2 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide A 9 1400 + 1421 aaaaaaaaaaaaaaaaaaaaaa >ponAbe2 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide A 9 1400 + 1424 aaaaaaaaaaaaaaaaaaaaaaaaa ->hg18 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 tetranucleotide [AATT][taat] 25 2535 + 2555 [aattaattaattaatt][taatt] indel/deletion 17 1 >panTro2 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 tetranucleotide [AATT][ttaa] 30 2535 + 2562 [aattaattaattaattaa]at[ttaattaa] indel/deletion at 19 1 >ponAbe2 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 tetranucleotide [AATT][taat] 28 2535 + 2555 [aattaattaattaatt][taatt] indel/deletion 17 1 >rheMac2 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 tetranucleotide [AATT][taat] 46 2535 + 2562 [aattaattaatt-----aatt][taattaa] indel/deletion 17 1 ->hg18 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide [T][T] 25 2802 + 2823 [tttttttt]c--[ttttttttttt] insertion c 9 1 >panTro2 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide [T][T] 30 2802 + 2823 [tttttttt]c[ttttttttttttt] insertion c 9 1 >ponAbe2 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide [T][t] 28 2802 + 2823 [tttt-------tttttt]c[tttt] indel/deletion c 11 1 ->hg18 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide [t][t][t][t][T] 27 3345 + 3380 [tt]c[tttt]c[tttt]c[tttt]c[ttt--ttttttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion c,c,c,c 3,8,13,18 4 >panTro2 115 hg18 chr22 16182279 16185645 panTro2 chr22 16205652 16209017 ponAbe2 chr22 13913643 13917021 rheMac2 chr10 61992364 61995689 mononucleotide [t][t][t][t][t][T] 30 3345 + 3380 [tt]c[tttt]c[tttt]c[tttt]c[tttt]c[ttttttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion c,c,c,c,c 3,8,13,18,23 5 ->hg18 118 hg18 chr22 16190841 16191000 panTro2 chr22 16214201 16214360 ponAbe2 chr22 13932445 13932603 rheMac2 chr10 62001165 62001330 mononucleotide [A][A][a][a] 0 6 + 37 [aaaaa]g[aaaaaaaaaa]g------[aaaa]g[aaaa] insertion,indel/deletion,indel/deletion g,g,g 6,17,22 3 >panTro2 118 hg18 chr22 16190841 16191000 panTro2 chr22 16214201 16214360 ponAbe2 chr22 13932445 13932603 rheMac2 chr10 62001165 62001330 mononucleotide [A][A][a][a] 0 6 + 37 [aaaaa]g[aaaaaaaaaa]g------[aaaa]g[aaaa] insertion,indel/deletion,indel/deletion g,g,g 6,17,22 3 >rheMac2 118 hg18 chr22 16190841 16191000 panTro2 chr22 16214201 16214360 ponAbe2 chr22 13932445 13932603 rheMac2 chr10 62001165 62001330 mononucleotide A 0 6 + 37 aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa ->hg18 121 hg18 chr22 16191297 16191670 panTro2 chr22 16214657 16215037 ponAbe2 chr22 13922971 13923347 rheMac2 chr10 62001444 62001733 mononucleotide A 8 372 + 381 aaaaaaaaaa >panTro2 121 hg18 chr22 16191297 16191670 panTro2 chr22 16214657 16215037 ponAbe2 chr22 13922971 13923347 rheMac2 chr10 62001444 62001733 mononucleotide A 2 372 + 382 aaaaaaaaaaa ->hg18 122 hg18 chr22 16191804 16192915 panTro2 chr22 16215171 16216287 ponAbe2 chr22 13933410 13934522 rheMac2 chr10 62002585 62003707 trinucleotide [AAT][taa] 1 130 + 148 [aataataataataat]t[taa] indel/deletion t 16 1 >panTro2 122 hg18 chr22 16191804 16192915 panTro2 chr22 16215171 16216287 ponAbe2 chr22 13933410 13934522 rheMac2 chr10 62002585 62003707 trinucleotide [AAT][taa] 1 130 + 148 [aataataataataat]t[taa] indel/deletion t 16 1 >ponAbe2 122 hg18 chr22 16191804 16192915 panTro2 chr22 16215171 16216287 ponAbe2 chr22 13933410 13934522 rheMac2 chr10 62002585 62003707 trinucleotide [AAT][taa] 1 130 + 148 [aataataataataat]t[taa] indel/deletion t 16 1 ->ponAbe2 122 hg18 chr22 16191804 16192915 panTro2 chr22 16215171 16216287 ponAbe2 chr22 13933410 13934522 rheMac2 chr10 62002585 62003707 trinucleotide [taa][ATA] 2 293 + 331 [taa]aaa[aaTAATAATA--------------------ATA] indel/deletion aaa 4 1 >hg18 122 hg18 chr22 16191804 16192915 panTro2 chr22 16215171 16216287 ponAbe2 chr22 13933410 13934522 rheMac2 chr10 62002585 62003707 trinucleotide ATA 2 299 + 331 aataataata--------------------ata >panTro2 122 hg18 chr22 16191804 16192915 panTro2 chr22 16215171 16216287 ponAbe2 chr22 13933410 13934522 rheMac2 chr10 62002585 62003707 trinucleotide ATA 2 299 + 331 aataataata--------------------ata >rheMac2 122 hg18 chr22 16191804 16192915 panTro2 chr22 16215171 16216287 ponAbe2 chr22 13933410 13934522 rheMac2 chr10 62002585 62003707 trinucleotide AAC 2 308 + 319 aacaacaacaac ->hg18 122 hg18 chr22 16191804 16192915 panTro2 chr22 16215171 16216287 ponAbe2 chr22 13933410 13934522 rheMac2 chr10 62002585 62003707 mononucleotide T 22 369 + 378 tttTTTTTTT >panTro2 122 hg18 chr22 16191804 16192915 panTro2 chr22 16215171 16216287 ponAbe2 chr22 13933410 13934522 rheMac2 chr10 62002585 62003707 mononucleotide T 22 369 + 378 tttTTTTTTT >ponAbe2 122 hg18 chr22 16191804 16192915 panTro2 chr22 16215171 16216287 ponAbe2 chr22 13933410 13934522 rheMac2 chr10 62002585 62003707 mononucleotide T 22 369 + 388 tttTTTTTTT---------T >rheMac2 122 hg18 chr22 16191804 16192915 panTro2 chr22 16215171 16216287 ponAbe2 chr22 13933410 13934522 rheMac2 chr10 62002585 62003707 mononucleotide T 2 369 + 385 tttTTTTTTTTTTTTTT ->hg18 122 hg18 chr22 16191804 16192915 panTro2 chr22 16215171 16216287 ponAbe2 chr22 13933410 13934522 rheMac2 chr10 62002585 62003707 mononucleotide A 31 789 + 806 aaaaaaaaaaaaaaaaaa >panTro2 122 hg18 chr22 16191804 16192915 panTro2 chr22 16215171 16216287 ponAbe2 chr22 13933410 13934522 rheMac2 chr10 62002585 62003707 mononucleotide A 32 789 + 811 aaaaaaaaaaaaaaaaaaaaaaa >ponAbe2 122 hg18 chr22 16191804 16192915 panTro2 chr22 16215171 16216287 ponAbe2 chr22 13933410 13934522 rheMac2 chr10 62002585 62003707 mononucleotide A 31 789 + 804 aaaaaaaaaaaaaaaa >rheMac2 122 hg18 chr22 16191804 16192915 panTro2 chr22 16215171 16216287 ponAbe2 chr22 13933410 13934522 rheMac2 chr10 62002585 62003707 mononucleotide A 14 789 + 809 aaaaaaaaaaaaaaaaaaaaa ->panTro2 122 hg18 chr22 16191804 16192915 panTro2 chr22 16215171 16216287 ponAbe2 chr22 13933410 13934522 rheMac2 chr10 62002585 62003707 tetranucleotide [caaa][AAAC] 32 1085 + 1107 [aaa-caaa]at-[aaaCAAACAAAC] indel/deletion at 8 1 >hg18 122 hg18 chr22 16191804 16192915 panTro2 chr22 16215171 16216287 ponAbe2 chr22 13933410 13934522 rheMac2 chr10 62002585 62003707 tetranucleotide [caaa][AAAC] 38 1089 + 1107 [caaa]aT-[AAACAAACAAAC] indel/deletion aT 5 1 >ponAbe2 122 hg18 chr22 16191804 16192915 panTro2 chr22 16215171 16216287 ponAbe2 chr22 13933410 13934522 rheMac2 chr10 62002585 62003707 tetranucleotide [aaca][AAAC] 39 1091 + 1107 [aaaca][aaacaaacaaac] indel/deletion 6 1 >rheMac2 122 hg18 chr22 16191804 16192915 panTro2 chr22 16215171 16216287 ponAbe2 chr22 13933410 13934522 rheMac2 chr10 62002585 62003707 mononucleotide A 28 1104 + 1113 AAAA-AAAAA ->hg18 123 hg18 chr22 16191804 16193531 panTro2 chr22 16215171 16216903 ponAbe2 chr22 13923482 13925211 rheMac2 chr10 62002585 62004319 trinucleotide [AAT][taa] 1 130 + 148 [aataataataataat]t[taa] indel/deletion t 16 1 >panTro2 123 hg18 chr22 16191804 16193531 panTro2 chr22 16215171 16216903 ponAbe2 chr22 13923482 13925211 rheMac2 chr10 62002585 62004319 trinucleotide [AAT][taa] 1 130 + 148 [aataataataataat]t[taa] indel/deletion t 16 1 >ponAbe2 123 hg18 chr22 16191804 16193531 panTro2 chr22 16215171 16216903 ponAbe2 chr22 13923482 13925211 rheMac2 chr10 62002585 62004319 trinucleotide [AAT][taa] 1 130 + 148 [aataataataataat]t[taa] indel/deletion t 16 1 ->ponAbe2 123 hg18 chr22 16191804 16193531 panTro2 chr22 16215171 16216903 ponAbe2 chr22 13923482 13925211 rheMac2 chr10 62002585 62004319 trinucleotide [taa][AAT] 2 293 + 331 [taa][aataataataata--------------------ata] indel/deletion 4 1 >hg18 123 hg18 chr22 16191804 16193531 panTro2 chr22 16215171 16216903 ponAbe2 chr22 13923482 13925211 rheMac2 chr10 62002585 62004319 trinucleotide ATA 2 299 + 331 aataataata--------------------ata >panTro2 123 hg18 chr22 16191804 16193531 panTro2 chr22 16215171 16216903 ponAbe2 chr22 13923482 13925211 rheMac2 chr10 62002585 62004319 trinucleotide ATA 2 299 + 331 aataataata--------------------ata >rheMac2 123 hg18 chr22 16191804 16193531 panTro2 chr22 16215171 16216903 ponAbe2 chr22 13923482 13925211 rheMac2 chr10 62002585 62004319 trinucleotide AAC 2 308 + 319 aacaacaacaac ->hg18 123 hg18 chr22 16191804 16193531 panTro2 chr22 16215171 16216903 ponAbe2 chr22 13923482 13925211 rheMac2 chr10 62002585 62004319 mononucleotide T 22 369 + 378 tttTTTTTTT >panTro2 123 hg18 chr22 16191804 16193531 panTro2 chr22 16215171 16216903 ponAbe2 chr22 13923482 13925211 rheMac2 chr10 62002585 62004319 mononucleotide T 22 369 + 378 tttTTTTTTT >ponAbe2 123 hg18 chr22 16191804 16193531 panTro2 chr22 16215171 16216903 ponAbe2 chr22 13923482 13925211 rheMac2 chr10 62002585 62004319 mononucleotide T 22 369 + 388 tttTTTTTTT---------T >rheMac2 123 hg18 chr22 16191804 16193531 panTro2 chr22 16215171 16216903 ponAbe2 chr22 13923482 13925211 rheMac2 chr10 62002585 62004319 mononucleotide T 2 369 + 385 tttTTTTTTTTTTTTTT ->hg18 123 hg18 chr22 16191804 16193531 panTro2 chr22 16215171 16216903 ponAbe2 chr22 13923482 13925211 rheMac2 chr10 62002585 62004319 mononucleotide A 31 789 + 806 aaaaaaaaaaaaaaaaaa >panTro2 123 hg18 chr22 16191804 16193531 panTro2 chr22 16215171 16216903 ponAbe2 chr22 13923482 13925211 rheMac2 chr10 62002585 62004319 mononucleotide A 32 789 + 811 aaaaaaaaaaaaaaaaaaaaaaa >ponAbe2 123 hg18 chr22 16191804 16193531 panTro2 chr22 16215171 16216903 ponAbe2 chr22 13923482 13925211 rheMac2 chr10 62002585 62004319 mononucleotide A 31 789 + 807 aaaaaaaaaaaaaaaaaaa >rheMac2 123 hg18 chr22 16191804 16193531 panTro2 chr22 16215171 16216903 ponAbe2 chr22 13923482 13925211 rheMac2 chr10 62002585 62004319 mononucleotide A 14 789 + 811 aaaaaaaaaaaaaaaaaa--aaa ->panTro2 123 hg18 chr22 16191804 16193531 panTro2 chr22 16215171 16216903 ponAbe2 chr22 13923482 13925211 rheMac2 chr10 62002585 62004319 tetranucleotide [caaa][AAAC] 32 1085 + 1107 [aaa-caaa]at-[aaaCAAACAAAC] indel/deletion at 8 1 >hg18 123 hg18 chr22 16191804 16193531 panTro2 chr22 16215171 16216903 ponAbe2 chr22 13923482 13925211 rheMac2 chr10 62002585 62004319 tetranucleotide [caaa][AAAC] 38 1089 + 1107 [caaa]aT-[AAACAAACAAAC] indel/deletion aT 5 1 >ponAbe2 123 hg18 chr22 16191804 16193531 panTro2 chr22 16215171 16216903 ponAbe2 chr22 13923482 13925211 rheMac2 chr10 62002585 62004319 tetranucleotide [aaca][AAAC] 36 1091 + 1107 [aaaca][aaacaaacaaac] indel/deletion 6 1 >rheMac2 123 hg18 chr22 16191804 16193531 panTro2 chr22 16215171 16216903 ponAbe2 chr22 13923482 13925211 rheMac2 chr10 62002585 62004319 mononucleotide A 28 1104 + 1113 AAAA-AAAAA ->hg18 128 hg18 chr22 16194063 16194915 panTro2 chr22 16217434 16218284 ponAbe2 chr22 13926001 13926852 rheMac2 chr10 62005180 62006020 mononucleotide [a][a][A] 11 643 + 661 [aaaaaa]c[aa]c[aaaaaaaaa] indel/deletion,indel/deletion c,c 7,10 2 >panTro2 128 hg18 chr22 16194063 16194915 panTro2 chr22 16217434 16218284 ponAbe2 chr22 13926001 13926852 rheMac2 chr10 62005180 62006020 mononucleotide [A][A] 9 643 + 661 [aaaa---aa]c[aaaaaaaaa] insertion c 7 1 >ponAbe2 128 hg18 chr22 16194063 16194915 panTro2 chr22 16217434 16218284 ponAbe2 chr22 13926001 13926852 rheMac2 chr10 62005180 62006020 mononucleotide [A][A][A] 10 643 + 664 [aaaaa--aaaaaaa]g[aaaaa]T[A] insertion,indel/deletion g,T 13,19 2 >rheMac2 128 hg18 chr22 16194063 16194915 panTro2 chr22 16217434 16218284 ponAbe2 chr22 13926001 13926852 rheMac2 chr10 62005180 62006020 mononucleotide [A][A] 9 644 + 664 [aaaa--aaaaaaaaaaaaa]T[A] indel/deletion T 18 1 ->hg18 128 hg18 chr22 16194063 16194915 panTro2 chr22 16217434 16218284 ponAbe2 chr22 13926001 13926852 rheMac2 chr10 62005180 62006020 tetranucleotide [GTTT][GTTT] 11 769 + 786 [GTTTGTTTGTTT]TG[GTTT] indel/deletion TG 13 1 >panTro2 128 hg18 chr22 16194063 16194915 panTro2 chr22 16217434 16218284 ponAbe2 chr22 13926001 13926852 rheMac2 chr10 62005180 62006020 tetranucleotide [GTTT][GTTT] 12 769 + 787 [GTTTGTTTGTTT]TG[G-TTT] indel/deletion TG 13 1 >ponAbe2 128 hg18 chr22 16194063 16194915 panTro2 chr22 16217434 16218284 ponAbe2 chr22 13926001 13926852 rheMac2 chr10 62005180 62006020 tetranucleotide [GTTT][GTTT] 12 769 + 786 [GTTTGTTTGTTT]TG[GTTT] indel/deletion TG 13 1 ->ponAbe2 129 hg18 chr22 16194416 16194709 panTro2 chr22 16217789 16218079 ponAbe2 chr22 13936108 13936398 rheMac2 chr10 62006020 62006309 mononucleotide A 2 282 + 296 aaaa---aa-aaaaa >rheMac2 129 hg18 chr22 16194416 16194709 panTro2 chr22 16217789 16218079 ponAbe2 chr22 13936108 13936398 rheMac2 chr10 62006020 62006309 mononucleotide A 3 282 + 296 aaaa---aa-aaaaa ->hg18 130 hg18 chr22 16194709 16194901 panTro2 chr22 16218079 16218270 ponAbe2 chr22 13936398 13936590 rheMac2 chr10 62005826 62006006 tetranucleotide [GTTT][GTTT] 0 112 + 129 [GTTTGTTTGTTT]TG[GTTT] indel/deletion TG 13 1 >panTro2 130 hg18 chr22 16194709 16194901 panTro2 chr22 16218079 16218270 ponAbe2 chr22 13936398 13936590 rheMac2 chr10 62005826 62006006 tetranucleotide [GTTT][GTTT] 0 112 + 130 [GTTTGTTTGTTT]TG[G-TTT] indel/deletion TG 13 1 >ponAbe2 130 hg18 chr22 16194709 16194901 panTro2 chr22 16218079 16218270 ponAbe2 chr22 13936398 13936590 rheMac2 chr10 62005826 62006006 tetranucleotide [GTTT][GTTT] 0 112 + 129 [GTTTGTTTGTTT]TG[GTTT] indel/deletion TG 13 1 ->ponAbe2 139 hg18 chr22 16196677 16196830 panTro2 chr22 16220038 16220191 ponAbe2 chr22 13938513 13938662 rheMac2 chr10 62008694 62008861 mononucleotide [A][a] 0 26 + 56 [aaaaaa--------------aaaaaaaa]g[aa] indel/deletion g 15 1 >hg18 139 hg18 chr22 16196677 16196830 panTro2 chr22 16220038 16220191 ponAbe2 chr22 13938513 13938662 rheMac2 chr10 62008694 62008861 mononucleotide [A][a] 0 27 + 60 [aaaaaaaaa--------------aaaaaaaa]g[aa] indel/deletion g 18 1 >panTro2 139 hg18 chr22 16196677 16196830 panTro2 chr22 16220038 16220191 ponAbe2 chr22 13938513 13938662 rheMac2 chr10 62008694 62008861 mononucleotide [A][a] 0 27 + 60 [aaaaaaaaa--------------aaaaaaaa]g[aa] indel/deletion g 18 1 >rheMac2 139 hg18 chr22 16196677 16196830 panTro2 chr22 16220038 16220191 ponAbe2 chr22 13938513 13938662 rheMac2 chr10 62008694 62008861 tetranucleotide [aaca][AAAC] 0 33 + 53 [aaaca][aaacaaacaaacaaac] indel/deletion 6 1 ->hg18 140 hg18 chr22 16196700 16196835 panTro2 chr22 16220061 16220203 ponAbe2 chr22 13943033 13943164 rheMac2 chr10 62008749 62008874 mononucleotide [A][a] 0 4 + 23 [aaaaaaaaaaaaaaaaa]g[aa] indel/deletion g 18 1 >panTro2 140 hg18 chr22 16196700 16196835 panTro2 chr22 16220061 16220203 ponAbe2 chr22 13943033 13943164 rheMac2 chr10 62008749 62008874 mononucleotide [A][a] 0 4 + 23 [aaaaaaaaaaaaaaaaa]g[aa] indel/deletion g 18 1 >ponAbe2 140 hg18 chr22 16196700 16196835 panTro2 chr22 16220061 16220203 ponAbe2 chr22 13943033 13943164 rheMac2 chr10 62008749 62008874 mononucleotide [A][A][A] 0 4 + 26 [AAAAAAAAAAAA]G[AA]------G[A] indel/deletion,indel/deletion G,G 13,16 2 ->hg18 141 hg18 chr22 16196846 16196948 panTro2 chr22 16220204 16220304 ponAbe2 chr22 13943164 13943257 rheMac2 chr10 62008874 62008967 mononucleotide A 0 84 + 102 AAAAAAAAAAAAAAAAAAA >panTro2 141 hg18 chr22 16196846 16196948 panTro2 chr22 16220204 16220304 ponAbe2 chr22 13943164 13943257 rheMac2 chr10 62008874 62008967 mononucleotide A 0 84 + 100 AAAAAAAAAAAAAAAAA >ponAbe2 141 hg18 chr22 16196846 16196948 panTro2 chr22 16220204 16220304 ponAbe2 chr22 13943164 13943257 rheMac2 chr10 62008874 62008967 mononucleotide A 0 84 + 93 AAAAAAAAAA >rheMac2 141 hg18 chr22 16196846 16196948 panTro2 chr22 16220204 16220304 ponAbe2 chr22 13943164 13943257 rheMac2 chr10 62008874 62008967 mononucleotide A 0 84 + 93 AAAAAAAAAA ->hg18 142 hg18 chr22 16196948 16197432 panTro2 chr22 16220304 16220790 ponAbe2 chr22 13943257 13943744 rheMac2 chr10 62008971 62009447 mononucleotide T 0 124 + 132 TTTTTTTTT >panTro2 142 hg18 chr22 16196948 16197432 panTro2 chr22 16220304 16220790 ponAbe2 chr22 13943257 13943744 rheMac2 chr10 62008971 62009447 mononucleotide T 0 124 + 134 TTTTTTTTTTT ->hg18 142 hg18 chr22 16196948 16197432 panTro2 chr22 16220304 16220790 ponAbe2 chr22 13943257 13943744 rheMac2 chr10 62008971 62009447 tetranucleotide [TTTA][attt] 7 369 + 398 [tatttatttatttatttatttattta][attt] indel/deletion 27 1 >panTro2 142 hg18 chr22 16196948 16197432 panTro2 chr22 16220304 16220790 ponAbe2 chr22 13943257 13943744 rheMac2 chr10 62008971 62009447 tetranucleotide [TATT][TTAT] 1 369 + 390 [TATTTATTTATTTA]C[TTATTTA] indel/deletion C 15 1 >ponAbe2 142 hg18 chr22 16196948 16197432 panTro2 chr22 16220304 16220790 ponAbe2 chr22 13943257 13943744 rheMac2 chr10 62008971 62009447 tetranucleotide [TTTA][attt] 4 369 + 398 [tatttatttatttatttatttattta][attt] indel/deletion 27 1 >rheMac2 142 hg18 chr22 16196948 16197432 panTro2 chr22 16220304 16220790 ponAbe2 chr22 13943257 13943744 rheMac2 chr10 62008971 62009447 tetranucleotide [TATT][attt] 3 369 + 386 [TAtttatttatt]cc[attt] indel/deletion cc 13 1 ->ponAbe2 145 hg18 chr22 16198180 16199022 panTro2 chr22 16221536 16222386 ponAbe2 chr22 13940015 13940869 rheMac2 chr10 62010149 62010986 trinucleotide TGT 0 99 + 117 tgttgttgttgttgttgtt ->hg18 146 hg18 chr22 16201082 16201318 panTro2 chr22 16224446 16224681 ponAbe2 chr22 13947403 13947635 rheMac2 chr10 62013365 62013600 mononucleotide A 0 76 + 102 aaaaaaaaaaaaaaaaaaaaaaaaaaa >panTro2 146 hg18 chr22 16201082 16201318 panTro2 chr22 16224446 16224681 ponAbe2 chr22 13947403 13947635 rheMac2 chr10 62013365 62013600 mononucleotide A 0 76 + 101 aaaaaaaaaaaaaaaaaaaaaaaaaa >ponAbe2 146 hg18 chr22 16201082 16201318 panTro2 chr22 16224446 16224681 ponAbe2 chr22 13947403 13947635 rheMac2 chr10 62013365 62013600 mononucleotide A 0 76 + 99 aaaaaaaaaaaaaaaaaaaaaaaa >rheMac2 146 hg18 chr22 16201082 16201318 panTro2 chr22 16224446 16224681 ponAbe2 chr22 13947403 13947635 rheMac2 chr10 62013365 62013600 mononucleotide A 0 76 + 102 aaaaaaaaaaaaaaaaaaaaaaaaaaa ->hg18 147 hg18 chr22 16202832 16203068 panTro2 chr22 16226288 16226525 ponAbe2 chr22 13949100 13949336 rheMac2 chr10 62015049 62015298 mononucleotide [T][T] 0 19 + 47 [T]C-[tttt------------tttttttttt] indel/deletion C 2 1 >panTro2 147 hg18 chr22 16202832 16203068 panTro2 chr22 16226288 16226525 ponAbe2 chr22 13949100 13949336 rheMac2 chr10 62015049 62015298 mononucleotide [T][T] 0 19 + 47 [T]C[ttttt------------tttttttttt] indel/deletion C 2 1 >ponAbe2 147 hg18 chr22 16202832 16203068 panTro2 chr22 16226288 16226525 ponAbe2 chr22 13949100 13949336 rheMac2 chr10 62015049 62015298 mononucleotide [t][T] 0 19 + 47 [t]g[ttttt------------tttttttttt] indel/deletion g 2 1 >rheMac2 147 hg18 chr22 16202832 16203068 panTro2 chr22 16226288 16226525 ponAbe2 chr22 13949100 13949336 rheMac2 chr10 62015049 62015298 mononucleotide [T][T][T][T] 0 19 + 47 [T]C[tttttt]g[ttttttttt]g[tttttttttt] indel/deletion,insertion,insertion C,g,g 2,9,19 3 ->hg18 148 hg18 chr22 16202850 16203153 panTro2 chr22 16229642 16229945 ponAbe2 chr22 13954016 13954318 rheMac2 chr10 62015080 62015383 mononucleotide [T][T] 0 1 + 16 [T]C[tttttttttttttt] indel/deletion C 2 1 >ponAbe2 148 hg18 chr22 16202850 16203153 panTro2 chr22 16229642 16229945 ponAbe2 chr22 13954016 13954318 rheMac2 chr10 62015080 62015383 mononucleotide [t][T] 0 1 + 16 [tt]g[ttttttttttttt] indel/deletion g 3 1 >rheMac2 148 hg18 chr22 16202850 16203153 panTro2 chr22 16229642 16229945 ponAbe2 chr22 13954016 13954318 rheMac2 chr10 62015080 62015383 mononucleotide [T][T] 0 1 + 16 [ttttt]g[tttttttttt] insertion g 6 1 >panTro2 148 hg18 chr22 16202850 16203153 panTro2 chr22 16229642 16229945 ponAbe2 chr22 13954016 13954318 rheMac2 chr10 62015080 62015383 mononucleotide [T][T] 0 2 + 16 [T]C[ttttttttttttt] indel/deletion C 2 1 ->rheMac2 150 hg18 chr22 16204201 16205349 panTro2 chr22 16227562 16228718 ponAbe2 chr22 13950471 13951610 rheMac2 chr10 62016134 62017323 mononucleotide [T][T][T][T] 1 121 + 151 [tttttttttttttttt]c[ttt]c[ttt]c[tttttt] indel/deletion,indel/deletion,indel/deletion C,C,C 17,21,25 4 >hg18 150 hg18 chr22 16204201 16205349 panTro2 chr22 16227562 16228718 ponAbe2 chr22 13950471 13951610 rheMac2 chr10 62016134 62017323 mononucleotide T 0 122 + 137 tttttttttttttttt >panTro2 150 hg18 chr22 16204201 16205349 panTro2 chr22 16227562 16228718 ponAbe2 chr22 13950471 13951610 rheMac2 chr10 62016134 62017323 mononucleotide T 0 122 + 143 tttttttttttttttttttttt >ponAbe2 150 hg18 chr22 16204201 16205349 panTro2 chr22 16227562 16228718 ponAbe2 chr22 13950471 13951610 rheMac2 chr10 62016134 62017323 mononucleotide T 0 122 + 139 tttttttttttttttttt ->ponAbe2 150 hg18 chr22 16204201 16205349 panTro2 chr22 16227562 16228718 ponAbe2 chr22 13950471 13951610 rheMac2 chr10 62016134 62017323 mononucleotide [T][T][T] 18 587 + 600 [TT]A[TTTTTTTTT]A[T] indel/deletion,indel/deletion A,A 3,13 2 ->hg18 150 hg18 chr22 16204201 16205349 panTro2 chr22 16227562 16228718 ponAbe2 chr22 13950471 13951610 rheMac2 chr10 62016134 62017323 mononucleotide T 25 638 + 653 tttttttttttttttt >panTro2 150 hg18 chr22 16204201 16205349 panTro2 chr22 16227562 16228718 ponAbe2 chr22 13950471 13951610 rheMac2 chr10 62016134 62017323 mononucleotide T 19 638 + 652 ttttttttttttttt >ponAbe2 150 hg18 chr22 16204201 16205349 panTro2 chr22 16227562 16228718 ponAbe2 chr22 13950471 13951610 rheMac2 chr10 62016134 62017323 mononucleotide T 34 638 + 650 ttttttttttttt >rheMac2 150 hg18 chr22 16204201 16205349 panTro2 chr22 16227562 16228718 ponAbe2 chr22 13950471 13951610 rheMac2 chr10 62016134 62017323 mononucleotide T 5 638 + 667 tttttttttttttttttttttttttttttt ->ponAbe2 151 hg18 chr22 16205659 16206162 panTro2 chr22 16231901 16232255 ponAbe2 chr22 13951912 13952300 rheMac2 chr10 62017632 62017991 mononucleotide N 1 69 + 78 nnnnnnnnnn ->panTro2 151 hg18 chr22 16205659 16206162 panTro2 chr22 16231901 16232255 ponAbe2 chr22 13951912 13952300 rheMac2 chr10 62017632 62017991 mononucleotide A 142 350 + 359 aaaaaaaaaa >ponAbe2 151 hg18 chr22 16205659 16206162 panTro2 chr22 16231901 16232255 ponAbe2 chr22 13951912 13952300 rheMac2 chr10 62017632 62017991 mononucleotide A 108 350 + 359 aaaaaaaaaa ->rheMac2 151 hg18 chr22 16205659 16206162 panTro2 chr22 16231901 16232255 ponAbe2 chr22 13951912 13952300 rheMac2 chr10 62017632 62017991 mononucleotide [A][A][A][a] 189 524 + 547 [aaaaaa]t[aaaaaaaaa]t[aaaaa]t[a] insertion,insertion,indel/deletion t,t,t 7,17,23 3 ->panTro2 152 hg18 chr22 16206370 16206471 panTro2 chr22 16232317 16232422 ponAbe2 chr22 13952362 13952463 rheMac2 chr10 62018053 62018147 tetranucleotide CAAA 0 92 + 105 caaacaaacaaaca >ponAbe2 152 hg18 chr22 16206370 16206471 panTro2 chr22 16232317 16232422 ponAbe2 chr22 13952362 13952463 rheMac2 chr10 62018053 62018147 mononucleotide A 4 97 + 105 aaaaaaaaa ->hg18 154 hg18 chr22 16207659 16208436 panTro2 chr22 16233601 16234374 ponAbe2 chr22 13958009 13958770 rheMac2 chr10 62018434 62019211 tetranucleotide TTTA 0 1 + 17 tttatttatttatttat >panTro2 154 hg18 chr22 16207659 16208436 panTro2 chr22 16233601 16234374 ponAbe2 chr22 13958009 13958770 rheMac2 chr10 62018434 62019211 tetranucleotide TTTA 0 1 + 17 tttatttatttatttat >ponAbe2 154 hg18 chr22 16207659 16208436 panTro2 chr22 16233601 16234374 ponAbe2 chr22 13958009 13958770 rheMac2 chr10 62018434 62019211 tetranucleotide TTTA 0 1 + 17 tttatttatttatttat >rheMac2 154 hg18 chr22 16207659 16208436 panTro2 chr22 16233601 16234374 ponAbe2 chr22 13958009 13958770 rheMac2 chr10 62018434 62019211 mononucleotide T 0 1 + 19 ttttttttttttttttttt ->hg18 155 hg18 chr22 16208903 16209221 panTro2 chr22 16234849 16235167 ponAbe2 chr22 13959228 13959547 rheMac2 chr10 62019670 62019992 mononucleotide [A][a] 2 168 + 178 [aaaaaaaaa]g[a] indel/deletion g 10 1 >panTro2 155 hg18 chr22 16208903 16209221 panTro2 chr22 16234849 16235167 ponAbe2 chr22 13959228 13959547 rheMac2 chr10 62019670 62019992 mononucleotide [A][A] 2 168 + 178 [aaaaaaaaA]G[A] indel/deletion G 10 1 >ponAbe2 155 hg18 chr22 16208903 16209221 panTro2 chr22 16234849 16235167 ponAbe2 chr22 13959228 13959547 rheMac2 chr10 62019670 62019992 mononucleotide [A][a] 2 168 + 179 [aaaaaaaaaa]g[a] indel/deletion g 11 1 >rheMac2 155 hg18 chr22 16208903 16209221 panTro2 chr22 16234849 16235167 ponAbe2 chr22 13959228 13959547 rheMac2 chr10 62019670 62019992 mononucleotide A 0 168 + 179 aaaaaaaaaaaa ->panTro2 156 hg18 chr22 16209221 16209985 panTro2 chr22 16235302 16236056 ponAbe2 chr22 13959547 13960301 rheMac2 chr10 62019992 62020662 mononucleotide [A][a] 0 142 + 172 [aaaaa----------aaaaaaaaaaaaaa]g[a] indel/deletion g 20 1 >ponAbe2 156 hg18 chr22 16209221 16209985 panTro2 chr22 16235302 16236056 ponAbe2 chr22 13959547 13960301 rheMac2 chr10 62019992 62020662 mononucleotide [A][a] 0 142 + 172 [aaaa-----------aaaaaaaaaaaaaa]g[a] indel/deletion g 19 1 >rheMac2 156 hg18 chr22 16209221 16209985 panTro2 chr22 16235302 16236056 ponAbe2 chr22 13959547 13960301 rheMac2 chr10 62019992 62020662 mononucleotide [A][a] 0 142 + 172 [aaaaaaaaaa-----aaaaaaaaaaaaaa]g[a] indel/deletion g 25 1 ->ponAbe2 158 hg18 chr22 16210949 16212037 panTro2 chr22 16237020 16238107 ponAbe2 chr22 13961104 13962189 rheMac2 chr10 62021648 62022704 mononucleotide T 3 613 + 621 TTTTTTTTT ->hg18 159 hg18 chr22 16212557 16212725 panTro2 chr22 16238619 16238804 ponAbe2 chr22 13962694 13962844 rheMac2 chr10 62023428 62023588 dinucleotide [ta][TA] 0 147 + 163 [ta][atATATATATATATA] indel/deletion 3 1 >panTro2 159 hg18 chr22 16212557 16212725 panTro2 chr22 16238619 16238804 ponAbe2 chr22 13962694 13962844 rheMac2 chr10 62023428 62023588 dinucleotide [ta][AT] 0 147 + 185 [ta][atatatatatatatatatatatatatatatatatata] indel/deletion 3 1 >rheMac2 159 hg18 chr22 16212557 16212725 panTro2 chr22 16238619 16238804 ponAbe2 chr22 13962694 13962844 rheMac2 chr10 62023428 62023588 mononucleotide T 0 150 + 185 ttttttt-------------------------tttt ->rheMac2 160 hg18 chr22 16213164 16213266 panTro2 chr22 16239243 16239345 ponAbe2 chr22 13963280 13963382 rheMac2 chr10 62024146 62024299 tetranucleotide.tetranucleotide CTCN.NTGT 0 35 + 60 [ctcNNNNNNNNNNNNNNNNNNNNtgt] NA.NA NA.NA NA.NA NA.NA 35.41 54.60 CTCNNNNNNNNNNNNNNNNN.NNNNNNNNNNNNNNNNNTGT ->hg18 162 hg18 chr22 16213663 16214633 panTro2 chr22 16239742 16240715 ponAbe2 chr22 13963822 13964810 rheMac2 chr10 62024734 62025603 tetranucleotide [TATt][TTTA] 0 77 + 98 [TTTATt][tttatttatttattta] indel/deletion 7 1 >panTro2 162 hg18 chr22 16213663 16214633 panTro2 chr22 16239742 16240715 ponAbe2 chr22 13963822 13964810 rheMac2 chr10 62024734 62025603 tetranucleotide [TATt][TTTA] 0 77 + 98 [TTTATt][tttatttatttattta] indel/deletion 7 1 >ponAbe2 162 hg18 chr22 16213663 16214633 panTro2 chr22 16239742 16240715 ponAbe2 chr22 13963822 13964810 rheMac2 chr10 62024734 62025603 tetranucleotide [TATt][TTTA] 0 77 + 98 [TTTATt][tttatttatttattta] indel/deletion 7 1 >rheMac2 162 hg18 chr22 16213663 16214633 panTro2 chr22 16239742 16240715 ponAbe2 chr22 13963822 13964810 rheMac2 chr10 62024734 62025603 tetranucleotide [ttta][ATTT][Attt] 0 81 + 105 [ttta]a[atttatttattt]GCTA[Attt] indel/deletion,indel/deletion a,GCTA 5,18 2 ->hg18 162 hg18 chr22 16213663 16214633 panTro2 chr22 16239742 16240715 ponAbe2 chr22 13963822 13964810 rheMac2 chr10 62024734 62025603 trinucleotide [TGT][GTT] 12 557 + 579 [TTGTTGTTG------TTGT]C[GTT] indel/deletion C 14 1 >panTro2 162 hg18 chr22 16213663 16214633 panTro2 chr22 16239742 16240715 ponAbe2 chr22 13963822 13964810 rheMac2 chr10 62024734 62025603 trinucleotide [GTT][gTT] 14 557 + 587 [ttgttgttgttg------ttgttgtt][ttgtt] indel/deletion 21 1 >rheMac2 162 hg18 chr22 16213663 16214633 panTro2 chr22 16239742 16240715 ponAbe2 chr22 13963822 13964810 rheMac2 chr10 62024734 62025603 compound [TTC][TGT] 12 568 + 709 [t------tcttcttcttcttc][tgt-------------------------------------------------------------------------------------------------------------tgttgttgt] >hg18 162 hg18 chr22 16213663 16214633 panTro2 chr22 16239742 16240715 ponAbe2 chr22 13963822 13964810 rheMac2 chr10 62024734 62025603 mononucleotide T 21 697 + 711 ttttttttttttttt >panTro2 162 hg18 chr22 16213663 16214633 panTro2 chr22 16239742 16240715 ponAbe2 chr22 13963822 13964810 rheMac2 chr10 62024734 62025603 mononucleotide T 20 697 + 713 ttttttttttttttttt >ponAbe2 162 hg18 chr22 16213663 16214633 panTro2 chr22 16239742 16240715 ponAbe2 chr22 13963822 13964810 rheMac2 chr10 62024734 62025603 mononucleotide T 1 697 + 709 ttttttttttttt ->panTro2 163 hg18 chr22 16214633 16215789 panTro2 chr22 16240715 16241866 ponAbe2 chr22 13964810 13965966 rheMac2 chr10 62025711 62026835 mononucleotide [T][T][T][T][T][T][t] 3 578 + 617 [TTTTTTT]C[Ttt]-c[tt]c[ttttttttt]a[ttttt]a[tttttt]g[t] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion C,C,C,a,a,g 8,12,15,25,31,38 7 >hg18 163 hg18 chr22 16214633 16215789 panTro2 chr22 16240715 16241866 ponAbe2 chr22 13964810 13965966 rheMac2 chr10 62025711 62026835 mononucleotide [t][T][T][T][t] 1 591 + 617 [tt]c[ttttttttt]a[ttttt]a[tttttt]g[t] indel/deletion,insertion,insertion,indel/deletion c,a,a,g 3,13,19,26 4 >rheMac2 163 hg18 chr22 16214633 16215789 panTro2 chr22 16240715 16241866 ponAbe2 chr22 13964810 13965966 rheMac2 chr10 62025711 62026835 mononucleotide [t][T] 38 592 + 607 [tt]c[ttttttttttttt] indel/deletion c 3 1 ->rheMac2 163 hg18 chr22 16214633 16215789 panTro2 chr22 16240715 16241866 ponAbe2 chr22 13964810 13965966 rheMac2 chr10 62025711 62026835 mononucleotide [T][T][T][T] 53 1080 + 1110 [T]G[tt]c[tt]c[ttt-------ttttttttttttt] indel/deletion,indel/deletion,indel/deletion G,C,C 2,5,8 3 >hg18 163 hg18 chr22 16214633 16215789 panTro2 chr22 16240715 16241866 ponAbe2 chr22 13964810 13965966 rheMac2 chr10 62025711 62026835 mononucleotide [t][T][T] 18 1086 + 1111 [t]c[ttt----tt]a[tttttttttttttt] indel/deletion,insertion c,a 2,8 2 >ponAbe2 163 hg18 chr22 16214633 16215789 panTro2 chr22 16240715 16241866 ponAbe2 chr22 13964810 13965966 rheMac2 chr10 62025711 62026835 mononucleotide [t][T] 22 1086 + 1111 [t]c[tttttttttttttttttttttttt] indel/deletion c 2 1 ->hg18 164 hg18 chr22 16215955 16216624 panTro2 chr22 16241866 16242377 ponAbe2 chr22 13965966 13966480 rheMac2 chr10 62026835 62027354 mononucleotide A 0 29 + 37 aaaaaaaaa ->panTro2 166 hg18 chr22 16225418 16225777 panTro2 chr22 16251086 16251445 ponAbe2 chr22 13977333 13977690 rheMac2 chr10 62034625 62035030 mononucleotide [a][a][A][A][A][A][A] 52 360 + 406 [aaaaaa]c[aaaaaa]c[aaaa]c[aaa]c[aaaaa---aaAAAA]C[AAAAAA]T[AA] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion c,c,C,C,C,T 7,14,19,23,35,42 7 >hg18 166 hg18 chr22 16225418 16225777 panTro2 chr22 16251086 16251445 ponAbe2 chr22 13977333 13977690 rheMac2 chr10 62034625 62035030 tetranucleotide [Aaac][AAAC][aaac] 52 370 + 400 [aaaca][aaacaaacaaaca---aa]a[aaacaaa] indel/deletion,indel/deletion ,a 6,21 2 >ponAbe2 166 hg18 chr22 16225418 16225777 panTro2 chr22 16251086 16251445 ponAbe2 chr22 13977333 13977690 rheMac2 chr10 62034625 62035030 tetranucleotide [Aaac][AAAC][aaac] 51 370 + 400 [aaaca][aaacaaacaaacaaacaaa][aaacaaa] indel/deletion,indel/deletion , 6,25 2 ->rheMac2 167 hg18 chr22 16225829 16226141 panTro2 chr22 16251497 16251809 ponAbe2 chr22 13977742 13978054 rheMac2 chr10 62035081 62035402 mononucleotide A 2 295 + 323 aaaaaaaaaaaaaaaaaaaaaaaaaaaaa >ponAbe2 167 hg18 chr22 16225829 16226141 panTro2 chr22 16251497 16251809 ponAbe2 chr22 13977742 13978054 rheMac2 chr10 62035081 62035402 mononucleotide A 11 315 + 323 aaaaaaaaa ->hg18 168 hg18 chr22 16226620 16226861 panTro2 chr22 16252283 16252525 ponAbe2 chr22 13978526 13978766 rheMac2 chr10 62035869 62036105 mononucleotide A 0 140 + 152 aaaaaaaaaaaaa >panTro2 168 hg18 chr22 16226620 16226861 panTro2 chr22 16252283 16252525 ponAbe2 chr22 13978526 13978766 rheMac2 chr10 62035869 62036105 mononucleotide A 0 140 + 153 aaaaaaaaaaaaaa ->rheMac2 169 hg18 chr22 16228611 16229326 panTro2 chr22 16254276 16254990 ponAbe2 chr22 13980734 13981450 rheMac2 chr10 62038216 62038934 trinucleotide TTG 2 287 + 298 TTGTTGTTGTTG >ponAbe2 169 hg18 chr22 16228611 16229326 panTro2 chr22 16254276 16254990 ponAbe2 chr22 13980734 13981450 rheMac2 chr10 62038216 62038934 mononucleotide T 6 297 + 305 TTTTTTTTT ->rheMac2 170 hg18 chr22 16233003 16233182 panTro2 chr22 16259985 16260165 ponAbe2 chr22 13986798 13986986 rheMac2 chr10 62044091 62044268 mononucleotide T 0 3 + 27 t-----------ttttttttttttt >panTro2 170 hg18 chr22 16233003 16233182 panTro2 chr22 16259985 16260165 ponAbe2 chr22 13986798 13986986 rheMac2 chr10 62044091 62044268 mononucleotide [T][t] 0 4 + 19 [tttttttttttttt]c[t] indel/deletion c 15 1 >ponAbe2 170 hg18 chr22 16233003 16233182 panTro2 chr22 16259985 16260165 ponAbe2 chr22 13986798 13986986 rheMac2 chr10 62044091 62044268 mononucleotide T 0 4 + 27 tttttttttttttttttttttttt ->hg18 173 hg18 chr22 16248118 16248938 panTro2 chr22 16275653 16276473 ponAbe2 chr22 14005346 14006166 rheMac2 chr10 62060235 62061054 mononucleotide [t][T] 10 602 + 612 [t]a[ttttttttt] indel/deletion a 2 1 >panTro2 173 hg18 chr22 16248118 16248938 panTro2 chr22 16275653 16276473 ponAbe2 chr22 14005346 14006166 rheMac2 chr10 62060235 62061054 mononucleotide [t][T] 10 602 + 612 [t]a[ttttttttt] indel/deletion a 2 1 ->hg18 175 hg18 chr22 16252266 16253239 panTro2 chr22 16279800 16280764 ponAbe2 chr22 14009691 14010669 rheMac2 chr10 62064432 62065405 mononucleotide [a][A][a] 1 306 + 322 [aaa]g[aaaaaaaaaaa]C[a] indel/deletion,indel/deletion g,C 4,16 2 >panTro2 175 hg18 chr22 16252266 16253239 panTro2 chr22 16279800 16280764 ponAbe2 chr22 14009691 14010669 rheMac2 chr10 62064432 62065405 mononucleotide [a][A][a] 1 306 + 322 [aaa]g-[aaaaaaaaaa]C[a] indel/deletion,indel/deletion g,C 4,15 2 >ponAbe2 175 hg18 chr22 16252266 16253239 panTro2 chr22 16279800 16280764 ponAbe2 chr22 14009691 14010669 rheMac2 chr10 62064432 62065405 mononucleotide [a][A][a] 0 306 + 322 [aaa]g[aaaaaaaaaaa]c[a] indel/deletion,indel/deletion g,c 4,16 2 >rheMac2 175 hg18 chr22 16252266 16253239 panTro2 chr22 16279800 16280764 ponAbe2 chr22 14009691 14010669 rheMac2 chr10 62064432 62065405 mononucleotide [a][A][a] 1 306 + 322 [aaa]g--[aaaaaaaaa]C[a] indel/deletion,indel/deletion g,C 4,14 2 ->panTro2 175 hg18 chr22 16252266 16253239 panTro2 chr22 16279800 16280764 ponAbe2 chr22 14009691 14010669 rheMac2 chr10 62064432 62065405 tetranucleotide TACA 2 342 + 354 tacatac-ataca ->panTro2 176 hg18 chr22 16253239 16254868 panTro2 chr22 16280764 16282372 ponAbe2 chr22 14010669 14012276 rheMac2 chr10 62065695 62067399 mononucleotide [t][t][t][T] 21 532 + 565 [tt]c[tttttt]a[tt]c[tttttt-tttttttttttttt] indel/deletion,indel/deletion,indel/deletion c,a,c 3,10,13 3 >rheMac2 176 hg18 chr22 16253239 16254868 panTro2 chr22 16280764 16282372 ponAbe2 chr22 14010669 14012276 rheMac2 chr10 62065695 62067399 mononucleotide [t][T][T] 10 532 + 565 [tt]c[tt---------------tttt]c[ttttttttt] indel/deletion,insertion c,c 3,10 2 >ponAbe2 176 hg18 chr22 16253239 16254868 panTro2 chr22 16280764 16282372 ponAbe2 chr22 14010669 14012276 rheMac2 chr10 62065695 62067399 tetranucleotide TTTA 7 538 + 559 tttattt--atttatttattta >hg18 176 hg18 chr22 16253239 16254868 panTro2 chr22 16280764 16282372 ponAbe2 chr22 14010669 14012276 rheMac2 chr10 62065695 62067399 mononucleotide T 9 548 + 565 ttt-tttttttttttttt ->hg18 176 hg18 chr22 16253239 16254868 panTro2 chr22 16280764 16282372 ponAbe2 chr22 14010669 14012276 rheMac2 chr10 62065695 62067399 compound [GCT][T] 10 845 + 885 [gctGCTGCTGCTGCt][tttttttttttttttttttttttttt] >panTro2 176 hg18 chr22 16253239 16254868 panTro2 chr22 16280764 16282372 ponAbe2 chr22 14010669 14012276 rheMac2 chr10 62065695 62067399 compound [GCT][T] 22 845 + 885 [gctGCTGCTGCTGC--------------t][tttttttttttt] >ponAbe2 176 hg18 chr22 16253239 16254868 panTro2 chr22 16280764 16282372 ponAbe2 chr22 14010669 14012276 rheMac2 chr10 62065695 62067399 trinucleotide TTC 9 846 + 877 cttcttcttcttc----------ttcttcttc >rheMac2 176 hg18 chr22 16253239 16254868 panTro2 chr22 16280764 16282372 ponAbe2 chr22 14010669 14012276 rheMac2 chr10 62065695 62067399 mononucleotide [t][T][t] 25 847 + 884 [tt]c[ttt----------------ttttttttttt]c[tttt] indel/deletion,indel/deletion c,c 3,18 2 ->hg18 176 hg18 chr22 16253239 16254868 panTro2 chr22 16280764 16282372 ponAbe2 chr22 14010669 14012276 rheMac2 chr10 62065695 62067399 mononucleotide [t][T][t] 12 1043 + 1062 [t]a-------[ttttttttt]g[t] indel/deletion,indel/deletion a,g 2,12 2 >panTro2 176 hg18 chr22 16253239 16254868 panTro2 chr22 16280764 16282372 ponAbe2 chr22 14010669 14012276 rheMac2 chr10 62065695 62067399 mononucleotide [t][T][t] 38 1043 + 1062 [t]a[tttttttttttttttt]g[t] indel/deletion,indel/deletion a,g 2,19 2 ->rheMac2 180 hg18 chr22 16260812 16261396 panTro2 chr22 16291637 16292230 ponAbe2 chr22 14020925 14021513 rheMac2 chr10 62076691 62077272 mononucleotide T 0 6 + 30 t------tt-----ttttttttttt >hg18 180 hg18 chr22 16260812 16261396 panTro2 chr22 16291637 16292230 ponAbe2 chr22 14020925 14021513 rheMac2 chr10 62076691 62077272 trinucleotide TTG 0 7 + 23 ttgttgttgttgttgtt >panTro2 180 hg18 chr22 16260812 16261396 panTro2 chr22 16291637 16292230 ponAbe2 chr22 14020925 14021513 rheMac2 chr10 62076691 62077272 trinucleotide TTG 0 7 + 29 ttgttgttgttgttgttgttgtt ->hg18 181 hg18 chr22 16265532 16265802 panTro2 chr22 16296575 16296841 ponAbe2 chr22 14027118 14027380 rheMac2 chr10 62081701 62081962 mononucleotide A 0 4 + 26 aaaaaaaaaaaaaaaaaaaaaaa >panTro2 181 hg18 chr22 16265532 16265802 panTro2 chr22 16296575 16296841 ponAbe2 chr22 14027118 14027380 rheMac2 chr10 62081701 62081962 compound [A][T] 0 4 + 30 [aaaaaaaaaaaaaaaaaa][ttttttttt] >ponAbe2 181 hg18 chr22 16265532 16265802 panTro2 chr22 16296575 16296841 ponAbe2 chr22 14027118 14027380 rheMac2 chr10 62081701 62081962 mononucleotide A 0 4 + 23 aaaaaaaaaaaaaaaaaaaa >rheMac2 181 hg18 chr22 16265532 16265802 panTro2 chr22 16296575 16296841 ponAbe2 chr22 14027118 14027380 rheMac2 chr10 62081701 62081962 mononucleotide A 0 4 + 14 aaaaaaaaaaa ->hg18 182 hg18 chr22 16268986 16269129 panTro2 chr22 16300025 16300164 ponAbe2 chr22 14030619 14030738 rheMac2 chr10 62085192 62085305 mononucleotide [T][T][T][T][T][T][T][T][T][T] 0 19 + 61 [T]G[TT]G[TT]G[TTTT]C[TT]G[ttttttttt]g[ttt]g[ttt]g[ttt]g[ttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion G,G,G,C,G,G,G,G,G 2,5,8,13,16,26,30,34,38 10 ->rheMac2 183 hg18 chr22 16274088 16276467 panTro2 chr22 16305968 16308354 ponAbe2 chr22 14036159 14038536 rheMac2 chr10 62090384 62092714 trinucleotide [TTC][TCT][ttc][tct] 0 176 + 218 [TTC]---[TCTTCttcttctt]tg[ttcttcttct----t][tcttctt] indel/deletion,indel/deletion,indel/deletion ,tg, 4,17,30 3 ->hg18 183 hg18 chr22 16274088 16276467 panTro2 chr22 16305968 16308354 ponAbe2 chr22 14036159 14038536 rheMac2 chr10 62090384 62092714 dinucleotide AT 27 1304 + 1315 ATATATA--TAT ->ponAbe2 183 hg18 chr22 16274088 16276467 panTro2 chr22 16305968 16308354 ponAbe2 chr22 14036159 14038536 rheMac2 chr10 62090384 62092714 mononucleotide [T][T] 37 1322 + 1332 [TTTTTTTTT]C[T] indel/deletion C 10 1 >rheMac2 183 hg18 chr22 16274088 16276467 panTro2 chr22 16305968 16308354 ponAbe2 chr22 14036159 14038536 rheMac2 chr10 62090384 62092714 mononucleotide [T][T] 23 1322 + 1334 [TTTTTTTTTTT]C[T] indel/deletion C 12 1 ->hg18 183 hg18 chr22 16274088 16276467 panTro2 chr22 16305968 16308354 ponAbe2 chr22 14036159 14038536 rheMac2 chr10 62090384 62092714 trinucleotide [TAT][ATT] 33 1512 + 1526 [TATTATTATTAT][ATT] indel/deletion 13 1 >panTro2 183 hg18 chr22 16274088 16276467 panTro2 chr22 16305968 16308354 ponAbe2 chr22 14036159 14038536 rheMac2 chr10 62090384 62092714 trinucleotide [TAT][ATT] 24 1512 + 1526 [TATTATTATTAT][ATT] indel/deletion 13 1 >rheMac2 183 hg18 chr22 16274088 16276467 panTro2 chr22 16305968 16308354 ponAbe2 chr22 14036159 14038536 rheMac2 chr10 62090384 62092714 trinucleotide [TAT][ATT] 23 1512 + 1526 [TATTATTATTAT][ATT] indel/deletion 13 1 ->hg18 183 hg18 chr22 16274088 16276467 panTro2 chr22 16305968 16308354 ponAbe2 chr22 14036159 14038536 rheMac2 chr10 62090384 62092714 tetranucleotide TAAA 41 1884 + 1895 TAAATAAATAAA >panTro2 183 hg18 chr22 16274088 16276467 panTro2 chr22 16305968 16308354 ponAbe2 chr22 14036159 14038536 rheMac2 chr10 62090384 62092714 tetranucleotide TAAA 32 1884 + 1895 TAAATAAATAAA >ponAbe2 183 hg18 chr22 16274088 16276467 panTro2 chr22 16305968 16308354 ponAbe2 chr22 14036159 14038536 rheMac2 chr10 62090384 62092714 tetranucleotide TAAA 43 1884 + 1895 TAAATAAATAAA >rheMac2 183 hg18 chr22 16274088 16276467 panTro2 chr22 16305968 16308354 ponAbe2 chr22 14036159 14038536 rheMac2 chr10 62090384 62092714 tetranucleotide TAAA 97 1884 + 1895 TAAATAAATAAA ->hg18 183 hg18 chr22 16274088 16276467 panTro2 chr22 16305968 16308354 ponAbe2 chr22 14036159 14038536 rheMac2 chr10 62090384 62092714 mononucleotide [T][T] 44 2020 + 2049 [TT]C-----------[TTTTTTTTTTTTTTTT] indel/deletion C 3 1 >panTro2 183 hg18 chr22 16274088 16276467 panTro2 chr22 16305968 16308354 ponAbe2 chr22 14036159 14038536 rheMac2 chr10 62090384 62092714 mononucleotide [T][T] 35 2020 + 2049 [TT]C---------[TTTTTTTTTTTTTTTTTT] indel/deletion C 3 1 >ponAbe2 183 hg18 chr22 16274088 16276467 panTro2 chr22 16305968 16308354 ponAbe2 chr22 14036159 14038536 rheMac2 chr10 62090384 62092714 mononucleotide [T][T][T] 60 2024 + 2049 [TTTTTT]G[TTTTT]G[TTTTTTTTTTTTT] insertion,insertion G,G 7,13 2 >rheMac2 183 hg18 chr22 16274088 16276467 panTro2 chr22 16305968 16308354 ponAbe2 chr22 14036159 14038536 rheMac2 chr10 62090384 62092714 mononucleotide [T][T] 106 2035 + 2049 [TTT]G[TTTTTTTTTTT] indel/deletion G 4 1 ->panTro2 185 hg18 chr22 16278521 16278901 panTro2 chr22 16310408 16310746 ponAbe2 chr22 14040530 14040864 rheMac2 chr10 62094706 62095012 trinucleotide GAA 0 22 + 113 gaag-----------------------------------------------------------------------aagaagaagaagaagaa >ponAbe2 185 hg18 chr22 16278521 16278901 panTro2 chr22 16310408 16310746 ponAbe2 chr22 14040530 14040864 rheMac2 chr10 62094706 62095012 trinucleotide AGA 0 22 + 117 agaagaag-----------------------------------------------------------------------aagaagaagaagaagaa >hg18 185 hg18 chr22 16278521 16278901 panTro2 chr22 16310408 16310746 ponAbe2 chr22 14040530 14040864 rheMac2 chr10 62094706 62095012 trinucleotide [AGA][aGA] 4 41 + 66 [gaagaagaagaagaagaaga]g[gaaga] indel/deletion g 21 1 >hg18 185 hg18 chr22 16278521 16278901 panTro2 chr22 16310408 16310746 ponAbe2 chr22 14040530 14040864 rheMac2 chr10 62094706 62095012 trinucleotide.trinucleotide [GAg][GAG].[gaa][AAG] 4 71 + 117 [gaggaagaggaggaggaggaggaggaagaaaagaagaagaagaagaa] indel/deletion.indel/deletion a. 6.7 1.1 67.91 92.113 [GAgga]a[GAGGAGGAGGAGGAGGAGGA].[gaagaa][AAGAAGAAGAAGAAGAA] ->ponAbe2 186 hg18 chr22 16278901 16279101 panTro2 chr22 16310746 16310946 ponAbe2 chr22 14040864 14041065 rheMac2 chr10 62095012 62095213 mononucleotide A 1 50 + 58 AAAAAAAAA ->hg18 187 hg18 chr22 16279101 16280012 panTro2 chr22 16310946 16311861 ponAbe2 chr22 14041065 14041970 rheMac2 chr10 62095213 62096130 mononucleotide A 2 626 + 634 AAAAAAAAA >panTro2 187 hg18 chr22 16279101 16280012 panTro2 chr22 16310946 16311861 ponAbe2 chr22 14041065 14041970 rheMac2 chr10 62095213 62096130 mononucleotide A 2 626 + 634 AAAAAAAAA >ponAbe2 187 hg18 chr22 16279101 16280012 panTro2 chr22 16310946 16311861 ponAbe2 chr22 14041065 14041970 rheMac2 chr10 62095213 62096130 mononucleotide A 10 626 + 634 AAAAAAAAA >rheMac2 187 hg18 chr22 16279101 16280012 panTro2 chr22 16310946 16311861 ponAbe2 chr22 14041065 14041970 rheMac2 chr10 62095213 62096130 mononucleotide [A][A] 0 626 + 638 [AAAAAAAAAA]T[AA] indel/deletion T 11 1 ->hg18 189 hg18 chr22 16282762 16283322 panTro2 chr22 16314263 16314822 ponAbe2 chr22 14046786 14047353 rheMac2 chr10 62099002 62099575 mononucleotide T 14 546 + 556 TTTTTTTTTTT >panTro2 189 hg18 chr22 16282762 16283322 panTro2 chr22 16314263 16314822 ponAbe2 chr22 14046786 14047353 rheMac2 chr10 62099002 62099575 mononucleotide T 15 546 + 556 TTTTTTTTTTT >ponAbe2 189 hg18 chr22 16282762 16283322 panTro2 chr22 16314263 16314822 ponAbe2 chr22 14046786 14047353 rheMac2 chr10 62099002 62099575 mononucleotide T 10 546 + 559 TTTTTTTTTTTTTT >rheMac2 189 hg18 chr22 16282762 16283322 panTro2 chr22 16314263 16314822 ponAbe2 chr22 14046786 14047353 rheMac2 chr10 62099002 62099575 mononucleotide T 9 546 + 564 ttttttttttttttttttt ->rheMac2 191 hg18 chr22 16285899 16286253 panTro2 chr22 16317398 16317751 ponAbe2 chr22 14049949 14050302 rheMac2 chr10 62102158 62102509 mononucleotide T 0 12 + 20 ttttttttt >hg18 191 hg18 chr22 16285899 16286253 panTro2 chr22 16317398 16317751 ponAbe2 chr22 14049949 14050302 rheMac2 chr10 62102158 62102509 mononucleotide T 0 13 + 22 tttttttttt >panTro2 191 hg18 chr22 16285899 16286253 panTro2 chr22 16317398 16317751 ponAbe2 chr22 14049949 14050302 rheMac2 chr10 62102158 62102509 mononucleotide T 0 13 + 21 ttttttttt >ponAbe2 191 hg18 chr22 16285899 16286253 panTro2 chr22 16317398 16317751 ponAbe2 chr22 14049949 14050302 rheMac2 chr10 62102158 62102509 mononucleotide T 0 13 + 22 tttttttttt ->hg18 194 hg18 chr22 16294954 16295267 panTro2 chr22 16326354 16326651 ponAbe2 chr22 14058839 14059156 rheMac2 chr10 62111426 62111772 tetranucleotide [ccct][TCCC] 4 52 + 71 [tccct]t[cctccctccctccc] indel/deletion t 6 1 >panTro2 194 hg18 chr22 16294954 16295267 panTro2 chr22 16326354 16326651 ponAbe2 chr22 14058839 14059156 rheMac2 chr10 62111426 62111772 tetranucleotide [ccct][TCCC] 20 52 + 71 [tccct]t[cctccctccctccc] indel/deletion t 6 1 >ponAbe2 194 hg18 chr22 16294954 16295267 panTro2 chr22 16326354 16326651 ponAbe2 chr22 14058839 14059156 rheMac2 chr10 62111426 62111772 tetranucleotide [ccct][TCCC] 0 52 + 71 [tccct]t[cctCCCTCCCTCCC] indel/deletion t 6 1 ->rheMac2 197 hg18 chr22 16304193 16305153 panTro2 chr22 16335577 16336579 ponAbe2 chr22 14068055 14068985 rheMac2 chr10 62120524 62121473 trinucleotide TAT 14 423 + 474 t------------attattattattattattattattattattattattatt >hg18 197 hg18 chr22 16304193 16305153 panTro2 chr22 16335577 16336579 ponAbe2 chr22 14068055 14068985 rheMac2 chr10 62120524 62121473 trinucleotide [tat][TTA] 36 425 + 474 [tat]act[ttattattattattattattattattattattattattattatt] indel/deletion act 4 1 >panTro2 197 hg18 chr22 16304193 16305153 panTro2 chr22 16335577 16336579 ponAbe2 chr22 14068055 14068985 rheMac2 chr10 62120524 62121473 trinucleotide [tat][TTA] 36 425 + 474 [tat]act[ttattattattattattattattattattattattattattatt] indel/deletion act 4 1 >ponAbe2 197 hg18 chr22 16304193 16305153 panTro2 chr22 16335577 16336579 ponAbe2 chr22 14068055 14068985 rheMac2 chr10 62120524 62121473 trinucleotide [tat][TTA] 22 425 + 474 [tat]act------------------------[ttattattattattattatt] indel/deletion act 4 1 ->panTro2 197 hg18 chr22 16304193 16305153 panTro2 chr22 16335577 16336579 ponAbe2 chr22 14068055 14068985 rheMac2 chr10 62120524 62121473 tetranucleotide.tetranucleotide GCNN.NNCA 36 824 + 837 [gcnnnnnnnnnnca] NA.NA NA.NA NA.NA NA.NA 788.790 799.801 GCNNNNNNNNNN.NNNNNNNNNNCA ->hg18 199 hg18 chr22 16306832 16308524 panTro2 chr22 16339378 16341068 ponAbe2 chr22 14070674 14072420 rheMac2 chr10 62123039 62124713 tetranucleotide [gttt][TTTG][gTTT] 3 82 + 114 [tgttt]tttt-[tttgttt--gtttg]tt[tttgttt] indel/deletion,indel/deletion tttt,tt 6,22 2 >panTro2 199 hg18 chr22 16306832 16308524 panTro2 chr22 16339378 16341068 ponAbe2 chr22 14070674 14072420 rheMac2 chr10 62123039 62124713 tetranucleotide [gttt][TTTG][tttg] 3 82 + 111 [tgttt]t[tttgtttgttt--gtttg]tt[tttg] indel/deletion,indel/deletion t,tt 6,23 2 >ponAbe2 199 hg18 chr22 16306832 16308524 panTro2 chr22 16339378 16341068 ponAbe2 chr22 14070674 14072420 rheMac2 chr10 62123039 62124713 tetranucleotide [gttt][TTTG][gTTT] 3 82 + 114 [tgttt]t----[tttgttt--gtttg]tt[tttgttt] indel/deletion,indel/deletion t,tt 6,19 2 ->rheMac2 199 hg18 chr22 16306832 16308524 panTro2 chr22 16339378 16341068 ponAbe2 chr22 14070674 14072420 rheMac2 chr10 62123039 62124713 mononucleotide [T][T] 32 1103 + 1184 [T]C[tt----------------tttt-----------------------------------------------------ttttt] indel/deletion C 2 1 >ponAbe2 199 hg18 chr22 16306832 16308524 panTro2 chr22 16339378 16341068 ponAbe2 chr22 14070674 14072420 rheMac2 chr10 62123039 62124713 tetranucleotide ATAA 27 1111 + 1122 ataaataaataa >hg18 199 hg18 chr22 16306832 16308524 panTro2 chr22 16339378 16341068 ponAbe2 chr22 14070674 14072420 rheMac2 chr10 62123039 62124713 tetranucleotide [TTTA][TTTA] 52 1124 + 1171 [tttatttattta][ttat-------------------------ttattta] indel/substitution 13 1 >panTro2 199 hg18 chr22 16306832 16308524 panTro2 chr22 16339378 16341068 ponAbe2 chr22 14070674 14072420 rheMac2 chr10 62123039 62124713 tetranucleotide [TTTA][TTTA] 52 1124 + 1179 [tttatttattta][ttat-------------------------ttatttattt----a] indel/substitution 13 1 ->ponAbe2 199 hg18 chr22 16306832 16308524 panTro2 chr22 16339378 16341068 ponAbe2 chr22 14070674 14072420 rheMac2 chr10 62123039 62124713 dinucleotide [CA][AC][CA] 31 1643 + 1657 [CA]G[ACACACACAC][CA] indel/deletion,indel/deletion G, 3,14 2 ->hg18 200 hg18 chr22 16308524 16312859 panTro2 chr22 16341068 16345387 ponAbe2 chr22 14072420 14076750 rheMac2 chr10 62125048 62129389 mononucleotide T 0 1 + 21 ttttttttttttttttttttt >panTro2 200 hg18 chr22 16308524 16312859 panTro2 chr22 16341068 16345387 ponAbe2 chr22 14072420 14076750 rheMac2 chr10 62125048 62129389 mononucleotide T 0 1 + 12 tttttttttttt >ponAbe2 200 hg18 chr22 16308524 16312859 panTro2 chr22 16341068 16345387 ponAbe2 chr22 14072420 14076750 rheMac2 chr10 62125048 62129389 mononucleotide T 0 1 + 21 ttttttttttttttttttttt >rheMac2 200 hg18 chr22 16308524 16312859 panTro2 chr22 16341068 16345387 ponAbe2 chr22 14072420 14076750 rheMac2 chr10 62125048 62129389 mononucleotide T 0 1 + 21 ttttttttttttttttttttt ->rheMac2 200 hg18 chr22 16308524 16312859 panTro2 chr22 16341068 16345387 ponAbe2 chr22 14072420 14076750 rheMac2 chr10 62125048 62129389 tetranucleotide [aatt][ATTA] 15 2590 + 2614 [aatt][tta------attaattaatta] indel/deletion 5 1 >hg18 200 hg18 chr22 16308524 16312859 panTro2 chr22 16341068 16345387 ponAbe2 chr22 14072420 14076750 rheMac2 chr10 62125048 62129389 tetranucleotide [TAtt][TTTA] 12 2594 + 2614 [TTAtt]----[tttatttattta] indel/deletion 6 1 >panTro2 200 hg18 chr22 16308524 16312859 panTro2 chr22 16341068 16345387 ponAbe2 chr22 14072420 14076750 rheMac2 chr10 62125048 62129389 tetranucleotide [TAtt][TTTA] 20 2594 + 2614 [TTAtt]----[tttatttattta] indel/deletion 6 1 >ponAbe2 200 hg18 chr22 16308524 16312859 panTro2 chr22 16341068 16345387 ponAbe2 chr22 14072420 14076750 rheMac2 chr10 62125048 62129389 tetranucleotide [TAtt][TTTA] 15 2594 + 2614 [TTAtt][tttatttatttattta] indel/deletion 6 1 ->ponAbe2 200 hg18 chr22 16308524 16312859 panTro2 chr22 16341068 16345387 ponAbe2 chr22 14072420 14076750 rheMac2 chr10 62125048 62129389 mononucleotide A 46 4002 + 4028 aaaaaaaaaaaaaa-----------aa >rheMac2 200 hg18 chr22 16308524 16312859 panTro2 chr22 16341068 16345387 ponAbe2 chr22 14072420 14076750 rheMac2 chr10 62125048 62129389 mononucleotide [A][A] 44 4002 + 4027 [aaaaaaaaaaaaaaaaaaaaaaaa]T[A] indel/deletion T 25 1 ->ponAbe2 201 hg18 chr22 16313012 16313701 panTro2 chr22 16345540 16346231 ponAbe2 chr22 14076903 14077585 rheMac2 chr10 62129738 62130429 mononucleotide [t][T] 0 82 + 92 [t]c[ttttttttt] indel/deletion c 2 1 ->hg18 207 hg18 chr22 16339795 16340090 panTro2 chr22 16374419 16374709 ponAbe2 chr22 14107998 14108305 rheMac2 chr10 62164924 62165227 mononucleotide [t][T] 1 282 + 309 [t]c[tttttttt----------------tt] indel/deletion c 2 1 >rheMac2 207 hg18 chr22 16339795 16340090 panTro2 chr22 16374419 16374709 ponAbe2 chr22 14107998 14108305 rheMac2 chr10 62164924 62165227 mononucleotide A 1 284 + 300 aaaaaaaaaaaaaaaaa >ponAbe2 207 hg18 chr22 16339795 16340090 panTro2 chr22 16374419 16374709 ponAbe2 chr22 14107998 14108305 rheMac2 chr10 62164924 62165227 mononucleotide A 5 292 + 312 aaaaaaaaaaaaaaaaaaaaa ->hg18 212 hg18 chr22 16355233 16355551 panTro2 chr22 16392606 16392919 ponAbe2 chr22 14122197 14122516 rheMac2 chr10 62179885 62180203 mononucleotide [A][A][A] 0 299 + 318 [aaaaaaa-aaaa]g[aaa]g[aaa] indel/deletion,indel/deletion G,G 12,16 2 >ponAbe2 212 hg18 chr22 16355233 16355551 panTro2 chr22 16392606 16392919 ponAbe2 chr22 14122197 14122516 rheMac2 chr10 62179885 62180203 mononucleotide [A][a] 0 299 + 318 [aaaaaaaaaaaaaaaa]g[aaa] indel/deletion g 17 1 >rheMac2 212 hg18 chr22 16355233 16355551 panTro2 chr22 16392606 16392919 ponAbe2 chr22 14122197 14122516 rheMac2 chr10 62179885 62180203 mononucleotide [A][a] 0 299 + 319 [aaaaaaa-aaaaaaaaa]g[aaa] indel/deletion g 17 1 ->hg18 213 hg18 chr22 16357149 16357449 panTro2 chr22 16394528 16394829 ponAbe2 chr22 14124116 14124421 rheMac2 chr10 62181828 62182143 mononucleotide A 0 116 + 124 aaaaaaaaa ->ponAbe2 213 hg18 chr22 16357149 16357449 panTro2 chr22 16394528 16394829 ponAbe2 chr22 14124116 14124421 rheMac2 chr10 62181828 62182143 compound [T][A] 1 270 + 306 [ttttt------------ttttttttt][aaaaaaaaaaa] >hg18 213 hg18 chr22 16357149 16357449 panTro2 chr22 16394528 16394829 ponAbe2 chr22 14124116 14124421 rheMac2 chr10 62181828 62182143 mononucleotide A 0 275 + 288 aaaaaaaaaaaaaa >panTro2 213 hg18 chr22 16357149 16357449 panTro2 chr22 16394528 16394829 ponAbe2 chr22 14124116 14124421 rheMac2 chr10 62181828 62182143 mononucleotide A 0 275 + 289 aaaaaaaaaaaaaaa >rheMac2 213 hg18 chr22 16357149 16357449 panTro2 chr22 16394528 16394829 ponAbe2 chr22 14124116 14124421 rheMac2 chr10 62181828 62182143 mononucleotide [A][A] 4 275 + 306 [aaaaaaaaaaaaaaaaaaaaaaaaaaaaa]G[AA] indel/deletion G 30 1 ->hg18 214 hg18 chr22 16358011 16358322 panTro2 chr22 16395393 16395698 ponAbe2 chr22 14124987 14125311 rheMac2 chr10 62182701 62183014 tetranucleotide TATT 0 1 + 29 ta-----tttatttatttatttatttatt >panTro2 214 hg18 chr22 16358011 16358322 panTro2 chr22 16395393 16395698 ponAbe2 chr22 14124987 14125311 rheMac2 chr10 62182701 62183014 tetranucleotide TTTA 0 1 + 16 tttatttatttattta >ponAbe2 214 hg18 chr22 16358011 16358322 panTro2 chr22 16395393 16395698 ponAbe2 chr22 14124987 14125311 rheMac2 chr10 62182701 62183014 tetranucleotide [TATT][TATT][ttat] 0 1 + 40 [tatttattt][tatttatttatttatttattt][ttatttattt] indel/substitution,indel/deletion , 10,31 2 >rheMac2 214 hg18 chr22 16358011 16358322 panTro2 chr22 16395393 16395698 ponAbe2 chr22 14124987 14125311 rheMac2 chr10 62182701 62183014 mononucleotide T 3 12 + 40 tttttttttttttttttt--------ttt ->ponAbe2 220 hg18 chr22 16380626 16381197 panTro2 chr22 16417996 16418569 ponAbe2 chr22 14147331 14147903 rheMac2 chr10 62204226 62204796 mononucleotide [T][t] 0 1 + 16 [tttttttttttttt]g[t] indel/deletion g 15 1 ->hg18 222 hg18 chr22 16384784 16385041 panTro2 chr22 16422463 16422717 ponAbe2 chr22 14154140 14154414 rheMac2 chr10 62209623 62209866 mononucleotide [A][a] 1 206 + 232 [aaaaaaaaaaaaaaaaaaaaaaa]g[aaa] indel/deletion g 24 1 >hg18 222 hg18 chr22 16384784 16385041 panTro2 chr22 16422463 16422717 ponAbe2 chr22 14154140 14154414 rheMac2 chr10 62209623 62209866 tetranucleotide GGGA 1 236 + 265 AGGGA-----------------GGGAGGGA >panTro2 222 hg18 chr22 16384784 16385041 panTro2 chr22 16422463 16422717 ponAbe2 chr22 14154140 14154414 rheMac2 chr10 62209623 62209866 mononucleotide [A][A][A] 1 206 + 229 [aaaaaaaaaaaaaaaa]g[aaa]g[aaa] indel/deletion,indel/deletion G,G 17,21 2 >panTro2 222 hg18 chr22 16384784 16385041 panTro2 chr22 16422463 16422717 ponAbe2 chr22 14154140 14154414 rheMac2 chr10 62209623 62209866 tetranucleotide AGGG 4 236 + 265 AGGGA-----------------GGGAGGGA >ponAbe2 222 hg18 chr22 16384784 16385041 panTro2 chr22 16422463 16422717 ponAbe2 chr22 14154140 14154414 rheMac2 chr10 62209623 62209866 mononucleotide A 1 206 + 218 aaaaaaaaaaaaa >rheMac2 222 hg18 chr22 16384784 16385041 panTro2 chr22 16422463 16422717 ponAbe2 chr22 14154140 14154414 rheMac2 chr10 62209623 62209866 mononucleotide [A][a][a] 1 206 + 230 [aaaaaaaaaaaaaaaa]g[aaaa]g[aaa] indel/deletion,indel/deletion g,g 17,22 2 >ponAbe2 222 hg18 chr22 16384784 16385041 panTro2 chr22 16422463 16422717 ponAbe2 chr22 14154140 14154414 rheMac2 chr10 62209623 62209866 mononucleotide [a][A] 1 235 + 256 [aaaa]g[aaannnnnnnnnnaaaa] indel/deletion g 5 1 ->hg18 223 hg18 chr22 16386225 16386609 panTro2 chr22 16423904 16424281 ponAbe2 chr22 14155619 14156009 rheMac2 chr10 62211053 62211446 mononucleotide [A][a] 6 286 + 310 [aaaaaaaaaaaaaaaaaaaaaa]g[aa] indel/deletion g 23 1 >panTro2 223 hg18 chr22 16386225 16386609 panTro2 chr22 16423904 16424281 ponAbe2 chr22 14155619 14156009 rheMac2 chr10 62211053 62211446 mononucleotide [A][a] 6 286 + 303 [aaaaaaaaaaaaaaa]g[aa] indel/deletion g 16 1 >ponAbe2 223 hg18 chr22 16386225 16386609 panTro2 chr22 16423904 16424281 ponAbe2 chr22 14155619 14156009 rheMac2 chr10 62211053 62211446 mononucleotide [A][a] 0 286 + 308 [aaaaaaaaaaaaaaaaaaaa]g[aa] indel/deletion g 21 1 >rheMac2 223 hg18 chr22 16386225 16386609 panTro2 chr22 16423904 16424281 ponAbe2 chr22 14155619 14156009 rheMac2 chr10 62211053 62211446 mononucleotide [A][a][a] 6 287 + 316 [aaaaaaaaaaaaaaaaaaaaaa]g[aaaa]g[aa] indel/deletion,indel/deletion g,g 23,28 2 ->rheMac2 225 hg18 chr22 16395656 16395975 panTro2 chr22 16434418 16434737 ponAbe2 chr22 14165654 14165967 rheMac2 chr10 62222362 62222683 mononucleotide [A][A][A][A][a][A] 0 283 + 314 [aaaaaaaaaa]g[aaaaa]g[aaa]g[aaaa]g[aaaa]T[A] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion g,G,G,g,T 11,17,21,26,31 6 ->rheMac2 227 hg18 chr22 16403797 16403930 panTro2 chr22 16442609 16442742 ponAbe2 chr22 14173962 14174095 rheMac2 chr10 62231151 62231284 mononucleotide A 2 96 + 109 aaaaaaaaaaaaaa ->hg18 228 hg18 chr22 16404026 16404207 panTro2 chr22 16442838 16443020 ponAbe2 chr22 14174191 14174366 rheMac2 chr10 62231380 62231564 mononucleotide A 0 161 + 182 aaaaaaaaaaaaaaa--aaaaa >panTro2 228 hg18 chr22 16404026 16404207 panTro2 chr22 16442838 16443020 ponAbe2 chr22 14174191 14174366 rheMac2 chr10 62231380 62231564 mononucleotide A 0 161 + 183 aaaaaaaaaaaaaaaa--aaaaa >ponAbe2 228 hg18 chr22 16404026 16404207 panTro2 chr22 16442838 16443020 ponAbe2 chr22 14174191 14174366 rheMac2 chr10 62231380 62231564 mononucleotide A 0 161 + 176 aaaaaaaaa--aaaaa >rheMac2 228 hg18 chr22 16404026 16404207 panTro2 chr22 16442838 16443020 ponAbe2 chr22 14174191 14174366 rheMac2 chr10 62231380 62231564 mononucleotide A 0 161 + 176 aaaaaaaaaaaaaaaa ->hg18 229 hg18 chr22 16404434 16404594 panTro2 chr22 16443247 16443402 ponAbe2 chr22 14174592 14174738 rheMac2 chr10 62231792 62231951 mononucleotide A 0 65 + 90 aaaaaaaaaaaaaaaaaaaaa-aaaa >panTro2 229 hg18 chr22 16404434 16404594 panTro2 chr22 16443247 16443402 ponAbe2 chr22 14174592 14174738 rheMac2 chr10 62231792 62231951 mononucleotide A 0 65 + 85 aaaaaaaaaaaaaaaaaaaaa >ponAbe2 229 hg18 chr22 16404434 16404594 panTro2 chr22 16443247 16443402 ponAbe2 chr22 14174592 14174738 rheMac2 chr10 62231792 62231951 mononucleotide A 0 65 + 73 aaaaaaaaa >rheMac2 229 hg18 chr22 16404434 16404594 panTro2 chr22 16443247 16443402 ponAbe2 chr22 14174592 14174738 rheMac2 chr10 62231792 62231951 mononucleotide [A][A][A] 2 65 + 90 [aaaaaaaaaaaaaa]g[aaa]g[aaaaaaa] indel/deletion,indel/deletion G,G 15,19 3 ->hg18 231 hg18 chr22 16409625 16409882 panTro2 chr22 16448413 16448662 ponAbe2 chr22 14179033 14179262 rheMac2 chr10 62236357 62236619 tetranucleotide TTTA 1 194 + 223 tttattta--tttatttatttatttattta >panTro2 231 hg18 chr22 16409625 16409882 panTro2 chr22 16448413 16448662 ponAbe2 chr22 14179033 14179262 rheMac2 chr10 62236357 62236619 tetranucleotide TTTA 1 194 + 213 tttatttatttatttattta >rheMac2 231 hg18 chr22 16409625 16409882 panTro2 chr22 16448413 16448662 ponAbe2 chr22 14179033 14179262 rheMac2 chr10 62236357 62236619 tetranucleotide [TATT][ATTT] 0 198 + 230 [TTTATT][tttatttatttatttatttatttattt] indel/deletion 7 1 ->ponAbe2 231 hg18 chr22 16409625 16409882 panTro2 chr22 16448413 16448662 ponAbe2 chr22 14179033 14179262 rheMac2 chr10 62236357 62236619 mononucleotide N 33 253 + 262 NNNNNNNNNN ->hg18 232 hg18 chr22 16416827 16417151 panTro2 chr22 16455999 16456343 ponAbe2 chr22 14186174 14186497 rheMac2 chr10 62244411 62244716 mononucleotide [t][t][T] 0 3 + 59 [tttt------------------tttt]c[tttt]c[tt--ttttttttttttttttttttt] indel/deletion,indel/deletion c,c 9,14 2 >panTro2 232 hg18 chr22 16416827 16417151 panTro2 chr22 16455999 16456343 ponAbe2 chr22 14186174 14186497 rheMac2 chr10 62244411 62244716 mononucleotide [t][t][t][t][t][T][T][T] 0 3 + 59 [ttttt]c[ttttt]c[tttt]c[tttt]c[tttt]c[tttt]c[ttt]c[ttttttttttttttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion c,c,c,c,c,C,C 6,12,17,22,27,32,36 8 >ponAbe2 232 hg18 chr22 16416827 16417151 panTro2 chr22 16455999 16456343 ponAbe2 chr22 14186174 14186497 rheMac2 chr10 62244411 62244716 mononucleotide [T][T][t][T][T][T][T] 0 3 + 59 [TTTTT]C[T---------------TTtt]c[tttt]c[t---ttt]c[ttt]c[ttt]c[ttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion C,c,c,C,C,C 6,12,17,22,26,30 7 ->ponAbe2 233 hg18 chr22 16418416 16418708 panTro2 chr22 16457582 16457874 ponAbe2 chr22 14187750 14188041 rheMac2 chr10 62246095 62246374 mononucleotide A 0 282 + 292 aaaaaaa-aaa >rheMac2 233 hg18 chr22 16418416 16418708 panTro2 chr22 16457582 16457874 ponAbe2 chr22 14187750 14188041 rheMac2 chr10 62246095 62246374 mononucleotide A 12 282 + 291 aaaaaaaaaa ->rheMac2 235 hg18 chr22 16424037 16424281 panTro2 chr22 16461649 16461897 ponAbe2 chr22 14191802 14192050 rheMac2 chr10 62250426 62250670 mononucleotide A 4 217 + 226 AAAAAAAAAA ->hg18 238 hg18 chr22 16429079 16429394 panTro2 chr22 16468186 16468501 ponAbe2 chr22 14198411 14198726 rheMac2 chr10 62253394 62253705 mononucleotide T 0 1 + 11 ttttttttttt >panTro2 238 hg18 chr22 16429079 16429394 panTro2 chr22 16468186 16468501 ponAbe2 chr22 14198411 14198726 rheMac2 chr10 62253394 62253705 mononucleotide T 0 1 + 11 ttttttttttt >ponAbe2 238 hg18 chr22 16429079 16429394 panTro2 chr22 16468186 16468501 ponAbe2 chr22 14198411 14198726 rheMac2 chr10 62253394 62253705 mononucleotide T 0 1 + 11 ttttttttttt >rheMac2 238 hg18 chr22 16429079 16429394 panTro2 chr22 16468186 16468501 ponAbe2 chr22 14198411 14198726 rheMac2 chr10 62253394 62253705 tetranucleotide TTTG 0 1 + 12 tttgtttgtttg ->rheMac2 239 hg18 chr22 16433046 16434399 panTro2 chr22 16471679 16473025 ponAbe2 chr22 14202454 14203828 rheMac2 chr10 62256401 62257702 mononucleotide [T][T] 0 158 + 169 [TTTTTTTTTT]C[T] indel/deletion C 11 1 ->panTro2 239 hg18 chr22 16433046 16434399 panTro2 chr22 16471679 16473025 ponAbe2 chr22 14202454 14203828 rheMac2 chr10 62256401 62257702 mononucleotide [A][a] 54 1141 + 1153 [aaaaaaaaaaa]t[a] indel/deletion t 12 1 ->hg18 241 hg18 chr22 16447262 16447557 panTro2 chr22 16485385 16485670 ponAbe2 chr22 14216803 14217089 rheMac2 chr10 62272868 62273152 mononucleotide A 0 286 + 295 aaaaaaaaaa ->hg18 244 hg18 chr22 16448374 16448583 panTro2 chr22 16486486 16486696 ponAbe2 chr22 14217908 14218130 rheMac2 chr10 62276003 62276204 mononucleotide [T][t][t][t][t][T][T][T][T][T][T][T][T][T] 0 3 + 74 [TTtt]a[tttt]a[tt]a[tt]a[ttt]a[tt-----tt]a[tt]a[tt]a[tt]a[tt]a[tt]a[tt]a[tt]a[tt-----------tttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion a,a,a,a,a,A,A,A,A,A,A,A,A 5,10,13,16,20,25,28,31,34,37,40,43,46 14 >rheMac2 244 hg18 chr22 16448374 16448583 panTro2 chr22 16486486 16486696 ponAbe2 chr22 14217908 14218130 rheMac2 chr10 62276003 62276204 tetranucleotide [ttta][ATTT][tatT] 0 9 + 49 [ttta]cta[ttatttatt------------tatt-t]ta[ttatt] indel/deletion,indel/deletion cta,ta 5,22 2 >ponAbe2 244 hg18 chr22 16448374 16448583 panTro2 chr22 16486486 16486696 ponAbe2 chr22 14217908 14218130 rheMac2 chr10 62276003 62276204 mononucleotide [T][T][T][T][T][T][T][T][T][T][T][T][T][T][T] 3 16 + 75 [tt]a[ttt]a[ttt]a[ttt]a[tttt]a[tt]a[tt]a[tt]a[tt]a[tt]a[tt]a[ttt]a[ttt]a[ttt]a[tttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion A,A,A,A,A,A,A,A,A,A,A,A,A,A 3,7,11,15,20,23,26,29,32,35,38,42,46,50 14 >panTro2 244 hg18 chr22 16448374 16448583 panTro2 chr22 16486486 16486696 ponAbe2 chr22 14217908 14218130 rheMac2 chr10 62276003 62276204 trinucleotide [att][ATT] 5 20 + 74 [ttatt]tt[ttattattattattattattattattatt----------attattatt] indel/deletion tt 6 1 ->rheMac2 245 hg18 chr22 16451937 16452100 panTro2 chr22 16489918 16490081 ponAbe2 chr22 14221378 14221540 rheMac2 chr10 62281175 62281331 mononucleotide T 0 2 + 18 ttttttttttttttttt >hg18 245 hg18 chr22 16451937 16452100 panTro2 chr22 16489918 16490081 ponAbe2 chr22 14221378 14221540 rheMac2 chr10 62281175 62281331 mononucleotide [T][T][T] 0 3 + 27 [ttttttttttt]c[ttttttt]g[ttttt] insertion,insertion c,g 12,20 2 >panTro2 245 hg18 chr22 16451937 16452100 panTro2 chr22 16489918 16490081 ponAbe2 chr22 14221378 14221540 rheMac2 chr10 62281175 62281331 mononucleotide [T][T][T] 0 3 + 27 [ttttttttttt]c[ttttttt]g[ttttt] insertion,insertion c,g 12,20 2 ->hg18 246 hg18 chr22 16454300 16454612 panTro2 chr22 16492266 16492576 ponAbe2 chr22 14223929 14224254 rheMac2 chr10 62283517 62283821 mononucleotide [A][A] 1 297 + 312 [aaaaaaaaaa]g[aaaaa] insertion g 11 1 >panTro2 246 hg18 chr22 16454300 16454612 panTro2 chr22 16492266 16492576 ponAbe2 chr22 14223929 14224254 rheMac2 chr10 62283517 62283821 mononucleotide [A][a] 1 297 + 311 [aaaaaaaaaaa]g[aaa] indel/deletion g 12 1 >ponAbe2 246 hg18 chr22 16454300 16454612 panTro2 chr22 16492266 16492576 ponAbe2 chr22 14223929 14224254 rheMac2 chr10 62283517 62283821 mononucleotide [A][a][a][a] 0 298 + 323 [aaaaaaaaaaaaaaa]g[aaaa]g[aaa]g[a] indel/deletion,indel/deletion,indel/deletion g,g,g 16,21,25 3 ->panTro2 249 hg18 chr22 16462378 16462688 panTro2 chr22 16501511 16501808 ponAbe2 chr22 14231966 14232275 rheMac2 chr10 62291004 62291274 mononucleotide [A][A] 0 1 + 25 [aaaaaaaAAAAAA]G--------[AAA] indel/deletion G 14 1 ->rheMac2 254 hg18 chr22 16476264 16476944 panTro2 chr22 16516135 16516817 ponAbe2 chr22 14249278 14249960 rheMac2 chr10 62307448 62308099 mononucleotide [a][A] 0 311 + 331 [a]c[aaaaaaaaaaaaaaaaaaa] indel/deletion c 2 1 ->hg18 254 hg18 chr22 16476264 16476944 panTro2 chr22 16516135 16516817 ponAbe2 chr22 14249278 14249960 rheMac2 chr10 62307448 62308099 mononucleotide [A][a][A] 12 481 + 495 [aaaaaaaaa]c[aaa]G[A] indel/deletion,indel/deletion c,G 10,14 2 >panTro2 254 hg18 chr22 16476264 16476944 panTro2 chr22 16516135 16516817 ponAbe2 chr22 14249278 14249960 rheMac2 chr10 62307448 62308099 mononucleotide [A][a][A] 12 481 + 497 [aaaaaaaaaaa]c[aaa]G[A] indel/deletion,indel/deletion c,G 12,16 2 >ponAbe2 254 hg18 chr22 16476264 16476944 panTro2 chr22 16516135 16516817 ponAbe2 chr22 14249278 14249960 rheMac2 chr10 62307448 62308099 mononucleotide [A][a][A] 12 481 + 497 [aaaaaaaaaaaa]g[aa]G[A] indel/deletion,indel/deletion g,G 13,16 2 >rheMac2 254 hg18 chr22 16476264 16476944 panTro2 chr22 16516135 16516817 ponAbe2 chr22 14249278 14249960 rheMac2 chr10 62307448 62308099 mononucleotide A 1 481 + 495 aaaaaaaaaaaaaaa ->ponAbe2 255 hg18 chr22 16479041 16479519 panTro2 chr22 16518919 16519400 ponAbe2 chr22 14249960 14250437 rheMac2 chr10 62308514 62308995 tetranucleotide [AATA][AATA] 0 75 + 96 [aaataaata][aaataaataaaTA] indel/substitution 10 1 >rheMac2 255 hg18 chr22 16479041 16479519 panTro2 chr22 16518919 16519400 ponAbe2 chr22 14249960 14250437 rheMac2 chr10 62308514 62308995 tetranucleotide AATA 2 75 + 96 aaat-----aaataaataaaTA >hg18 255 hg18 chr22 16479041 16479519 panTro2 chr22 16518919 16519400 ponAbe2 chr22 14249960 14250437 rheMac2 chr10 62308514 62308995 tetranucleotide [aata][AATA] 0 78 + 96 [taaata][aaataaataaaTA] indel/deletion 7 1 >panTro2 255 hg18 chr22 16479041 16479519 panTro2 chr22 16518919 16519400 ponAbe2 chr22 14249960 14250437 rheMac2 chr10 62308514 62308995 tetranucleotide [aata][AATA] 0 78 + 96 [taaata][aaataaataaaTA] indel/deletion 7 1 ->hg18 255 hg18 chr22 16479041 16479519 panTro2 chr22 16518919 16519400 ponAbe2 chr22 14249960 14250437 rheMac2 chr10 62308514 62308995 mononucleotide [A][a] 0 405 + 433 [aaaaaaaaaaaaaaaa-------aa]g[aaa] indel/deletion g 19 1 >panTro2 255 hg18 chr22 16479041 16479519 panTro2 chr22 16518919 16519400 ponAbe2 chr22 14249960 14250437 rheMac2 chr10 62308514 62308995 mononucleotide [A][a] 0 405 + 436 [aaaaaaaaaaaaaaaaaaa-------aa]g[aaa] indel/deletion g 22 1 >ponAbe2 255 hg18 chr22 16479041 16479519 panTro2 chr22 16518919 16519400 ponAbe2 chr22 14249960 14250437 rheMac2 chr10 62308514 62308995 mononucleotide [A][a] 0 405 + 432 [aaaaaaaaaaaaaaa-------aa]g[aaa] indel/deletion g 18 1 >rheMac2 255 hg18 chr22 16479041 16479519 panTro2 chr22 16518919 16519400 ponAbe2 chr22 14249960 14250437 rheMac2 chr10 62308514 62308995 mononucleotide A 7 405 + 428 aaaaaaaaaaaaaaaaaaaaaaaa ->rheMac2 258 hg18 chr22 16485075 16485451 panTro2 chr22 16524627 16525000 ponAbe2 chr22 14256511 14256888 rheMac2 chr10 62316852 62317227 mononucleotide [A][A][A][A] 2 333 + 357 [aaa]t[aaa]t[aa-----aaaaaaaa]G[A] indel/deletion,indel/deletion,indel/deletion T,T,G 4,8,19 3 >ponAbe2 258 hg18 chr22 16485075 16485451 panTro2 chr22 16524627 16525000 ponAbe2 chr22 14256511 14256888 rheMac2 chr10 62316852 62317227 mononucleotide [A][A][A][A][A] 5 345 + 375 [aaaaaaaaaaaaAAA]G[AAA]G[AAAA]G[AAAA]C[A] indel/deletion,indel/deletion,indel/deletion,indel/deletion G,G,G,C 16,20,25,30 5 ->hg18 259 hg18 chr22 16489104 16489422 panTro2 chr22 16528648 16528967 ponAbe2 chr22 14260557 14260876 rheMac2 chr10 62322657 62322978 tetranucleotide [Attt][TTTA][tatt] 0 26 + 49 [Attt]tg[tttatttattta]a[tattt] indel/deletion,indel/deletion tg,a 5,19 2 ->hg18 259 hg18 chr22 16489104 16489422 panTro2 chr22 16528648 16528967 ponAbe2 chr22 14260557 14260876 rheMac2 chr10 62322657 62322978 mononucleotide T 1 205 + 219 ttttttttttttttt >panTro2 259 hg18 chr22 16489104 16489422 panTro2 chr22 16528648 16528967 ponAbe2 chr22 14260557 14260876 rheMac2 chr10 62322657 62322978 mononucleotide T 0 205 + 221 ttttttttttttttttt >rheMac2 259 hg18 chr22 16489104 16489422 panTro2 chr22 16528648 16528967 ponAbe2 chr22 14260557 14260876 rheMac2 chr10 62322657 62322978 mononucleotide [t][T] 14 206 + 227 [tt]g[ttttttttttttttttttt] indel/deletion g 3 1 >ponAbe2 259 hg18 chr22 16489104 16489422 panTro2 chr22 16528648 16528967 ponAbe2 chr22 14260557 14260876 rheMac2 chr10 62322657 62322978 mononucleotide [T][T] 13 213 + 227 [ttttt]c[ttttttttt] insertion c 6 1 ->hg18 260 hg18 chr22 16492543 16492711 panTro2 chr22 16532057 16532209 ponAbe2 chr22 14262487 14262661 rheMac2 chr10 62326808 62326962 dinucleotide [ca][AC] 0 39 + 77 [ca]t------[acacacacacacacacacacacacacacac] indel/deletion t 3 1 >panTro2 260 hg18 chr22 16492543 16492711 panTro2 chr22 16532057 16532209 ponAbe2 chr22 14262487 14262661 rheMac2 chr10 62326808 62326962 dinucleotide [ca][AC] 0 39 + 77 [ca]t----------------------[acacacaCACACAC] indel/deletion t 3 1 >ponAbe2 260 hg18 chr22 16492543 16492711 panTro2 chr22 16532057 16532209 ponAbe2 chr22 14262487 14262661 rheMac2 chr10 62326808 62326962 dinucleotide [ca][AC] 0 39 + 77 [ca]t[acacacacacacacacacacacacacacacacacac] indel/deletion t 3 1 >rheMac2 260 hg18 chr22 16492543 16492711 panTro2 chr22 16532057 16532209 ponAbe2 chr22 14262487 14262661 rheMac2 chr10 62326808 62326962 dinucleotide CA 0 39 + 77 cac--------------------acacacaCACACACAC ->hg18 261 hg18 chr22 16493338 16493666 panTro2 chr22 16532791 16533159 ponAbe2 chr22 14263121 14263443 rheMac2 chr10 62327198 62327521 mononucleotide [T][t][t][T] 0 6 + 81 [TT]C[ttttt]c[tt-------------------------------------------tt]c--[ttttttttttttttttt] indel/deletion,indel/deletion,indel/deletion C,c,c 3,9,14 3 >ponAbe2 261 hg18 chr22 16493338 16493666 panTro2 chr22 16532791 16533159 ponAbe2 chr22 14263121 14263443 rheMac2 chr10 62327198 62327521 mononucleotide [t][T][T] 0 6 + 81 [tt]c[ttttt]c[tt---------------------------------------------------tttttttttttttt] indel/deletion,insertion c,c 3,9 2 >rheMac2 261 hg18 chr22 16493338 16493666 panTro2 chr22 16532791 16533159 ponAbe2 chr22 14263121 14263443 rheMac2 chr10 62327198 62327521 mononucleotide T 13 15 + 81 tt------------------------------------------------ttttttttttttttttt >panTro2 261 hg18 chr22 16493338 16493666 panTro2 chr22 16532791 16533159 ponAbe2 chr22 14263121 14263443 rheMac2 chr10 62327198 62327521 mononucleotide T 0 65 + 81 ttttttttttttttttt ->hg18 262 hg18 chr22 16493666 16495952 panTro2 chr22 16533669 16535925 ponAbe2 chr22 14263443 14265663 rheMac2 chr10 62327521 62329724 mononucleotide T 8 214 + 227 tttttttttttttt >panTro2 262 hg18 chr22 16493666 16495952 panTro2 chr22 16533669 16535925 ponAbe2 chr22 14263443 14265663 rheMac2 chr10 62327521 62329724 mononucleotide T 4 214 + 230 ttttttttttttttttt >ponAbe2 262 hg18 chr22 16493666 16495952 panTro2 chr22 16533669 16535925 ponAbe2 chr22 14263443 14265663 rheMac2 chr10 62327521 62329724 mononucleotide T 8 214 + 230 ttttttttttttttttt ->panTro2 262 hg18 chr22 16493666 16495952 panTro2 chr22 16533669 16535925 ponAbe2 chr22 14263443 14265663 rheMac2 chr10 62327521 62329724 compound [AT][T] 12 764 + 822 [atatatatatatatatatatatatat][ttttttttttttttttttttttttttttttttt] >hg18 262 hg18 chr22 16493666 16495952 panTro2 chr22 16533669 16535925 ponAbe2 chr22 14263443 14265663 rheMac2 chr10 62327521 62329724 compound [TG][TA][T] 18 777 + 856 [tgtgtgtgtgtg][tatatatatatatatatatatatatatatatatata][tttttttttttttttttttttttttttttttt] >rheMac2 262 hg18 chr22 16493666 16495952 panTro2 chr22 16533669 16535925 ponAbe2 chr22 14263443 14265663 rheMac2 chr10 62327521 62329724 mononucleotide T 78 844 + 856 ttttttttttttt ->hg18 262 hg18 chr22 16493666 16495952 panTro2 chr22 16533669 16535925 ponAbe2 chr22 14263443 14265663 rheMac2 chr10 62327521 62329724 mononucleotide [T][T][T][T] 24 1868 + 1900 [tt]c[tt]c[tt]c------[tttttttttttttttttt] indel/deletion,indel/deletion,indel/deletion C,C,C 3,6,9 3 >panTro2 262 hg18 chr22 16493666 16495952 panTro2 chr22 16533669 16535925 ponAbe2 chr22 14263443 14265663 rheMac2 chr10 62327521 62329724 mononucleotide [T][T][T][T][T] 52 1868 + 1900 [tt]c[tt]c[tt]c--------[tt]c[ttttttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion C,C,C,C 3,6,9,12 4 >ponAbe2 262 hg18 chr22 16493666 16495952 panTro2 chr22 16533669 16535925 ponAbe2 chr22 14263443 14265663 rheMac2 chr10 62327521 62329724 mononucleotide [T][T][T][T][T][T] 88 1868 + 1900 [tt]c[tt]c[tt]c--------[tt]c[tt]c[tttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion C,C,C,C,C 3,6,9,12,15 5 >rheMac2 262 hg18 chr22 16493666 16495952 panTro2 chr22 16533669 16535925 ponAbe2 chr22 14263443 14265663 rheMac2 chr10 62327521 62329724 mononucleotide [T][T][T][T][T][T][T] 114 1869 + 1901 [T]C[TT]C[tt]c[tt]c[tt]c[tt]c[tttttttttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion C,C,C,C,C,C 2,5,8,11,14,17 6 ->ponAbe2 266 hg18 chr22 16503660 16503955 panTro2 chr22 16543976 16544270 ponAbe2 chr22 14273642 14273935 rheMac2 chr10 62336815 62337106 mononucleotide T 0 1 + 14 tttttttttttttt >hg18 266 hg18 chr22 16503660 16503955 panTro2 chr22 16543976 16544270 ponAbe2 chr22 14273642 14273935 rheMac2 chr10 62336815 62337106 mononucleotide [t][T] 0 3 + 14 [t]a[tttttttttt] indel/deletion a 2 1 >panTro2 266 hg18 chr22 16503660 16503955 panTro2 chr22 16543976 16544270 ponAbe2 chr22 14273642 14273935 rheMac2 chr10 62336815 62337106 mononucleotide T 1 3 + 14 tttttttttttt ->hg18 267 hg18 chr22 16504903 16505258 panTro2 chr22 16545218 16545573 ponAbe2 chr22 14274880 14275235 rheMac2 chr10 62338162 62338571 mononucleotide T 0 1 + 13 ttttttttttttt >panTro2 267 hg18 chr22 16504903 16505258 panTro2 chr22 16545218 16545573 ponAbe2 chr22 14274880 14275235 rheMac2 chr10 62338162 62338571 mononucleotide T 0 1 + 13 ttttttttttttt >ponAbe2 267 hg18 chr22 16504903 16505258 panTro2 chr22 16545218 16545573 ponAbe2 chr22 14274880 14275235 rheMac2 chr10 62338162 62338571 mononucleotide T 0 1 + 13 ttttttttttttt ->hg18 269 hg18 chr22 16507197 16508088 panTro2 chr22 16547518 16548406 ponAbe2 chr22 14277180 14278082 rheMac2 chr10 62341934 62342766 mononucleotide [t][T][T] 2 374 + 400 [ttt]c-[tttttttttttttttt]c[ttttt] indel/deletion,insertion c,c 4,21 2 >panTro2 269 hg18 chr22 16507197 16508088 panTro2 chr22 16547518 16548406 ponAbe2 chr22 14277180 14278082 rheMac2 chr10 62341934 62342766 mononucleotide [t][T][T] 2 374 + 400 [ttt]c---[tttttttttttttt]c[ttttt] indel/deletion,insertion c,c 4,19 2 >ponAbe2 269 hg18 chr22 16507197 16508088 panTro2 chr22 16547518 16548406 ponAbe2 chr22 14277180 14278082 rheMac2 chr10 62341934 62342766 mononucleotide [t][T][T] 2 374 + 400 [ttt]c[ttttttttttttttttt]c[ttttt] indel/deletion,insertion c,c 4,22 2 >rheMac2 269 hg18 chr22 16507197 16508088 panTro2 chr22 16547518 16548406 ponAbe2 chr22 14277180 14278082 rheMac2 chr10 62341934 62342766 mononucleotide [t][T] 51 375 + 400 [tt]c-----------[tttttttttttt] indel/deletion c 3 1 ->rheMac2 269 hg18 chr22 16507197 16508088 panTro2 chr22 16547518 16548406 ponAbe2 chr22 14277180 14278082 rheMac2 chr10 62341934 62342766 mononucleotide [T][T] 66 797 + 829 [t--------------tttttt]g[ttttttttttt] insertion g 8 1 >hg18 269 hg18 chr22 16507197 16508088 panTro2 chr22 16547518 16548406 ponAbe2 chr22 14277180 14278082 rheMac2 chr10 62341934 62342766 mononucleotide T 3 798 + 818 ttttttttttttttttttttt >panTro2 269 hg18 chr22 16507197 16508088 panTro2 chr22 16547518 16548406 ponAbe2 chr22 14277180 14278082 rheMac2 chr10 62341934 62342766 mononucleotide T 5 798 + 817 tttttttttttttttttttt >ponAbe2 269 hg18 chr22 16507197 16508088 panTro2 chr22 16547518 16548406 ponAbe2 chr22 14277180 14278082 rheMac2 chr10 62341934 62342766 mononucleotide T 2 798 + 828 ttttttttttttttttttttttttttttttt ->hg18 270 hg18 chr22 16509503 16510141 panTro2 chr22 16550598 16551221 ponAbe2 chr22 14279479 14280097 rheMac2 chr10 62343719 62344272 dinucleotide TG 3 155 + 189 tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt >hg18 270 hg18 chr22 16509503 16510141 panTro2 chr22 16550598 16551221 ponAbe2 chr22 14279479 14280097 rheMac2 chr10 62343719 62344272 compound [AT][T][T][T] 7 203 + 264 [ata---tatatatatatatatatatat][ttttttttttttttttttttttt]c[ttttt]c[ttttt] >panTro2 270 hg18 chr22 16509503 16510141 panTro2 chr22 16550598 16551221 ponAbe2 chr22 14279479 14280097 rheMac2 chr10 62343719 62344272 dinucleotide TG 3 155 + 193 tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt >panTro2 270 hg18 chr22 16509503 16510141 panTro2 chr22 16550598 16551221 ponAbe2 chr22 14279479 14280097 rheMac2 chr10 62343719 62344272 dinucleotide [ta][at][TA] 3 200 + 228 [ta]c[atat]tt[tatatatatatatatatata] indel/deletion,indel/deletion c,tt 3,8 2 >ponAbe2 270 hg18 chr22 16509503 16510141 panTro2 chr22 16550598 16551221 ponAbe2 chr22 14279479 14280097 rheMac2 chr10 62343719 62344272 dinucleotide TG 1 155 + 193 tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt >ponAbe2 270 hg18 chr22 16509503 16510141 panTro2 chr22 16550598 16551221 ponAbe2 chr22 14279479 14280097 rheMac2 chr10 62343719 62344272 compound [AT][T] 1 203 + 264 [ata---tatatatatatatatat]---[ttt----------------------ttttttttttt] >rheMac2 270 hg18 chr22 16509503 16510141 panTro2 chr22 16550598 16551221 ponAbe2 chr22 14279479 14280097 rheMac2 chr10 62343719 62344272 mononucleotide [t][T] 58 213 + 264 [t]a[tt------------ttt----------------------ttttttttttt] indel/deletion a 2 1 ->panTro2 272 hg18 chr22 16510662 16511208 panTro2 chr22 16551772 16552319 ponAbe2 chr22 14280732 14281283 rheMac2 chr10 62345189 62345740 tetranucleotide.tetranucleotide CCNN.NNGA 8 11 + 24 [ccnnnnnnnnnnga] NA.NA NA.NA NA.NA NA.NA 3.5 14.16 CCNNNNNNNNNN.NNNNNNNNNNGA ->hg18 272 hg18 chr22 16510662 16511208 panTro2 chr22 16551772 16552319 ponAbe2 chr22 14280732 14281283 rheMac2 chr10 62345189 62345740 mononucleotide [A][a] 15 240 + 256 [aaaaaaaaaaaaa]g[aaa] indel/deletion g 14 1 >panTro2 272 hg18 chr22 16510662 16511208 panTro2 chr22 16551772 16552319 ponAbe2 chr22 14280732 14281283 rheMac2 chr10 62345189 62345740 mononucleotide [A][a] 15 240 + 257 [aaaaaaaaaaaaaa]g[aaa] indel/deletion g 15 1 >ponAbe2 272 hg18 chr22 16510662 16511208 panTro2 chr22 16551772 16552319 ponAbe2 chr22 14280732 14281283 rheMac2 chr10 62345189 62345740 mononucleotide [A][a] 10 240 + 256 [aaaaaaaaaaaaa]g[aaa] indel/deletion g 14 1 >rheMac2 272 hg18 chr22 16510662 16511208 panTro2 chr22 16551772 16552319 ponAbe2 chr22 14280732 14281283 rheMac2 chr10 62345189 62345740 mononucleotide A 10 240 + 256 aaaaaaaaaaaaaaaaa ->rheMac2 273 hg18 chr22 16511268 16511676 panTro2 chr22 16552379 16552790 ponAbe2 chr22 14281343 14281751 rheMac2 chr10 62346104 62346511 compound [A][T] 0 30 + 50 [aaaaaaaaaaaa][ttttttttt] >rheMac2 273 hg18 chr22 16511268 16511676 panTro2 chr22 16552379 16552790 ponAbe2 chr22 14281343 14281751 rheMac2 chr10 62346104 62346511 mononucleotide [A][a] 0 55 + 66 [aaaaaaaaaa]t[a] indel/deletion t 11 1 >hg18 273 hg18 chr22 16511268 16511676 panTro2 chr22 16552379 16552790 ponAbe2 chr22 14281343 14281751 rheMac2 chr10 62346104 62346511 mononucleotide A 6 55 + 64 aAAAAAAAAA >panTro2 273 hg18 chr22 16511268 16511676 panTro2 chr22 16552379 16552790 ponAbe2 chr22 14281343 14281751 rheMac2 chr10 62346104 62346511 mononucleotide [a][A] 6 55 + 67 [aA]G[AAAAAAAAAA] indel/deletion G 3 1 >ponAbe2 273 hg18 chr22 16511268 16511676 panTro2 chr22 16552379 16552790 ponAbe2 chr22 14281343 14281751 rheMac2 chr10 62346104 62346511 mononucleotide A 6 55 + 64 aAAAAAAAAA ->ponAbe2 273 hg18 chr22 16511268 16511676 panTro2 chr22 16552379 16552790 ponAbe2 chr22 14281343 14281751 rheMac2 chr10 62346104 62346511 tetranucleotide TAAA 10 159 + 172 taaataaataaata ->hg18 274 hg18 chr22 16511786 16512574 panTro2 chr22 16552899 16553683 ponAbe2 chr22 14281861 14282659 rheMac2 chr10 62346934 62347743 mononucleotide T 0 82 + 95 tttttttttttttt >panTro2 274 hg18 chr22 16511786 16512574 panTro2 chr22 16552899 16553683 ponAbe2 chr22 14281861 14282659 rheMac2 chr10 62346934 62347743 mononucleotide T 0 82 + 94 ttttttttttttt >ponAbe2 274 hg18 chr22 16511786 16512574 panTro2 chr22 16552899 16553683 ponAbe2 chr22 14281861 14282659 rheMac2 chr10 62346934 62347743 mononucleotide T 0 82 + 96 ttttttttttttttt ->hg18 274 hg18 chr22 16511786 16512574 panTro2 chr22 16552899 16553683 ponAbe2 chr22 14281861 14282659 rheMac2 chr10 62346934 62347743 mononucleotide T 24 515 + 524 tttttttttt >panTro2 274 hg18 chr22 16511786 16512574 panTro2 chr22 16552899 16553683 ponAbe2 chr22 14281861 14282659 rheMac2 chr10 62346934 62347743 mononucleotide T 27 515 + 523 ttttttttt >ponAbe2 274 hg18 chr22 16511786 16512574 panTro2 chr22 16552899 16553683 ponAbe2 chr22 14281861 14282659 rheMac2 chr10 62346934 62347743 mononucleotide T 16 515 + 526 tttttttttttt >rheMac2 274 hg18 chr22 16511786 16512574 panTro2 chr22 16552899 16553683 ponAbe2 chr22 14281861 14282659 rheMac2 chr10 62346934 62347743 mononucleotide T 11 515 + 532 tttttttttttttttttt ->panTro2 278 hg18 chr22 16513745 16514466 panTro2 chr22 16555121 16555849 ponAbe2 chr22 14283815 14284535 rheMac2 chr10 62349247 62349947 mononucleotide [T][T][T] 0 10 + 42 [T]-------C[tt]c[tttttttttttttttt----t] indel/deletion,indel/deletion C,C 2,5 2 >ponAbe2 278 hg18 chr22 16513745 16514466 panTro2 chr22 16555121 16555849 ponAbe2 chr22 14283815 14284535 rheMac2 chr10 62349247 62349947 mononucleotide [T][T][T] 0 10 + 42 [T]C[tt]c[ttttttttttttttttttttttt----t] indel/deletion,indel/deletion C,C 2,5 2 >rheMac2 278 hg18 chr22 16513745 16514466 panTro2 chr22 16555121 16555849 ponAbe2 chr22 14283815 14284535 rheMac2 chr10 62349247 62349947 mononucleotide T 0 10 + 37 t-------tttttttttttttttttttt >hg18 278 hg18 chr22 16513745 16514466 panTro2 chr22 16555121 16555849 ponAbe2 chr22 14283815 14284535 rheMac2 chr10 62349247 62349947 mononucleotide T 6 19 + 42 ttttttttttttttttttt----t ->hg18 278 hg18 chr22 16513745 16514466 panTro2 chr22 16555121 16555849 ponAbe2 chr22 14283815 14284535 rheMac2 chr10 62349247 62349947 tetranucleotide TATT 16 405 + 437 tatttatttatttatttatttatttatttattt >ponAbe2 278 hg18 chr22 16513745 16514466 panTro2 chr22 16555121 16555849 ponAbe2 chr22 14283815 14284535 rheMac2 chr10 62349247 62349947 mononucleotide [t][t][t][t][T] 10 405 + 437 [t]c[ttt]c[ttt]g[ttt]c[t-------ttttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion c,c,g,c 2,6,10,14 4 >rheMac2 278 hg18 chr22 16513745 16514466 panTro2 chr22 16555121 16555849 ponAbe2 chr22 14283815 14284535 rheMac2 chr10 62349247 62349947 mononucleotide [T][T][T][T][T] 22 405 + 437 [t]c[ttt]c[ttt]c[ttt]c[tt------ttttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion C,C,C,C 2,6,10,14 4 >panTro2 278 hg18 chr22 16513745 16514466 panTro2 chr22 16555121 16555849 ponAbe2 chr22 14283815 14284535 rheMac2 chr10 62349247 62349947 tetranucleotide TTTA 25 407 + 453 tttatttatttatttatttatttatttatttatttatttatttattt ->ponAbe2 279 hg18 chr22 16514765 16515469 panTro2 chr22 16556149 16556853 ponAbe2 chr22 14284835 14285541 rheMac2 chr10 62349947 62350646 mononucleotide T 0 203 + 212 T-TTTttttt ->rheMac2 279 hg18 chr22 16514765 16515469 panTro2 chr22 16556149 16556853 ponAbe2 chr22 14284835 14285541 rheMac2 chr10 62349947 62350646 mononucleotide [t][T] 6 448 + 462 [ttt]c[ttttttttttt] indel/deletion c 4 1 ->hg18 281 hg18 chr22 16517907 16518233 panTro2 chr22 16559616 16559942 ponAbe2 chr22 14288311 14288633 rheMac2 chr10 62352767 62353079 mononucleotide T 4 164 + 178 ttttttttttttttt >panTro2 281 hg18 chr22 16517907 16518233 panTro2 chr22 16559616 16559942 ponAbe2 chr22 14288311 14288633 rheMac2 chr10 62352767 62353079 mononucleotide T 4 164 + 177 tttttttttttttt >ponAbe2 281 hg18 chr22 16517907 16518233 panTro2 chr22 16559616 16559942 ponAbe2 chr22 14288311 14288633 rheMac2 chr10 62352767 62353079 mononucleotide [T][t] 4 164 + 181 [ttttttttttt]-----a[t] indel/deletion a 12 1 >rheMac2 281 hg18 chr22 16517907 16518233 panTro2 chr22 16559616 16559942 ponAbe2 chr22 14288311 14288633 rheMac2 chr10 62352767 62353079 mononucleotide T 0 164 + 174 ttttttttttt ->hg18 281 hg18 chr22 16517907 16518233 panTro2 chr22 16559616 16559942 ponAbe2 chr22 14288311 14288633 rheMac2 chr10 62352767 62353079 mononucleotide [T][t] 4 289 + 306 [tttttttttttttt]c[ttt] indel/deletion c 15 1 >panTro2 281 hg18 chr22 16517907 16518233 panTro2 chr22 16559616 16559942 ponAbe2 chr22 14288311 14288633 rheMac2 chr10 62352767 62353079 mononucleotide [T][t] 5 289 + 307 [ttttttttttttttt]c[ttt] indel/deletion c 16 1 >ponAbe2 281 hg18 chr22 16517907 16518233 panTro2 chr22 16559616 16559942 ponAbe2 chr22 14288311 14288633 rheMac2 chr10 62352767 62353079 mononucleotide [T][T] 10 289 + 304 [tttttttttt]c[ttttt] insertion c 11 1 ->hg18 282 hg18 chr22 16519114 16519881 panTro2 chr22 16560794 16561561 ponAbe2 chr22 14289525 14290299 rheMac2 chr10 62353951 62354558 mononucleotide T 0 1 + 20 tttttttttttttttttttt >hg18 282 hg18 chr22 16519114 16519881 panTro2 chr22 16560794 16561561 ponAbe2 chr22 14289525 14290299 rheMac2 chr10 62353951 62354558 dinucleotide [tc][CT] 0 30 + 44 [tctc]a[ctctctctct] indel/deletion a 5 1 >panTro2 282 hg18 chr22 16519114 16519881 panTro2 chr22 16560794 16561561 ponAbe2 chr22 14289525 14290299 rheMac2 chr10 62353951 62354558 mononucleotide [T][T] 0 1 + 20 [ttttttttt]g[tttttttttt] insertion g 10 1 >panTro2 282 hg18 chr22 16519114 16519881 panTro2 chr22 16560794 16561561 ponAbe2 chr22 14289525 14290299 rheMac2 chr10 62353951 62354558 dinucleotide [Tc][CT] 0 30 + 44 [tct]ta[ctctctctct] indel/deletion ta 4 1 >ponAbe2 282 hg18 chr22 16519114 16519881 panTro2 chr22 16560794 16561561 ponAbe2 chr22 14289525 14290299 rheMac2 chr10 62353951 62354558 mononucleotide T 0 1 + 20 tttttttttttttttttttt >ponAbe2 282 hg18 chr22 16519114 16519881 panTro2 chr22 16560794 16561561 ponAbe2 chr22 14289525 14290299 rheMac2 chr10 62353951 62354558 dinucleotide [tc][CT] 0 30 + 44 [tctc]a[ctctctctct] indel/deletion a 5 1 >rheMac2 282 hg18 chr22 16519114 16519881 panTro2 chr22 16560794 16561561 ponAbe2 chr22 14289525 14290299 rheMac2 chr10 62353951 62354558 mononucleotide [T][T] 5 7 + 20 [T]A[tttttttttttt] indel/deletion A 2 1 >rheMac2 282 hg18 chr22 16519114 16519881 panTro2 chr22 16560794 16561561 ponAbe2 chr22 14289525 14290299 rheMac2 chr10 62353951 62354558 dinucleotide [tc][CT] 5 30 + 44 [tctc]a[ctctctctct] indel/deletion a 5 1 ->ponAbe2 282 hg18 chr22 16519114 16519881 panTro2 chr22 16560794 16561561 ponAbe2 chr22 14289525 14290299 rheMac2 chr10 62353951 62354558 mononucleotide T 2 475 + 496 tttttttttttttttttttttt ->rheMac2 282 hg18 chr22 16519114 16519881 panTro2 chr22 16560794 16561561 ponAbe2 chr22 14289525 14290299 rheMac2 chr10 62353951 62354558 mononucleotide [T][t] 172 647 + 657 [ttttttttt]g[t] indel/deletion g 10 1 ->rheMac2 283 hg18 chr22 16525101 16525264 panTro2 chr22 16566820 16566983 ponAbe2 chr22 14295873 14296036 rheMac2 chr10 62357869 62358035 tetranucleotide [caaa][AACA] 0 142 + 162 [caaa][aaacaaacaaacaaaCA] indel/deletion 5 1 ->hg18 284 hg18 chr22 16527050 16527652 panTro2 chr22 16568762 16569363 ponAbe2 chr22 14304635 14305239 rheMac2 chr10 62362006 62362611 mononucleotide [c][C] 3 132 + 145 [cc]a--[ccccccccc] indel/deletion a 3 1 >rheMac2 284 hg18 chr22 16527050 16527652 panTro2 chr22 16568762 16569363 ponAbe2 chr22 14304635 14305239 rheMac2 chr10 62362006 62362611 mononucleotide [c][C] 2 133 + 145 [c]a[ccccccccccc] indel/deletion a 2 1 ->ponAbe2 286 hg18 chr22 16528292 16528986 panTro2 chr22 16570007 16570708 ponAbe2 chr22 14306151 14306882 rheMac2 chr10 62363477 62364165 tetranucleotide [tatt][TTTA] 2 709 + 726 [tttatt][tttatttattta] indel/deletion 7 1 ->hg18 287 hg18 chr22 16528986 16530504 panTro2 chr22 16570708 16572228 ponAbe2 chr22 14307178 14308700 rheMac2 chr10 62364175 62365680 dinucleotide [TA][ta] 0 26 + 40 [tatatatatat]t[tat] indel/deletion t 12 1 >panTro2 287 hg18 chr22 16528986 16530504 panTro2 chr22 16570708 16572228 ponAbe2 chr22 14307178 14308700 rheMac2 chr10 62364175 62365680 dinucleotide [TA][ta] 0 26 + 40 [tatatatatat]t[tat] indel/deletion t 12 1 ->hg18 287 hg18 chr22 16528986 16530504 panTro2 chr22 16570708 16572228 ponAbe2 chr22 14307178 14308700 rheMac2 chr10 62364175 62365680 tetranucleotide TTAT 0 212 + 243 ttattta----------tttatttatttattt >panTro2 287 hg18 chr22 16528986 16530504 panTro2 chr22 16570708 16572228 ponAbe2 chr22 14307178 14308700 rheMac2 chr10 62364175 62365680 tetranucleotide TTTA 0 215 + 243 ttta----------tttatttatttattt >ponAbe2 287 hg18 chr22 16528986 16530504 panTro2 chr22 16570708 16572228 ponAbe2 chr22 14307178 14308700 rheMac2 chr10 62364175 62365680 mononucleotide T 4 223 + 244 tttttttttttttttttttttt ->hg18 287 hg18 chr22 16528986 16530504 panTro2 chr22 16570708 16572228 ponAbe2 chr22 14307178 14308700 rheMac2 chr10 62364175 62365680 mononucleotide [t][T] 18 474 + 498 [tt]c-[ttttttttttttttttttttt] indel/deletion c 3 1 >panTro2 287 hg18 chr22 16528986 16530504 panTro2 chr22 16570708 16572228 ponAbe2 chr22 14307178 14308700 rheMac2 chr10 62364175 62365680 mononucleotide [t][T] 18 474 + 498 [tt]c[tttttttttttttttttttttt] indel/deletion c 3 1 >ponAbe2 287 hg18 chr22 16528986 16530504 panTro2 chr22 16570708 16572228 ponAbe2 chr22 14307178 14308700 rheMac2 chr10 62364175 62365680 mononucleotide [t][T] 11 474 + 498 [tt]c----------[tttttttttttt] indel/deletion c 3 1 >rheMac2 287 hg18 chr22 16528986 16530504 panTro2 chr22 16570708 16572228 ponAbe2 chr22 14307178 14308700 rheMac2 chr10 62364175 62365680 mononucleotide [t][T] 19 474 + 498 [tt]c--[tttttttttttttttttttt] indel/deletion c 3 1 ->rheMac2 287 hg18 chr22 16528986 16530504 panTro2 chr22 16570708 16572228 ponAbe2 chr22 14307178 14308700 rheMac2 chr10 62364175 62365680 trinucleotide TTG 21 1312 + 1332 ttgttgttgttgttg---ttg ->hg18 288 hg18 chr22 16530504 16532780 panTro2 chr22 16572228 16574499 ponAbe2 chr22 14308869 14311163 rheMac2 chr10 62365694 62367970 mononucleotide [t][t][T] 6 282 + 308 [t]a[tt]c----------[tttttttttttt] indel/deletion,indel/deletion a,c 2,5 2 >panTro2 288 hg18 chr22 16530504 16532780 panTro2 chr22 16572228 16574499 ponAbe2 chr22 14308869 14311163 rheMac2 chr10 62365694 62367970 mononucleotide [t][t][T] 14 282 + 308 [t]a[tt]c------[tttttttttttttttt] indel/deletion,indel/deletion a,c 2,5 2 >ponAbe2 288 hg18 chr22 16530504 16532780 panTro2 chr22 16572228 16574499 ponAbe2 chr22 14308869 14311163 rheMac2 chr10 62365694 62367970 mononucleotide [t][t][T][T] 4 282 + 308 [t]a[tt]c[tttttttttt]c[ttttttttttt] indel/deletion,indel/deletion,insertion a,c,c 2,5,16 3 >rheMac2 288 hg18 chr22 16530504 16532780 panTro2 chr22 16572228 16574499 ponAbe2 chr22 14308869 14311163 rheMac2 chr10 62365694 62367970 mononucleotide [t][T] 13 284 + 308 [tt]c-------[ttttttttttttttt] indel/deletion c 3 1 ->ponAbe2 288 hg18 chr22 16530504 16532780 panTro2 chr22 16572228 16574499 ponAbe2 chr22 14308869 14311163 rheMac2 chr10 62365694 62367970 mononucleotide [t][T][T] 8 729 + 761 [t]g[tttttt--------tt]g-[ttttttttttttt] indel/deletion,insertion g,g 2,11 2 >rheMac2 288 hg18 chr22 16530504 16532780 panTro2 chr22 16572228 16574499 ponAbe2 chr22 14308869 14311163 rheMac2 chr10 62365694 62367970 trinucleotide [gtt][TTG][gTT] 22 729 + 755 [tgtt]ttt[ttgttgttgttg]ttt[ttgtt] indel/deletion,indel/deletion ttt,ttt 5,20 2 >hg18 288 hg18 chr22 16530504 16532780 panTro2 chr22 16572228 16574499 ponAbe2 chr22 14308869 14311163 rheMac2 chr10 62365694 62367970 mononucleotide [t][T][t] 18 731 + 761 [t]g[tt--------------ttttttttttt]c[t] indel/deletion,indel/deletion g,c 2,16 2 >panTro2 288 hg18 chr22 16530504 16532780 panTro2 chr22 16572228 16574499 ponAbe2 chr22 14308869 14311163 rheMac2 chr10 62365694 62367970 mononucleotide [t][T][t] 24 731 + 761 [t]g[tt--------------ttttttttttt]c[t] indel/deletion,indel/deletion g,c 2,16 2 ->hg18 288 hg18 chr22 16530504 16532780 panTro2 chr22 16572228 16574499 ponAbe2 chr22 14308869 14311163 rheMac2 chr10 62365694 62367970 mononucleotide [t][T][T][T] 32 1315 + 1358 [t]g[ttt]c[ttt]c[ttt--------------ttttttttttttttttt] indel/deletion,indel/deletion,indel/deletion g,C,C 2,6,10 3 >panTro2 288 hg18 chr22 16530504 16532780 panTro2 chr22 16572228 16574499 ponAbe2 chr22 14308869 14311163 rheMac2 chr10 62365694 62367970 mononucleotide [t][T][T][T][T][T] 38 1315 + 1358 [t]g[ttt]c[ttt]c[ttt]c-------------[ttt]c[ttttttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion g,C,C,C,C 2,6,10,14,18 5 >ponAbe2 288 hg18 chr22 16530504 16532780 panTro2 chr22 16572228 16574499 ponAbe2 chr22 14308869 14311163 rheMac2 chr10 62365694 62367970 mononucleotide [t][T][T][T][T][T] 17 1315 + 1358 [t]g[ttt]c[ttt]c[ttt]c----------[ttt]c[tttttttttttttttt] indel/deletion,indel/deletion,indel/deletion,indel/deletion,indel/deletion g,C,C,C,C 2,6,10,14,18 5 ->hg18 289 hg18 chr22 16532780 16533507 panTro2 chr22 16574499 16575228 ponAbe2 chr22 14311163 14311893 rheMac2 chr10 62368292 62368969 mononucleotide T 2 362 + 379 tttttttttttttttttt >panTro2 289 hg18 chr22 16532780 16533507 panTro2 chr22 16574499 16575228 ponAbe2 chr22 14311163 14311893 rheMac2 chr10 62368292 62368969 mononucleotide T 2 362 + 382 ttttttttttttttttttttt >ponAbe2 289 hg18 chr22 16532780 16533507 panTro2 chr22 16574499 16575228 ponAbe2 chr22 14311163 14311893 rheMac2 chr10 62368292 62368969 mononucleotide T 0 362 + 380 ttttttttttttttttttt >rheMac2 289 hg18 chr22 16532780 16533507 panTro2 chr22 16574499 16575228 ponAbe2 chr22 14311163 14311893 rheMac2 chr10 62368292 62368969 mononucleotide [T][T] 34 362 + 383 [tttttttttttt]c[ttttttttt] insertion c 13 1 ->hg18 290 hg18 chr22 16534328 16534487 panTro2 chr22 16576046 16576207 ponAbe2 chr22 14313785 14313947 rheMac2 chr10 62369483 62369667 mononucleotide A 0 4 + 18 aaaaaaaaaaaaaaa >hg18 290 hg18 chr22 16534328 16534487 panTro2 chr22 16576046 16576207 ponAbe2 chr22 14313785 14313947 rheMac2 chr10 62369483 62369667 tetranucleotide TTTA 6 34 + 45 TTTATTTAttta >panTro2 290 hg18 chr22 16534328 16534487 panTro2 chr22 16576046 16576207 ponAbe2 chr22 14313785 14313947 rheMac2 chr10 62369483 62369667 mononucleotide A 0 4 + 20 aaaaaaaaaaaaaaaaa >panTro2 290 hg18 chr22 16534328 16534487 panTro2 chr22 16576046 16576207 ponAbe2 chr22 14313785 14313947 rheMac2 chr10 62369483 62369667 tetranucleotide TTTA 4 34 + 45 tttatttattta >ponAbe2 290 hg18 chr22 16534328 16534487 panTro2 chr22 16576046 16576207 ponAbe2 chr22 14313785 14313947 rheMac2 chr10 62369483 62369667 mononucleotide A 0 4 + 21 aaaaaaaaaaaaaaaaaa >ponAbe2 290 hg18 chr22 16534328 16534487 panTro2 chr22 16576046 16576207 ponAbe2 chr22 14313785 14313947 rheMac2 chr10 62369483 62369667 tetranucleotide TTTA 3 34 + 52 TTTatttatttatttattt >rheMac2 290 hg18 chr22 16534328 16534487 panTro2 chr22 16576046 16576207 ponAbe2 chr22 14313785 14313947 rheMac2 chr10 62369483 62369667 mononucleotide A 0 4 + 24 aaaaaaaaaaaaaaaaaaaaa ->rheMac2 290 hg18 chr22 16534328 16534487 panTro2 chr22 16576046 16576207 ponAbe2 chr22 14313785 14313947 rheMac2 chr10 62369483 62369667 mononucleotide T 9 181 + 193 ttttttttttttt ->hg18 291 hg18 chr22 16536127 16536247 panTro2 chr22 16577847 16577964 ponAbe2 chr22 14315614 14315728 rheMac2 chr10 62371299 62371410 mononucleotide T 0 1 + 18 tttttttttttttttttt >panTro2 291 hg18 chr22 16536127 16536247 panTro2 chr22 16577847 16577964 ponAbe2 chr22 14315614 14315728 rheMac2 chr10 62371299 62371410 mononucleotide T 0 1 + 15 ttttttttttttttt >ponAbe2 291 hg18 chr22 16536127 16536247 panTro2 chr22 16577847 16577964 ponAbe2 chr22 14315614 14315728 rheMac2 chr10 62371299 62371410 mononucleotide T 0 1 + 18 tttttttttttttttttt ->hg18 292 hg18 chr22 16537105 16537420 panTro2 chr22 16578816 16579132 ponAbe2 chr22 14316789 14317107 rheMac2 chr10 62372265 62372564 mononucleotide [A][A][A][A] 14 281 + 309 [aaaaaaaaaaaaaaaaa]g[aaa]g[aaa]g[aaa] indel/deletion,indel/deletion,indel/deletion G,G,G 18,22,26 3 >panTro2 292 hg18 chr22 16537105 16537420 panTro2 chr22 16578816 16579132 ponAbe2 chr22 14316789 14317107 rheMac2 chr10 62372265 62372564 mononucleotide [A][A][A][A] 14 281 + 310 [aaaaaaaaaaaaaaaaaa]g[aaa]g[aaa]g[aaa] indel/deletion,indel/deletion,indel/deletion G,G,G 19,23,27 3 ->panTro2 295 hg18 chr22 16547342 16549221 panTro2 chr22 16589056 16590930 ponAbe2 chr22 14325074 14327001 rheMac2 chr10 62382569 62384469 mononucleotide [T][T] 1 156 + 198 [tttttt]g-----------------[ttttttttttttttttttt] insertion g 7 1 >hg18 295 hg18 chr22 16547342 16549221 panTro2 chr22 16589056 16590930 ponAbe2 chr22 14325074 14327001 rheMac2 chr10 62382569 62384469 mononucleotide [t][T] 1 163 + 178 [t]a[tttttttttttttt] indel/deletion a 2 1 >ponAbe2 295 hg18 chr22 16547342 16549221 panTro2 chr22 16589056 16590930 ponAbe2 chr22 14325074 14327001 rheMac2 chr10 62382569 62384469 mononucleotide T 0 172 + 199 tttttttttttttttttttttttttttt ->rheMac2 295 hg18 chr22 16547342 16549221 panTro2 chr22 16589056 16590930 ponAbe2 chr22 14325074 14327001 rheMac2 chr10 62382569 62384469 mononucleotide [T][t][T] 107 763 + 790 [T]G[tttt]c[t------------tttttttt] indel/deletion,indel/deletion G,c 2,7 2 >hg18 295 hg18 chr22 16547342 16549221 panTro2 chr22 16589056 16590930 ponAbe2 chr22 14325074 14327001 rheMac2 chr10 62382569 62384469 trinucleotide [TTG][gtT] 123 770 + 786 [ttgttgttgttg]c[tgtt] indel/deletion c 13 1 >panTro2 295 hg18 chr22 16547342 16549221 panTro2 chr22 16589056 16590930 ponAbe2 chr22 14325074 14327001 rheMac2 chr10 62382569 62384469 trinucleotide [TTG][gtT] 120 770 + 786 [ttgttgttgttg]c[tgtt] indel/deletion c 13 1 >ponAbe2 295 hg18 chr22 16547342 16549221 panTro2 chr22 16589056 16590930 ponAbe2 chr22 14325074 14327001 rheMac2 chr10 62382569 62384469 trinucleotide [TTG][gtT] 91 770 + 786 [ttgttgttgttg]c[tgtt] indel/deletion c 13 1 ->hg18 295 hg18 chr22 16547342 16549221 panTro2 chr22 16589056 16590930 ponAbe2 chr22 14325074 14327001 rheMac2 chr10 62382569 62384469 mononucleotide [T][T][T] 140 1312 + 1353 [tttttt]c[ttttt]c[ttttttttttttttttttttttttttttt] insertion,insertion c,c 7,13 2 >panTro2 295 hg18 chr22 16547342 16549221 panTro2 chr22 16589056 16590930 ponAbe2 chr22 14325074 14327001 rheMac2 chr10 62382569 62384469 mononucleotide [T][T][T] 137 1312 + 1353 [tttttt]c[ttttt]c--------[ttttttttttttttttttttt] insertion,insertion c,c 7,13 2 >ponAbe2 295 hg18 chr22 16547342 16549221 panTro2 chr22 16589056 16590930 ponAbe2 chr22 14325074 14327001 rheMac2 chr10 62382569 62384469 mononucleotide [T][T][T][t] 95 1312 + 1355 [tttttt]c[ttttt]c--------------[ttttttttttttttt]g[t] insertion,insertion,indel/deletion c,c,g 7,13,29 3 >rheMac2 295 hg18 chr22 16547342 16549221 panTro2 chr22 16589056 16590930 ponAbe2 chr22 14325074 14327001 rheMac2 chr10 62382569 62384469 mononucleotide [T][T][T][T][t] 138 1312 + 1353 [tttttt]c[ttttt]c------------[ttttt]c[ttttttttt]c[t] insertion,insertion,insertion,indel/deletion c,c,c,c 7,13,19,29 4 ->rheMac2 295 hg18 chr22 16547342 16549221 panTro2 chr22 16589056 16590930 ponAbe2 chr22 14325074 14327001 rheMac2 chr10 62382569 62384469 mononucleotide [a][A] 161 1885 + 1895 [a]c[aaaaaaaaa] indel/deletion c 2 1 ->panTro2 295 hg18 chr22 16547342 16549221 panTro2 chr22 16589056 16590930 ponAbe2 chr22 14325074 14327001 rheMac2 chr10 62382569 62384469 mononucleotide A 185 2051 + 2059 aaaaaaaaa >ponAbe2 295 hg18 chr22 16547342 16549221 panTro2 chr22 16589056 16590930 ponAbe2 chr22 14325074 14327001 rheMac2 chr10 62382569 62384469 mononucleotide A 137 2051 + 2064 aaaaaaaaaaaaaa >rheMac2 295 hg18 chr22 16547342 16549221 panTro2 chr22 16589056 16590930 ponAbe2 chr22 14325074 14327001 rheMac2 chr10 62382569 62384469 mononucleotide [A][A] 169 2053 + 2069 [aaaaa]c[aaaaaaaaaaa] insertion c 6 1 ->ponAbe2 297 hg18 chr22 16550407 16550708 panTro2 chr22 16592355 16592659 ponAbe2 chr22 14328231 14328545 rheMac2 chr10 62386999 62387286 mononucleotide T 1 177 + 201 tttttttttttttttttttttnttt >rheMac2 297 hg18 chr22 16550407 16550708 panTro2 chr22 16592355 16592659 ponAbe2 chr22 14328231 14328545 rheMac2 chr10 62386999 62387286 mononucleotide T 1 177 + 196 t---tttttttttttttttt >hg18 297 hg18 chr22 16550407 16550708 panTro2 chr22 16592355 16592659 ponAbe2 chr22 14328231 14328545 rheMac2 chr10 62386999 62387286 mononucleotide T 0 178 + 193 tttttttttttttttt >panTro2 297 hg18 chr22 16550407 16550708 panTro2 chr22 16592355 16592659 ponAbe2 chr22 14328231 14328545 rheMac2 chr10 62386999 62387286 mononucleotide T 0 178 + 196 ttttttttttttttttttt ->hg18 299 hg18 chr22 16552326 16552639 panTro2 chr22 16594278 16594591 ponAbe2 chr22 14330196 14330515 rheMac2 chr10 62388973 62389286 mononucleotide A 4 287 + 304 aaaaaaaaaaaaaaaaaa >panTro2 299 hg18 chr22 16552326 16552639 panTro2 chr22 16594278 16594591 ponAbe2 chr22 14330196 14330515 rheMac2 chr10 62388973 62389286 mononucleotide A 4 287 + 305 aaaaaaaaaaaaaaaaaaa >ponAbe2 299 hg18 chr22 16552326 16552639 panTro2 chr22 16594278 16594591 ponAbe2 chr22 14330196 14330515 rheMac2 chr10 62388973 62389286 mononucleotide A 0 287 + 305 aaaaaaaaaaaaaaaaaaa >rheMac2 299 hg18 chr22 16552326 16552639 panTro2 chr22 16594278 16594591 ponAbe2 chr22 14330196 14330515 rheMac2 chr10 62388973 62389286 mononucleotide A 4 287 + 307 aaaaaaaaaaaaaaaaaaaaa ->hg18 301 hg18 chr22 16559769 16560194 panTro2 chr22 16601694 16602118 ponAbe2 chr22 14337739 14338171 rheMac2 chr10 62395845 62396273 mononucleotide A 0 135 + 149 aaaaaaaaaaaaaaa >panTro2 301 hg18 chr22 16559769 16560194 panTro2 chr22 16601694 16602118 ponAbe2 chr22 14337739 14338171 rheMac2 chr10 62395845 62396273 mononucleotide A 0 135 + 148 aaaaaaaaaaaaaa >rheMac2 301 hg18 chr22 16559769 16560194 panTro2 chr22 16601694 16602118 ponAbe2 chr22 14337739 14338171 rheMac2 chr10 62395845 62396273 mononucleotide A 0 135 + 152 aaaaaaaaaaaaaaaaaa >ponAbe2 301 hg18 chr22 16559769 16560194 panTro2 chr22 16601694 16602118 ponAbe2 chr22 14337739 14338171 rheMac2 chr10 62395845 62396273 mononucleotide A 0 136 + 154 aaaaaaaaaaaaaaaaaaa ->panTro2 302 hg18 chr22 16567898 16568183 panTro2 chr22 16611410 16611697 ponAbe2 chr22 14347411 14347701 rheMac2 chr10 62405712 62406009 tetranucleotide [AAAC][aAAC] 0 141 + 167 [caaacaaacaaacaaacaaac]aa[aAAC] indel/deletion aa 22 1 >ponAbe2 302 hg18 chr22 16567898 16568183 panTro2 chr22 16611410 16611697 ponAbe2 chr22 14347411 14347701 rheMac2 chr10 62405712 62406009 tetranucleotide [CAAA][aaaC] 0 141 + 162 [caaacaaacaaacaaa][aaa--C] indel/deletion 17 1 >rheMac2 302 hg18 chr22 16567898 16568183 panTro2 chr22 16611410 16611697 ponAbe2 chr22 14347411 14347701 rheMac2 chr10 62405712 62406009 mononucleotide A 0 143 + 167 aaaaaaaaaaaaaaaaaaaaaaaaa ->rheMac2 302 hg18 chr22 16567898 16568183 panTro2 chr22 16611410 16611697 ponAbe2 chr22 14347411 14347701 rheMac2 chr10 62405712 62406009 mononucleotide T 0 183 + 199 t----tttttttttttt >hg18 302 hg18 chr22 16567898 16568183 panTro2 chr22 16611410 16611697 ponAbe2 chr22 14347411 14347701 rheMac2 chr10 62405712 62406009 mononucleotide T 15 184 + 198 ttttttttttttttt >panTro2 302 hg18 chr22 16567898 16568183 panTro2 chr22 16611410 16611697 ponAbe2 chr22 14347411 14347701 rheMac2 chr10 62405712 62406009 mononucleotide T 3 184 + 199 tttttttttttttttt >ponAbe2 302 hg18 chr22 16567898 16568183 panTro2 chr22 16611410 16611697 ponAbe2 chr22 14347411 14347701 rheMac2 chr10 62405712 62406009 mononucleotide T 11 184 + 198 ttttttttttttttt ->ponAbe2 303 hg18 chr22 16568576 16569324 panTro2 chr22 16612103 16612846 ponAbe2 chr22 14348040 14348764 rheMac2 chr10 62406403 62407140 mononucleotide C 8 442 + 450 ccccccccc ->hg18 303 hg18 chr22 16568576 16569324 panTro2 chr22 16612103 16612846 ponAbe2 chr22 14348040 14348764 rheMac2 chr10 62406403 62407140 mononucleotide [T][T] 1 518 + 535 [TT]G[TTTTTTTTTTTTTTT] indel/deletion G 3 1 >panTro2 303 hg18 chr22 16568576 16569324 panTro2 chr22 16612103 16612846 ponAbe2 chr22 14348040 14348764 rheMac2 chr10 62406403 62407140 mononucleotide [T][T][T] 4 518 + 535 [TT]G--[TT]G[TTTTTTTTTT] indel/deletion,indel/deletion G,G 3,6 2 >rheMac2 303 hg18 chr22 16568576 16569324 panTro2 chr22 16612103 16612846 ponAbe2 chr22 14348040 14348764 rheMac2 chr10 62406403 62407140 mononucleotide [T][T] 5 518 + 535 [TT]G----[TTTTTTTTTTT] indel/deletion G 3 1 ->hg18 304 hg18 chr22 16569363 16569569 panTro2 chr22 16612885 16613091 ponAbe2 chr22 14348803 14349006 rheMac2 chr10 62407178 62407391 tetranucleotide GTCT 8 196 + 207 GTCTGTCTGTCT >panTro2 304 hg18 chr22 16569363 16569569 panTro2 chr22 16612885 16613091 ponAbe2 chr22 14348803 14349006 rheMac2 chr10 62407178 62407391 tetranucleotide GTCT 8 196 + 207 GTCTGTCTGTCT >ponAbe2 304 hg18 chr22 16569363 16569569 panTro2 chr22 16612885 16613091 ponAbe2 chr22 14348803 14349006 rheMac2 chr10 62407178 62407391 tetranucleotide GTCT 11 196 + 207 GTCTGTCTGTCT ->hg18 308 hg18 chr22 16572797 16572984 panTro2 chr22 16616296 16616480 ponAbe2 chr22 14354459 14354641 rheMac2 chr10 62410186 62410371 mononucleotide [A][A] 2 39 + 65 [aaaaaaaaaaaaaaaaaaaaaaaaa]G[A] indel/deletion G 26 1 >panTro2 308 hg18 chr22 16572797 16572984 panTro2 chr22 16616296 16616480 ponAbe2 chr22 14354459 14354641 rheMac2 chr10 62410186 62410371 mononucleotide A 2 39 + 65 aaaaaaaaaaaaaaaaaaaaaaa---a >ponAbe2 308 hg18 chr22 16572797 16572984 panTro2 chr22 16616296 16616480 ponAbe2 chr22 14354459 14354641 rheMac2 chr10 62410186 62410371 mononucleotide A 2 39 + 65 aaaaaaaaaaaaaaaaaaaaa-----a >rheMac2 308 hg18 chr22 16572797 16572984 panTro2 chr22 16616296 16616480 ponAbe2 chr22 14354459 14354641 rheMac2 chr10 62410186 62410371 mononucleotide [A][A] 0 39 + 67 [aaaaaaaaaaaaaaaaaaaaaaa---a]G[A] indel/deletion G 25 1 ->hg18 309 hg18 chr22 16573089 16573369 panTro2 chr22 16616587 16616866 ponAbe2 chr22 14354748 14355029 rheMac2 chr10 62410478 62410762 mononucleotide A 7 104 + 114 aaaaaaaaaaa >panTro2 309 hg18 chr22 16573089 16573369 panTro2 chr22 16616587 16616866 ponAbe2 chr22 14354748 14355029 rheMac2 chr10 62410478 62410762 mononucleotide A 7 104 + 113 aaaaaaaaaa >ponAbe2 309 hg18 chr22 16573089 16573369 panTro2 chr22 16616587 16616866 ponAbe2 chr22 14354748 14355029 rheMac2 chr10 62410478 62410762 mononucleotide A 6 104 + 114 aaaaaaaaaaa >rheMac2 309 hg18 chr22 16573089 16573369 panTro2 chr22 16616587 16616866 ponAbe2 chr22 14354748 14355029 rheMac2 chr10 62410478 62410762 mononucleotide A 1 104 + 114 aaaaaaaaaaa ->hg18 310 hg18 chr22 16573668 16574108 panTro2 chr22 16617165 16617619 ponAbe2 chr22 14355343 14355794 rheMac2 chr10 62410762 62411204 mononucleotide T 2 405 + 415 ttttttttttt >panTro2 310 hg18 chr22 16573668 16574108 panTro2 chr22 16617165 16617619 ponAbe2 chr22 14355343 14355794 rheMac2 chr10 62410762 62411204 mononucleotide T 2 405 + 429 ttttttttttttttttttttttttt >ponAbe2 310 hg18 chr22 16573668 16574108 panTro2 chr22 16617165 16617619 ponAbe2 chr22 14355343 14355794 rheMac2 chr10 62410762 62411204 mononucleotide [T][T] 0 405 + 424 [ttttt]c[tttttttttttttt] insertion c 6 1 >rheMac2 310 hg18 chr22 16573668 16574108 panTro2 chr22 16617165 16617619 ponAbe2 chr22 14355343 14355794 rheMac2 chr10 62410762 62411204 mononucleotide [T][T] 2 405 + 417 [TT]A[tttttttttt] indel/deletion A 3 1 ->ponAbe2 311 hg18 chr22 16577884 16578116 panTro2 chr22 16621672 16621855 ponAbe2 chr22 14359850 14360047 rheMac2 chr10 62415528 62415770 dinucleotide [at][TA] 0 1 + 16 [at]tt[tatatatatata] indel/deletion tt 3 1 >ponAbe2 311 hg18 chr22 16577884 16578116 panTro2 chr22 16621672 16621855 ponAbe2 chr22 14359850 14360047 rheMac2 chr10 62415528 62415770 tetranucleotide [tgtt][GTTT] 45 71 + 94 [ttgtt]g[ttgtttgtttgtttgttt] indel/deletion g 6 1 >panTro2 311 hg18 chr22 16577884 16578116 panTro2 chr22 16621672 16621855 ponAbe2 chr22 14359850 14360047 rheMac2 chr10 62415528 62415770 compound [TA][TTAT] 0 3 + 94 [TATATATATATATA-----------------------------------------------------------t][ttatttatttatttattt] >hg18 311 hg18 chr22 16577884 16578116 panTro2 chr22 16621672 16621855 ponAbe2 chr22 14359850 14360047 rheMac2 chr10 62415528 62415770 compound [TA][T] 0 5 + 95 [tatatatatata----------tatatatatatatatatatatatatatatatatatat][tttttttttttttttttttttttttttttttt] >rheMac2 311 hg18 chr22 16577884 16578116 panTro2 chr22 16621672 16621855 ponAbe2 chr22 14359850 14360047 rheMac2 chr10 62415528 62415770 dinucleotide [GT][tg] 0 6 + 41 [gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt]a[tgt] indel/deletion a 33 1 >rheMac2 311 hg18 chr22 16577884 16578116 panTro2 chr22 16621672 16621855 ponAbe2 chr22 14359850 14360047 rheMac2 chr10 62415528 62415770 compound [TG][AT][T] 0 45 + 92 [tgtgtgtgtgtgtgt][atatatatatatatat][ttttttttttttttttt] ->hg18 313 hg18 chr22 16582282 16582611 panTro2 chr22 16631108 16631432 ponAbe2 chr22 14363989 14364311 rheMac2 chr10 62419764 62420106 mononucleotide A 34 346 + 363 aaaaaaaaaaaaaaaaaa >panTro2 313 hg18 chr22 16582282 16582611 panTro2 chr22 16631108 16631432 ponAbe2 chr22 14363989 14364311 rheMac2 chr10 62419764 62420106 mononucleotide A 34 346 + 358 aaaaaaaaaaaaa >ponAbe2 313 hg18 chr22 16582282 16582611 panTro2 chr22 16631108 16631432 ponAbe2 chr22 14363989 14364311 rheMac2 chr10 62419764 62420106 mononucleotide A 34 346 + 356 aaaaaaaaaaa >rheMac2 313 hg18 chr22 16582282 16582611 panTro2 chr22 16631108 16631432 ponAbe2 chr22 14363989 14364311 rheMac2 chr10 62419764 62420106 mononucleotide A 15 346 + 357 aaaaaaaaaaaa ->hg18 314 hg18 chr22 16586456 16586708 panTro2 chr22 16637105 16637357 ponAbe2 chr22 14368804 14369056 rheMac2 chr10 62422807 62423062 mononucleotide A 1 243 + 254 aaaaa--aaaaa >panTro2 314 hg18 chr22 16586456 16586708 panTro2 chr22 16637105 16637357 ponAbe2 chr22 14368804 14369056 rheMac2 chr10 62422807 62423062 mononucleotide A 1 243 + 255 aaaaa--aaaaaa >ponAbe2 314 hg18 chr22 16586456 16586708 panTro2 chr22 16637105 16637357 ponAbe2 chr22 14368804 14369056 rheMac2 chr10 62422807 62423062 mononucleotide A 1 243 + 255 aaaaa--aaaaaa -UNDONE: 0 ->hg18 6 hg18 chr22 16087148 16087683 panTro2 chr22 16098278 16098811 ponAbe2 chr22 13792105 13792643 mononucleotide A 0 275 + 286 aaaaaaaaaaaa >panTro2 6 hg18 chr22 16087148 16087683 panTro2 chr22 16098278 16098811 ponAbe2 chr22 13792105 13792643 mononucleotide A 0 275 + 284 aaaaaaaaaa >ponAbe2 6 hg18 chr22 16087148 16087683 panTro2 chr22 16098278 16098811 ponAbe2 chr22 13792105 13792643 mononucleotide A 10 275 + 299 aaaaaaaaaaaaaaaaaaaaaaaaa ->hg18 7 hg18 chr22 16087849 16088212 panTro2 chr22 16098811 16099174 ponAbe2 chr22 13792797 13793158 mononucleotide [A][a] 0 247 + 264 [aaaaaaaaaaaaa]g[aaaa] indel/deletion g 14 1 >panTro2 7 hg18 chr22 16087849 16088212 panTro2 chr22 16098811 16099174 ponAbe2 chr22 13792797 13793158 mononucleotide [A][a] 0 247 + 264 [aaaaaaaaaaaaa]g[aaaa] indel/deletion g 14 1 >ponAbe2 7 hg18 chr22 16087849 16088212 panTro2 chr22 16098811 16099174 ponAbe2 chr22 13792797 13793158 mononucleotide A 0 247 + 265 aaaaaaaaaaaaaaaaaaa ->hg18 15 hg18 chr22 16134988 16135166 panTro2 chr22 16151662 16151839 ponAbe2 chr22 13856716 13856882 mononucleotide [A][a][a] 0 32 + 58 [aaaaaaaaaaaaaaaaaaaa]g[aaa]g[aa] indel/deletion,indel/deletion g,g 21,25 2 >panTro2 15 hg18 chr22 16134988 16135166 panTro2 chr22 16151662 16151839 ponAbe2 chr22 13856716 13856882 mononucleotide [A][A] 0 32 + 53 [aaaaaaaaaaaaaaaaaaaa]G[A] indel/deletion G 21 1 >ponAbe2 15 hg18 chr22 16134988 16135166 panTro2 chr22 16151662 16151839 ponAbe2 chr22 13856716 13856882 mononucleotide [A][a] 0 32 + 52 [aaaaaaaaaaaaaaaaaaa]g[a] indel/deletion g 20 1 ->hg18 15 hg18 chr22 16134988 16135166 panTro2 chr22 16151662 16151839 ponAbe2 chr22 13856716 13856882 tetranucleotide TTTC 0 163 + 177 TTTCTTTCTTTCTTT >panTro2 15 hg18 chr22 16134988 16135166 panTro2 chr22 16151662 16151839 ponAbe2 chr22 13856716 13856882 tetranucleotide TTTC 0 163 + 178 TTTCTTTCTTTC-TTt ->hg18 16 hg18 chr22 16135373 16135835 panTro2 chr22 16152046 16152515 ponAbe2 chr22 13857060 13857523 trinucleotide ATT 3 291 + 305 attattattattatt >hg18 16 hg18 chr22 16135373 16135835 panTro2 chr22 16152046 16152515 ponAbe2 chr22 13857060 13857523 trinucleotide TTA 9 317 + 331 ttattattattatta >panTro2 16 hg18 chr22 16135373 16135835 panTro2 chr22 16152046 16152515 ponAbe2 chr22 13857060 13857523 trinucleotide ATT 1 291 + 311 attattattattattattatt >panTro2 16 hg18 chr22 16135373 16135835 panTro2 chr22 16152046 16152515 ponAbe2 chr22 13857060 13857523 mononucleotide [t][t][t][T][t] 1 315 + 341 [ttttttt]a[tt]a[tt]a[tt-ttttttt]a[tt] indel/deletion,indel/deletion,indel/deletion,indel/deletion a,a,a,a 8,11,14,24 4 >ponAbe2 16 hg18 chr22 16135373 16135835 panTro2 chr22 16152046 16152515 ponAbe2 chr22 13857060 13857523 trinucleotide ATT 0 291 + 305 ATTATTATTATTAtt ->ponAbe2 17 hg18 chr22 16138405 16138678 panTro2 chr22 16154962 16155235 ponAbe2 chr22 13860739 13861013 mononucleotide [a][a][A] 2 102 + 117 [a]c[aaa]g[aaaaaaaaaa] indel/deletion,indel/deletion c,g 2,6 2 ->ponAbe2 17 hg18 chr22 16138405 16138678 panTro2 chr22 16154962 16155235 ponAbe2 chr22 13860739 13861013 dinucleotide [ta][AT] 2 263 + 276 [ta][aTATATATATAT] indel/deletion 3 1 ->ponAbe2 18 hg18 chr22 16152746 16153006 panTro2 chr22 16173465 16173724 ponAbe2 chr22 13879267 13879525 mononucleotide [t][t][T] 0 4 + 27 [ttt]c[tttt]c[tt-tttttttttttt] indel/deletion,indel/deletion c,c 4,9 2 >hg18 18 hg18 chr22 16152746 16153006 panTro2 chr22 16173465 16173724 ponAbe2 chr22 13879267 13879525 compound [TC][T] 0 6 + 27 [tctctctctct][ttttttttttt] >panTro2 18 hg18 chr22 16152746 16153006 panTro2 chr22 16173465 16173724 ponAbe2 chr22 13879267 13879525 mononucleotide [t][T] 0 12 + 27 [t]c[t-tttttttttttt] indel/deletion c 2 1 ->hg18 19 hg18 chr22 16153006 16153180 panTro2 chr22 16174091 16174261 ponAbe2 chr22 13880170 13880342 mononucleotide T 0 51 + 68 tttttttttttttttttt >ponAbe2 19 hg18 chr22 16153006 16153180 panTro2 chr22 16174091 16174261 ponAbe2 chr22 13880170 13880342 mononucleotide T 0 51 + 67 ttttttttttttttttt ->hg18 25 hg18 chr22 16191114 16191297 panTro2 chr22 16214474 16214657 ponAbe2 chr22 13922788 13922971 tetranucleotide TGTA 0 157 + 168 TGTATGTATGTA >panTro2 25 hg18 chr22 16191114 16191297 panTro2 chr22 16214474 16214657 ponAbe2 chr22 13922788 13922971 tetranucleotide TGTA 0 157 + 168 TGTATGTATGTA ->hg18 26 hg18 chr22 16191670 16191804 panTro2 chr22 16215037 16215171 ponAbe2 chr22 13923347 13923482 mononucleotide A 0 1 + 9 aaaaaaaaa >panTro2 26 hg18 chr22 16191670 16191804 panTro2 chr22 16215037 16215171 ponAbe2 chr22 13923347 13923482 mononucleotide A 0 1 + 9 aaaaaaaaa >ponAbe2 26 hg18 chr22 16191670 16191804 panTro2 chr22 16215037 16215171 ponAbe2 chr22 13923347 13923482 mononucleotide A 0 1 + 9 aaaaaaaaa ->hg18 27 hg18 chr22 16196102 16196229 panTro2 chr22 16219461 16219588 ponAbe2 chr22 13937929 13938060 tetranucleotide CAAA 0 1 + 12 caaacaaacaaa >panTro2 27 hg18 chr22 16196102 16196229 panTro2 chr22 16219461 16219588 ponAbe2 chr22 13937929 13938060 tetranucleotide CAAA 0 1 + 12 caaacaaacaaa ->hg18 28 hg18 chr22 16204023 16204201 panTro2 chr22 16227427 16227562 ponAbe2 chr22 13950296 13950471 mononucleotide T 0 19 + 32 tttttttttttttt ->hg18 29 hg18 chr22 16206162 16207659 panTro2 chr22 16232109 16233601 ponAbe2 chr22 13956476 13958009 mononucleotide A 0 1 + 9 aaaaaaaaa >panTro2 29 hg18 chr22 16206162 16207659 panTro2 chr22 16232109 16233601 ponAbe2 chr22 13956476 13958009 mononucleotide A 0 1 + 9 aaaaaaaaa >ponAbe2 29 hg18 chr22 16206162 16207659 panTro2 chr22 16232109 16233601 ponAbe2 chr22 13956476 13958009 mononucleotide A 0 1 + 9 AAAAAAAAA ->hg18 29 hg18 chr22 16206162 16207659 panTro2 chr22 16232109 16233601 ponAbe2 chr22 13956476 13958009 compound [CAAA][AT] 1 301 + 365 [caaacaaacaaacaaacaaa]---------------------------------[ATATATATATAt] >panTro2 29 hg18 chr22 16206162 16207659 panTro2 chr22 16232109 16233601 ponAbe2 chr22 13956476 13958009 compound [CAAA][AT] 1 301 + 369 [caaacaaacaaacaaacaaacaaa]---------------------------------[ATATATATATAt] >ponAbe2 29 hg18 chr22 16206162 16207659 panTro2 chr22 16232109 16233601 ponAbe2 chr22 13956476 13958009 compound [A][TA] 5 306 + 344 [aaaaaaaaaaaaaaaaaaa][tatatatatatatatatata] >ponAbe2 29 hg18 chr22 16206162 16207659 panTro2 chr22 16232109 16233601 ponAbe2 chr22 13956476 13958009 dinucleotide [AT][TA] 5 348 + 369 [atatatatatat]g[tatatatat] indel/substitution g 13 1 ->hg18 29 hg18 chr22 16206162 16207659 panTro2 chr22 16232109 16233601 ponAbe2 chr22 13956476 13958009 mononucleotide T 41 789 + 800 tttttttttttt >panTro2 29 hg18 chr22 16206162 16207659 panTro2 chr22 16232109 16233601 ponAbe2 chr22 13956476 13958009 mononucleotide T 37 789 + 799 ttttttttttt ->hg18 29 hg18 chr22 16206162 16207659 panTro2 chr22 16232109 16233601 ponAbe2 chr22 13956476 13958009 dinucleotide [at][TA][at] 41 1106 + 1119 [at][tatatatata][at] indel/deletion,indel/deletion , 3,13 2 >panTro2 29 hg18 chr22 16206162 16207659 panTro2 chr22 16232109 16233601 ponAbe2 chr22 13956476 13958009 dinucleotide [at][TA][at] 38 1106 + 1119 [at][tatatatata][at] indel/deletion,indel/deletion , 3,13 2 >ponAbe2 29 hg18 chr22 16206162 16207659 panTro2 chr22 16232109 16233601 ponAbe2 chr22 13956476 13958009 dinucleotide [at][TA][at] 5 1106 + 1119 [at][tatatatata][at] indel/deletion,indel/deletion , 3,13 2 ->ponAbe2 30 hg18 chr22 16206471 16206727 panTro2 chr22 16232422 16232678 ponAbe2 chr22 13952463 13952752 dinucleotide TA 0 9 + 29 atatatatatatatatatata >ponAbe2 30 hg18 chr22 16206471 16206727 panTro2 chr22 16232422 16232678 ponAbe2 chr22 13952463 13952752 dinucleotide [at][TA][TA] 0 33 + 55 [at][tatatatatat]g[tatatatat] indel/deletion,indel/substitution ,g 3,14 2 >hg18 30 hg18 chr22 16206471 16206727 panTro2 chr22 16232422 16232678 ponAbe2 chr22 13952463 13952752 dinucleotide AT 0 11 + 55 ATA---------------------------------TATATATAt >panTro2 30 hg18 chr22 16206471 16206727 panTro2 chr22 16232422 16232678 ponAbe2 chr22 13952463 13952752 dinucleotide AT 0 11 + 55 ATA---------------------------------TATATATAt ->hg18 31 hg18 chr22 16206825 16207793 panTro2 chr22 16232776 16233735 ponAbe2 chr22 13952853 13953821 mononucleotide T 0 85 + 96 tttttttttttt >panTro2 31 hg18 chr22 16206825 16207793 panTro2 chr22 16232776 16233735 ponAbe2 chr22 13952853 13953821 mononucleotide T 0 85 + 95 ttttttttttt ->hg18 31 hg18 chr22 16206825 16207793 panTro2 chr22 16232776 16233735 ponAbe2 chr22 13952853 13953821 dinucleotide [at][TA][at] 0 402 + 415 [at][tatatatata][at] indel/deletion,indel/deletion , 3,13 2 >panTro2 31 hg18 chr22 16206825 16207793 panTro2 chr22 16232776 16233735 ponAbe2 chr22 13952853 13953821 dinucleotide [at][TA][at] 1 402 + 415 [at][tatatatata][at] indel/deletion,indel/deletion , 3,13 2 >ponAbe2 31 hg18 chr22 16206825 16207793 panTro2 chr22 16232776 16233735 ponAbe2 chr22 13952853 13953821 dinucleotide [at][TA][at] 0 402 + 415 [at][tatatatata][at] indel/deletion,indel/deletion , 3,13 2 ->hg18 31 hg18 chr22 16206825 16207793 panTro2 chr22 16232776 16233735 ponAbe2 chr22 13952853 13953821 tetranucleotide ATTT 0 826 + 851 atttatttatttatttatttatttat >panTro2 31 hg18 chr22 16206825 16207793 panTro2 chr22 16232776 16233735 ponAbe2 chr22 13952853 13953821 tetranucleotide ATTT 5 826 + 847 atttatttatttatttatttat >ponAbe2 31 hg18 chr22 16206825 16207793 panTro2 chr22 16232776 16233735 ponAbe2 chr22 13952853 13953821 tetranucleotide [ATTT][TTTA] 0 826 + 851 [atttattt]c[tttatttatttatttat] indel/substitution c 9 1 ->hg18 37 hg18 chr22 16235765 16235912 panTro2 chr22 16263272 16263417 ponAbe2 chr22 13989737 13989887 mononucleotide A 0 139 + 147 aaaaaaaaa >ponAbe2 37 hg18 chr22 16235765 16235912 panTro2 chr22 16263272 16263417 ponAbe2 chr22 13989737 13989887 mononucleotide A 1 139 + 151 aaaaaaaaaaaaa ->hg18 41 hg18 chr22 16280795 16281802 panTro2 chr22 16312322 16313301 ponAbe2 chr22 14045798 14046786 mononucleotide [t][T] 5 352 + 362 [t]g[ttttttttt] indel/deletion g 2 1 ->hg18 41 hg18 chr22 16280795 16281802 panTro2 chr22 16312322 16313301 ponAbe2 chr22 14045798 14046786 mononucleotide [t][T] 6 965 + 976 [t]c[tttttttttt] indel/deletion c 2 1 >panTro2 41 hg18 chr22 16280795 16281802 panTro2 chr22 16312322 16313301 ponAbe2 chr22 14045798 14046786 mononucleotide [t][T] 26 965 + 977 [t]c[ttttttttttt] indel/deletion c 2 1 >ponAbe2 41 hg18 chr22 16280795 16281802 panTro2 chr22 16312322 16313301 ponAbe2 chr22 14045798 14046786 mononucleotide [t][T] 23 965 + 975 [t]c[ttttttttt] indel/deletion c 2 1 ->hg18 44 hg18 chr22 16305944 16306832 panTro2 chr22 16338488 16339378 ponAbe2 chr22 14069777 14070674 tetranucleotide [TCAT][TTCA] 6 642 + 665 [tcATTCATTCATT]AG[TTCATTCAT] indel/deletion AG 14 1 >panTro2 44 hg18 chr22 16305944 16306832 panTro2 chr22 16338488 16339378 ponAbe2 chr22 14069777 14070674 tetranucleotide [TCAT][TTCA] 4 642 + 665 [tcattcattcattc]g[ttcattcat] indel/substitution g 15 1 >ponAbe2 44 hg18 chr22 16305944 16306832 panTro2 chr22 16338488 16339378 ponAbe2 chr22 14069777 14070674 tetranucleotide [TCAT][TTCA] 3 642 + 665 [tcattcattcattc]g[ttcattcat] indel/substitution g 15 1 ->hg18 44 hg18 chr22 16305944 16306832 panTro2 chr22 16338488 16339378 ponAbe2 chr22 14069777 14070674 mononucleotide [A][A] 6 753 + 775 [AAAAAAAA------AAAA]G[AAAA] indel/deletion G 13 1 >panTro2 44 hg18 chr22 16305944 16306832 panTro2 chr22 16338488 16339378 ponAbe2 chr22 14069777 14070674 mononucleotide [A][A] 4 753 + 775 [AAAAAAAA------AAAA]G[AAAA] indel/deletion G 13 1 ->hg18 47 hg18 chr22 16316020 16316365 panTro2 chr22 16348554 16348899 ponAbe2 chr22 14079950 14080294 tetranucleotide GTTT 0 47 + 59 Gtttgtttgtttg >panTro2 47 hg18 chr22 16316020 16316365 panTro2 chr22 16348554 16348899 ponAbe2 chr22 14079950 14080294 tetranucleotide GTTT 0 47 + 59 Gtttgtttgtttg >ponAbe2 47 hg18 chr22 16316020 16316365 panTro2 chr22 16348554 16348899 ponAbe2 chr22 14079950 14080294 tetranucleotide GTTT 0 47 + 59 Gtttgtttgtttg ->ponAbe2 50 hg18 chr22 16320821 16321001 panTro2 chr22 16354379 16354557 ponAbe2 chr22 14084722 14084897 mononucleotide [T][T] 0 5 + 26 [TT]A[t-----ttttttttttttt] indel/deletion A 3 1 >hg18 50 hg18 chr22 16320821 16321001 panTro2 chr22 16354379 16354557 ponAbe2 chr22 14084722 14084897 mononucleotide T 0 9 + 26 tttttttttttttttttt >panTro2 50 hg18 chr22 16320821 16321001 panTro2 chr22 16354379 16354557 ponAbe2 chr22 14084722 14084897 mononucleotide T 0 9 + 24 tttttttttttttttt ->hg18 51 hg18 chr22 16340090 16340357 panTro2 chr22 16374709 16374969 ponAbe2 chr22 14108305 14108572 mononucleotide A 0 1 + 9 aaaaaaaaa >panTro2 51 hg18 chr22 16340090 16340357 panTro2 chr22 16374709 16374969 ponAbe2 chr22 14108305 14108572 mononucleotide A 0 1 + 9 aaaaaaaaa >ponAbe2 51 hg18 chr22 16340090 16340357 panTro2 chr22 16374709 16374969 ponAbe2 chr22 14108305 14108572 mononucleotide A 0 1 + 9 aaaaaaaaa ->hg18 52 hg18 chr22 16358956 16359267 panTro2 chr22 16396334 16396645 ponAbe2 chr22 14126270 14126577 mononucleotide [A][a] 0 285 + 306 [aaaaaaaaaaaaaaaaaaa]g[aa] indel/deletion g 20 1 >panTro2 52 hg18 chr22 16358956 16359267 panTro2 chr22 16396334 16396645 ponAbe2 chr22 14126270 14126577 mononucleotide [a][A][a] 0 285 + 306 [aaaa]g[aaaaaaaaaaaaaa]g[aa] indel/deletion,indel/deletion g,g 5,20 2 >ponAbe2 52 hg18 chr22 16358956 16359267 panTro2 chr22 16396334 16396645 ponAbe2 chr22 14126270 14126577 mononucleotide [A][a] 0 285 + 303 [aaaaaaaaaaaaaaaa]g[aa] indel/deletion g 17 1 ->hg18 53 hg18 chr22 16360382 16360598 panTro2 chr22 16397754 16397983 ponAbe2 chr22 14127692 14127914 mononucleotide A 0 208 + 216 aaaaaaaaa >panTro2 53 hg18 chr22 16360382 16360598 panTro2 chr22 16397754 16397983 ponAbe2 chr22 14127692 14127914 mononucleotide A 0 208 + 229 aaaaaaaaaaaaaaaaaaaaaa >ponAbe2 53 hg18 chr22 16360382 16360598 panTro2 chr22 16397754 16397983 ponAbe2 chr22 14127692 14127914 mononucleotide A 0 208 + 221 aaaaaaaaaaaaaa ->panTro2 54 hg18 chr22 16369643 16369937 panTro2 chr22 16407018 16407311 ponAbe2 chr22 14136647 14136940 mononucleotide [T][t] 0 158 + 169 [tttttt-ttt]g[t] indel/deletion g 10 1 >ponAbe2 54 hg18 chr22 16369643 16369937 panTro2 chr22 16407018 16407311 ponAbe2 chr22 14136647 14136940 mononucleotide [T][t] 0 158 + 169 [tttttt-ttt]a[t] indel/deletion a 10 1 >hg18 54 hg18 chr22 16369643 16369937 panTro2 chr22 16407018 16407311 ponAbe2 chr22 14136647 14136940 dinucleotide GT 0 163 + 173 tgtgtgtgtgt ->hg18 57 hg18 chr22 16389101 16389406 panTro2 chr22 16426999 16427304 ponAbe2 chr22 14158770 14159051 mononucleotide A 1 296 + 306 aaaaaaaaaaa >panTro2 57 hg18 chr22 16389101 16389406 panTro2 chr22 16426999 16427304 ponAbe2 chr22 14158770 14159051 mononucleotide A 1 296 + 306 aaaaaaaaaaa >ponAbe2 57 hg18 chr22 16389101 16389406 panTro2 chr22 16426999 16427304 ponAbe2 chr22 14158770 14159051 mononucleotide A 25 296 + 306 aaaaaaaaaaa ->hg18 58 hg18 chr22 16394195 16394393 panTro2 chr22 16432578 16432752 ponAbe2 chr22 14163638 14163812 tetranucleotide TTTA 0 1 + 13 atttatttattta >panTro2 58 hg18 chr22 16394195 16394393 panTro2 chr22 16432578 16432752 ponAbe2 chr22 14163638 14163812 tetranucleotide TTTA 0 1 + 13 atttatttattta >ponAbe2 58 hg18 chr22 16394195 16394393 panTro2 chr22 16432578 16432752 ponAbe2 chr22 14163638 14163812 tetranucleotide ATTT 0 1 + 17 atttatttatttattta ->ponAbe2 59 hg18 chr22 16399175 16399400 panTro2 chr22 16437955 16438175 ponAbe2 chr22 14169293 14169504 dinucleotide AT 7 184 + 201 aTA------TATATATAT ->hg18 61 hg18 chr22 16428466 16429079 panTro2 chr22 16467564 16468186 ponAbe2 chr22 14197796 14198411 mononucleotide [t][T] 0 152 + 180 [t]c[ttttttttttttttttttttttttttt] indel/deletion c 2 1 >panTro2 61 hg18 chr22 16428466 16429079 panTro2 chr22 16467564 16468186 ponAbe2 chr22 14197796 14198411 mononucleotide T 3 159 + 180 tttttttttttttttttttttt >ponAbe2 61 hg18 chr22 16428466 16429079 panTro2 chr22 16467564 16468186 ponAbe2 chr22 14197796 14198411 mononucleotide T 3 159 + 180 tttttttttttttttttttttt ->panTro2 61 hg18 chr22 16428466 16429079 panTro2 chr22 16467564 16468186 ponAbe2 chr22 14197796 14198411 mononucleotide T 9 614 + 631 tttttttttttttttttt ->hg18 64 hg18 chr22 16434672 16436474 panTro2 chr22 16473032 16474856 ponAbe2 chr22 14204096 14205926 trinucleotide [ATT][TAT] 7 231 + 280 [ttattattattatta----------------------ttattatt]TA[TAT] indel/deletion TA 24 1 >panTro2 64 hg18 chr22 16434672 16436474 panTro2 chr22 16473032 16474856 ponAbe2 chr22 14204096 14205926 trinucleotide [TAT][ATT][TAT] 7 231 + 280 [ttattattattattattattattattattattattat][ttattatt]TA[TAT] indel/substitution,indel/deletion ,TA 38,46 2 >ponAbe2 64 hg18 chr22 16434672 16436474 panTro2 chr22 16473032 16474856 ponAbe2 chr22 14204096 14205926 tetranucleotide [TATT][TATT] 4 237 + 291 [TTATT]A[ttatttatttatttatt--------tatttatttatttatttatttatt] indel/deletion A 6 1 ->hg18 64 hg18 chr22 16434672 16436474 panTro2 chr22 16473032 16474856 ponAbe2 chr22 14204096 14205926 mononucleotide [A][A][a] 56 1803 + 1827 [aaaaaaaaaaa]g[aaaaaaaaaa]g[aa] insertion,indel/deletion g,g 12,23 2 >panTro2 64 hg18 chr22 16434672 16436474 panTro2 chr22 16473032 16474856 ponAbe2 chr22 14204096 14205926 mononucleotide [A][A][A][A] 33 1803 + 1826 [aaaaaaaaaa]g[aaaaaaa]g[aa]g[aa] indel/deletion,indel/deletion,indel/deletion g,G,G 11,19,22 3 >ponAbe2 64 hg18 chr22 16434672 16436474 panTro2 chr22 16473032 16474856 ponAbe2 chr22 14204096 14205926 mononucleotide A 17 1803 + 1816 aaaaaaaaaaaaaa ->hg18 65 hg18 chr22 16436747 16438269 panTro2 chr22 16475129 16476649 ponAbe2 chr22 14206204 14207755 mononucleotide [T][T] 20 916 + 939 [T]A[tt--tttttttttttttttttt] indel/deletion A 2 1 >panTro2 65 hg18 chr22 16436747 16438269 panTro2 chr22 16475129 16476649 ponAbe2 chr22 14206204 14207755 mononucleotide [T][T] 20 916 + 939 [T]A----[tttttttttttttttttt] indel/deletion A 2 1 >ponAbe2 65 hg18 chr22 16436747 16438269 panTro2 chr22 16475129 16476649 ponAbe2 chr22 14206204 14207755 tetranucleotide TTTA 0 916 + 933 tatttatttatttattta ->panTro2 70 hg18 chr22 16446992 16447262 panTro2 chr22 16485149 16485385 ponAbe2 chr22 14216620 14216803 compound [A][GAAA][GAAG][AAAG] 0 167 + 268 [aaaa--aaaaaaaaaaaaaaaa][gaaagaaaGAa--------------------------------ag][gaaggaaggaaggaaggaaggaag][aaagaaagaaa] >hg18 70 hg18 chr22 16446992 16447262 panTro2 chr22 16485149 16485385 ponAbe2 chr22 14216620 14216803 compound [AAAG][GGAA][GA][AAGA] 0 174 + 268 [aaagaaagaaagaaagaaagaaagaa][ggaaggaaggaaggaaggaagga][gagagagagagagagagagagaga][aagaaagaaagaaagaaagaaa] ->ponAbe2 71 hg18 chr22 16449509 16449675 panTro2 chr22 16487488 16487654 ponAbe2 chr22 14218953 14219119 tetranucleotide [AAAT][ataa] 0 1 + 19 [aaataaataaataaa][ataa] indel/deletion 16 1 ->panTro2 73 hg18 chr22 16465142 16465314 panTro2 chr22 16504609 16504783 ponAbe2 chr22 14235468 14235643 mononucleotide [T][T] 0 3 + 21 [T]C-[tttttttttttttttt] indel/deletion C 2 1 >ponAbe2 73 hg18 chr22 16465142 16465314 panTro2 chr22 16504609 16504783 ponAbe2 chr22 14235468 14235643 mononucleotide [T][T] 0 3 + 21 [T]C[ttttttttttttttttt] indel/deletion C 2 1 >hg18 73 hg18 chr22 16465142 16465314 panTro2 chr22 16504609 16504783 ponAbe2 chr22 14235468 14235643 mononucleotide [T][t] 0 5 + 18 [tttttttttt]c[ttt] indel/deletion c 11 1 ->hg18 74 hg18 chr22 16465314 16465951 panTro2 chr22 16504783 16505420 ponAbe2 chr22 14237512 14238145 tetranucleotide TTAT 0 217 + 229 TTATTTATTTATT >panTro2 74 hg18 chr22 16465314 16465951 panTro2 chr22 16504783 16505420 ponAbe2 chr22 14237512 14238145 tetranucleotide TTAT 0 217 + 229 TTATTTATTTATT >ponAbe2 74 hg18 chr22 16465314 16465951 panTro2 chr22 16504783 16505420 ponAbe2 chr22 14237512 14238145 tetranucleotide TTAT 3 217 + 229 ttatttatttatt ->hg18 74 hg18 chr22 16465314 16465951 panTro2 chr22 16504783 16505420 ponAbe2 chr22 14237512 14238145 trinucleotide ATT 0 409 + 423 ATTATTATTATTAtt >panTro2 74 hg18 chr22 16465314 16465951 panTro2 chr22 16504783 16505420 ponAbe2 chr22 14237512 14238145 trinucleotide ATT 0 409 + 423 Attattattattatt >ponAbe2 74 hg18 chr22 16465314 16465951 panTro2 chr22 16504783 16505420 ponAbe2 chr22 14237512 14238145 trinucleotide ATT 3 409 + 423 attattattattatt ->panTro2 75 hg18 chr22 16467819 16468711 panTro2 chr22 16507291 16508219 ponAbe2 chr22 14240608 14241491 trinucleotide NTG 0 129 + 141 gnnnnnnnnnntg ->hg18 75 hg18 chr22 16467819 16468711 panTro2 chr22 16507291 16508219 ponAbe2 chr22 14240608 14241491 mononucleotide [A][a][a][a][a] 40 193 + 230 [aaaaaaaaaaaaaaaaaa]g[aaaa]g[aaaa]g[aaaa]g[aaaa] indel/deletion,indel/deletion,indel/deletion,indel/deletion g,g,g,g 19,24,29,34 4 >panTro2 75 hg18 chr22 16467819 16468711 panTro2 chr22 16507291 16508219 ponAbe2 chr22 14240608 14241491 mononucleotide [A][A][a][a] 0 193 + 225 [aaaaaaaaaaaaa]g[a----aaaa]g[aaaa]g[aaaa] insertion,indel/deletion,indel/deletion g,g,g 14,20,25 3 ->hg18 75 hg18 chr22 16467819 16468711 panTro2 chr22 16507291 16508219 ponAbe2 chr22 14240608 14241491 mononucleotide [t][T] 48 687 + 715 [t]c-----[tttttttttttttttttttttt] indel/deletion c 2 1 >panTro2 75 hg18 chr22 16467819 16468711 panTro2 chr22 16507291 16508219 ponAbe2 chr22 14240608 14241491 mononucleotide [t][T] 12 687 + 715 [t]c-----[tttttttttttttttttttttt] indel/deletion c 2 1 >ponAbe2 75 hg18 chr22 16467819 16468711 panTro2 chr22 16507291 16508219 ponAbe2 chr22 14240608 14241491 mononucleotide [t][T] 62 687 + 715 [t]c[ttttttttttttttttttttttttttt] indel/deletion c 2 1 ->hg18 77 hg18 chr22 16481320 16482141 panTro2 chr22 16520891 16521719 ponAbe2 chr22 14252230 14253119 mononucleotide A 0 128 + 151 aaaaaaaaaaaaaaaaaaaaaaaa >panTro2 77 hg18 chr22 16481320 16482141 panTro2 chr22 16520891 16521719 ponAbe2 chr22 14252230 14253119 mononucleotide A 0 128 + 145 aaaaaaaaaaaaaaaaaa >ponAbe2 77 hg18 chr22 16481320 16482141 panTro2 chr22 16520891 16521719 ponAbe2 chr22 14252230 14253119 mononucleotide A 0 128 + 137 aaaaaaaaaa ->ponAbe2 77 hg18 chr22 16481320 16482141 panTro2 chr22 16520891 16521719 ponAbe2 chr22 14252230 14253119 trinucleotide NCT 14 307 + 319 tnnnnnnnnnnct ->panTro2 80 hg18 chr22 16484374 16485075 panTro2 chr22 16523925 16524627 ponAbe2 chr22 14255781 14256511 mononucleotide A 31 574 + 582 AAAAAAAAA ->hg18 87 hg18 chr22 16511676 16511786 panTro2 chr22 16552790 16552899 ponAbe2 chr22 14281751 14281861 mononucleotide [T][t] 0 24 + 37 [ttttttttt]c[tttt] indel/deletion c 10 1 >ponAbe2 87 hg18 chr22 16511676 16511786 panTro2 chr22 16552790 16552899 ponAbe2 chr22 14281751 14281861 mononucleotide [T][t] 0 24 + 37 [ttttttttt]c[tttt] indel/deletion c 10 1 ->ponAbe2 89 hg18 chr22 16513470 16513745 panTro2 chr22 16554844 16555121 ponAbe2 chr22 14283544 14283815 mononucleotide T 0 8 + 21 tttttttttttttt ->hg18 92 hg18 chr22 16520282 16520759 panTro2 chr22 16561957 16562427 ponAbe2 chr22 14290687 14291154 mononucleotide [t][T] 0 1 + 17 [tttt]c[tttttttttttt] indel/deletion c 5 1 >panTro2 92 hg18 chr22 16520282 16520759 panTro2 chr22 16561957 16562427 ponAbe2 chr22 14290687 14291154 mononucleotide [t][T] 0 1 + 17 [tttt]c[tttttttttttt] indel/deletion c 5 1 >ponAbe2 92 hg18 chr22 16520282 16520759 panTro2 chr22 16561957 16562427 ponAbe2 chr22 14290687 14291154 mononucleotide [t][T] 0 1 + 17 [tttt]c[tttttttttttt] indel/deletion c 5 1 ->hg18 92 hg18 chr22 16520282 16520759 panTro2 chr22 16561957 16562427 ponAbe2 chr22 14290687 14291154 mononucleotide T 4 168 + 176 ttttttttt >panTro2 92 hg18 chr22 16520282 16520759 panTro2 chr22 16561957 16562427 ponAbe2 chr22 14290687 14291154 mononucleotide [T][t] 4 168 + 179 [tttttttttt]g[t] indel/deletion g 11 1 >ponAbe2 92 hg18 chr22 16520282 16520759 panTro2 chr22 16561957 16562427 ponAbe2 chr22 14290687 14291154 mononucleotide [T][t] 0 168 + 179 [ttttttttt]-g[t] indel/deletion g 10 1 ->hg18 92 hg18 chr22 16520282 16520759 panTro2 chr22 16561957 16562427 ponAbe2 chr22 14290687 14291154 mononucleotide [t][T] 4 308 + 332 [ttt]c[ttttttttttttttttttttt] indel/deletion c 4 1 >panTro2 92 hg18 chr22 16520282 16520759 panTro2 chr22 16561957 16562427 ponAbe2 chr22 14290687 14291154 mononucleotide [t][T] 4 308 + 332 [ttt]c-------[tttttttttttttt] indel/deletion c 4 1 ->ponAbe2 94 hg18 chr22 16524956 16525101 panTro2 chr22 16566675 16566820 ponAbe2 chr22 14295730 14295873 mononucleotide A 0 126 + 138 aaaaaa--aaaaa ->panTro2 97 hg18 chr22 16546791 16547342 panTro2 chr22 16588511 16589056 ponAbe2 chr22 14324513 14325074 trinucleotide [TAA][AAT] 5 290 + 315 [TAA]ACA[aataataataataataataa] indel/deletion ACA 4 1 >ponAbe2 97 hg18 chr22 16546791 16547342 panTro2 chr22 16588511 16589056 ponAbe2 chr22 14324513 14325074 mononucleotide A 0 291 + 306 aaaaa------aaaaa >hg18 97 hg18 chr22 16546791 16547342 panTro2 chr22 16588511 16589056 ponAbe2 chr22 14324513 14325074 trinucleotide [AAT][AAT] 5 292 + 315 [aata]---[aataataataataataa] indel/deletion 5 1 ->hg18 97 hg18 chr22 16546791 16547342 panTro2 chr22 16588511 16589056 ponAbe2 chr22 14324513 14325074 trinucleotide GTG 13 547 + 567 gtggtggt---ggtggtggtg ->panTro2 99 hg18 chr22 16567388 16567767 panTro2 chr22 16610896 16611272 ponAbe2 chr22 14346895 14347276 mononucleotide A 3 365 + 382 A---AAAAAAAAAAAAAA >hg18 99 hg18 chr22 16567388 16567767 panTro2 chr22 16610896 16611272 ponAbe2 chr22 14346895 14347276 mononucleotide A 3 369 + 382 AAAAAAAAAAAAAA >ponAbe2 99 hg18 chr22 16567388 16567767 panTro2 chr22 16610896 16611272 ponAbe2 chr22 14346895 14347276 mononucleotide A 1 371 + 382 AAAAAAAAAAAA ->hg18 101 hg18 chr22 16573369 16573668 panTro2 chr22 16616866 16617165 ponAbe2 chr22 14355029 14355343 mononucleotide [A][A][A][a] 3 277 + 302 [aaaaaaaa]t[aaaaa]t[aaaaaaaaa]t[a] insertion,insertion,indel/deletion t,t,t 9,15,25 3 >ponAbe2 101 hg18 chr22 16573369 16573668 panTro2 chr22 16616866 16617165 ponAbe2 chr22 14355029 14355343 tetranucleotide [AAat][TAAA] 0 294 + 313 [aaataa]g[taaataaataaat] indel/deletion g 7 1 -UNDONE: 0 +>rheMac2 1 hg18 chr22 16115000 16115212 panTro2 chr22 16131432 16131644 ponAbe2 chr22 13834301 13834513 rheMac2 chr10 61914657 61914870 calJac1 Contig13114 14954 15124 mononucleotide A 1 198 + 206 aaaaaaaaa +>calJac1 4 hg18 chr22 16118223 16119141 panTro2 chr22 16134653 16135572 ponAbe2 chr22 13837634 13838553 rheMac2 chr10 61918520 61919424 calJac1 Contig13114 15842 16747 tetranucleotide AAAC 1 182 + 193 AAACAAACAAAC +>hg18 4 hg18 chr22 16118223 16119141 panTro2 chr22 16134653 16135572 ponAbe2 chr22 13837634 13838553 rheMac2 chr10 61918520 61919424 calJac1 Contig13114 15842 16747 mononucleotide T 7 568 + 577 TTTTTTTTTT >panTro2 4 hg18 chr22 16118223 16119141 panTro2 chr22 16134653 16135572 ponAbe2 chr22 13837634 13838553 rheMac2 chr10 61918520 61919424 calJac1 Contig13114 15842 16747 mononucleotide T 6 568 + 577 TTTTTTTTTT >ponAbe2 4 hg18 chr22 16118223 16119141 panTro2 chr22 16134653 16135572 ponAbe2 chr22 13837634 13838553 rheMac2 chr10 61918520 61919424 calJac1 Contig13114 15842 16747 mononucleotide T 5 568 + 576 TTTTTTTTT >rheMac2 4 hg18 chr22 16118223 16119141 panTro2 chr22 16134653 16135572 ponAbe2 chr22 13837634 13838553 rheMac2 chr10 61918520 61919424 calJac1 Contig13114 15842 16747 mononucleotide T 22 568 + 579 TTTTTTTTTTTT +>ponAbe2 4 hg18 chr22 16118223 16119141 panTro2 chr22 16134653 16135572 ponAbe2 chr22 13837634 13838553 rheMac2 chr10 61918520 61919424 calJac1 Contig13114 15842 16747 tetranucleotide GAGG 8 821 + 833 GAGGGAGGGAGGG +>hg18 5 hg18 chr22 16119141 16119363 panTro2 chr22 16135572 16135794 ponAbe2 chr22 13838553 13838774 rheMac2 chr10 61919424 61919654 calJac1 Contig13114 16747 16966 dinucleotide [TC][TC] 0 21 + 34 [TCT]G[TCTCTCTCTC] indel/deletion G 4 1 >panTro2 5 hg18 chr22 16119141 16119363 panTro2 chr22 16135572 16135794 ponAbe2 chr22 13838553 13838774 rheMac2 chr10 61919424 61919654 calJac1 Contig13114 16747 16966 dinucleotide [TC][TC] 0 21 + 34 [TCT]G[TCTCTCTCTC] indel/deletion G 4 1 >ponAbe2 5 hg18 chr22 16119141 16119363 panTro2 chr22 16135572 16135794 ponAbe2 chr22 13838553 13838774 rheMac2 chr10 61919424 61919654 calJac1 Contig13114 16747 16966 dinucleotide [TC][TC] 0 21 + 34 [TCT]G[TCTCTCTCTC] indel/deletion G 4 1 >rheMac2 5 hg18 chr22 16119141 16119363 panTro2 chr22 16135572 16135794 ponAbe2 chr22 13838553 13838774 rheMac2 chr10 61919424 61919654 calJac1 Contig13114 16747 16966 dinucleotide [TC][TC] 0 21 + 34 [TCT]G[TCTCTCTCTC] indel/deletion G 4 1 >calJac1 5 hg18 chr22 16119141 16119363 panTro2 chr22 16135572 16135794 ponAbe2 chr22 13838553 13838774 rheMac2 chr10 61919424 61919654 calJac1 Contig13114 16747 16966 dinucleotide [TC][TC] 0 21 + 34 [TCT]G[TCTCTCTCTC] indel/deletion G 4 1 diff -r c802de6bf0ba697d9a5038ab41dfa1425f0c296f -r 753130def2f89698bb95a554ce76c7ea8c5102d7 test-data/regVariation/microsatellite/Galaxy17_unmasked_results.txt --- a/test-data/regVariation/microsatellite/Galaxy17_unmasked_results.txt +++ b/test-data/regVariation/microsatellite/Galaxy17_unmasked_results.txt @@ -1,46 +1,1 @@ -hg18.chr22 16153057 16153074 A 1 -C ins=,imot:0:tt;dels= ,9:t>c -panTro2 2 hg18:tttttttttttttttttt,ponAbe2:--tttttttttttttttt,panTro2:-----ttttctttttttt HCO -hg18.chr22 16484916 16484924 A 1 +C ins=,imotf:0:A;dels= NA +panTro2 2 hg18:-AAAAAAAA,ponAbe2:-AAAAAAAA,panTro2:AAAAAAAAA HCO -hg18.chr22 14869543 14869551 ATAG 4 +C ins=,imotf:0:TATC;dels= ,4:A>T,7:C>T +panTro2 2 hg18:----AATCTATC,ponAbe2:----AATTTATC,panTro2:TATCTATCTATC,rheMac2:-----ATCTATC HCOR -hg18.chr22 15242524 15242530 A 1 +O ins=,imot:2:tt;dels= ,3:t>c +ponAbe2 2 hg18:tt--ttttt,ponAbe2:ttttttttt,panTro2:tt-cttttt,rheMac2:at--ttttt HCOR -hg18.chr22 15243122 15243131 A 1 +C ins=;dels=,dmot:3:a,dmotf:0:AAAA ,8:a>t,4:a>t N:U:L:L -1 hg18:----taaaaaaa--a,ponAbe2:---aaaaataaa--a,panTro2:aaaaaaaaaaaa--a,rheMac2:----aaaaaaaacta HCOR -hg18.chr22 15569056 15569065 AC 2 -H NA ,3:C>A -hg18 2 hg18:ACAAACACAC,ponAbe2:ACACACACAC,panTro2:ACACACACAC,rheMac2:ACATACACAC HCOR -hg18.chr22 16131711 16131722 ATGC 4 +O NA ,2:C>T +ponAbe2 2 hg18:CACGCATGCATG,ponAbe2:CATGCATGCATG,panTro2:CACGCATGCATG,rheMac2:CACGCGTGCATG HCOR -hg18.chr22 16139207 16139219 A 1 +H.+O|-C ins=,imot:8:tt;dels=,dmot:10:ttttt ,6:t>g,0:t>a -panTro2 2 hg18:tttttttt--ttttt,ponAbe2:ttttttttttttttt,panTro2:atttttgt-------,rheMac2:ttttttgt------- HCOR -hg18.chr22 16197071 16197080 A 1 +HC ins=,imot:0:TT;dels= NA +hg18.+panTro2 / +hg18:panTro2 1 hg18:--TTTTTTTTT,ponAbe2:--CTTTTTTTT,panTro2:TTTTTTTTTTT,rheMac2:---ATTTGTTT HCOR -hg18.chr22 16198276 16198290 AAC 3 +O ins=,imotf:0:tgt;dels=,dnon:3:tg ,8:t>C +ponAbe2 2 hg18:-----CTGCTGTTGTTGTT,ponAbe2:tgttgttgttgttgttgtt,panTro2:---tgctgctgttgttgtt,rheMac2:-----gtgttgtcattgtt HCOR -hg18.chr22 16205989 16205998 A 1 -H NA ,5:a>g -hg18 2 hg18:aaaaagaaaa,ponAbe2:aaaaaaaaaa,panTro2:aaaaaaaaaa,rheMac2:actaaaa--- HCOR -hg18.chr22 16211560 16211568 A 1 +O ins=,imotf:0:T;dels= NA +ponAbe2 2 hg18:-TTTTTTTT,ponAbe2:TTTTTTTTT,panTro2:-TTTTTTTT,rheMac2:-TTTTTTTT HCOR -hg18.chr22 16226759 16226772 A 1 +HC ins=,imot:1:a,imot:0:a,imotf:9:a;dels=,dnon:9:t NA +hg18:panTro2 2 hg18:-aaaaaaaaaaaaa,ponAbe2:--aaaaaaataaaa,panTro2:aaaaaaaaaaaaaa,rheMac2:--aaaaaaataaaa HCOR -hg18.chr22 16252607 16252619 ATAC 4 +C ins=;dels=,dnon:7:t NA +panTro2 2 hg18:tacatactataca,ponAbe2:tacatactataca,panTro2:tacatac-ataca,rheMac2:tacat---ataca HCOR -hg18.chr22 16275365 16275374 AT 2 +H NA ,11:C>T +hg18 2 hg18:ATATATA--TAT,ponAbe2:ATATATA--TAC,panTro2:ATATATA--TAC,rheMac2:ATATATATCTAC HCOR -hg18.chr22 16278949 16278957 A 1 +O ins=,imotf:0:A;dels= NA +ponAbe2 2 hg18:-AAAAAAAA,ponAbe2:AAAAAAAAA,panTro2:-AAAAAAAA,rheMac2:-AAAAAAAA HCOR -hg18.chr22 16357265 16357273 A 1 +H ins=,imot:1:a;dels= NA +hg18 2 hg18:aaaaaaaaa,ponAbe2:a-aaaaaaa,panTro2:acaaaaaaa,rheMac2:a-aaaaaaa HCOR -hg18.chr22 16511417 16511430 AAAT 4 +O NA ,5:G>a +ponAbe2 2 hg18:TAAATGAATAAATA,ponAbe2:taaataaataaata,panTro2:TAAATGAATAAATA,rheMac2:TAAACGAATAAATA HCOR -hg18.chr22 16514967 16514975 A 1 +O ins=;dels=,dmot:0:T ,8:tt>AA -hg18:panTro2 2 hg18:--TTTttttt,ponAbe2:T-TTTttttt,panTro2:--TTTTTTAA,rheMac2:TGTTTTTTTA HCOR -hg18.chr22 16569017 16569025 G 1 +O ins=;dels=,dnon:2:t ,6:c>t,7:c>g +ponAbe2 2 hg18:cctccccgc,ponAbe2:ccccccccc,panTro2:cctccctgc,rheMac2:cctccctcc HCOR -hg18.chr22 16092969 16092977 A 1 +C ins=,imotf:0:a;dels=,dmotf:1:A NA +panTro2 2 hg18:-AAAAAAAA,ponAbe2:-AAAAAAAA,calJac1:-AAAAGAAA,panTro2:aaaaaaaaa,rheMac2:--AAAAAAA HCORM -hg18.chr22 16097890 16097904 ATGG 4 +HCO ins=,imotf:4:TGGA,imotf:0:TGGA;dels= NA +hg18:panTro2:ponAbe2 2 hg18:----TGGATGGATGGATG,ponAbe2:TGGATGGATGGATGGATG,calJac1:--------TGGATGGATG,panTro2:----TGGATGGATGGATG,rheMac2:--------TGGATGGATG HCORM -hg18.chr22 16119035 16119047 AGGG 4 +O NA ,1:G>A +ponAbe2 2 hg18:GGGGGAGGGAGGG,ponAbe2:GAGGGAGGGAGGG,calJac1:GGGGAAGGGAGGG,panTro2:GGGGGAGGGAGGG,rheMac2:GGGGGAGGGAGGG HCORM -hg18.chr22 16124562 16124574 AAAT 4 -HC NA ,8:T>c -hg18:panTro2 2 hg18:taaataaacaaaT,ponAbe2:TAAATAAATAAAT,calJac1:TAAATAAATAAAT,panTro2:taaataaacaaaT,rheMac2:TAAATAAATAAAT HCORM -hg18.chr22 16175530 16175540 AC 2 +HCO ins=;dels=,dmotf:0:GT ,2:G>A N:U:L:L -1 hg18:GTGTGTGTGTG,ponAbe2:GTGTGTGTGTG,calJac1:--GTGTGTGTG,panTro2:GTGTGTGTGTG,rheMac2:--ATGTGTGTG HCORM -hg18.chr22 16197071 16197080 A 1 +HC ins=,imot:0:TT,imot:2:T;dels= ,7:T>G +hg18:panTro2 2 hg18:--TTTTTTTTT,ponAbe2:--CTTTTTTTT,calJac1:----ACTTTTT,panTro2:TTTTTTTTTTT,rheMac2:---ATTTGTTT HCORM -hg18.chr22 16198276 16198290 AAC 3 +O ins=,inon:3:tg,imotf:0:tgt;dels=,dnon:3:tg ,8:t>C,12:TG>ca,5:C>t,5:C>g +hg18:panTro2:ponAbe2,-hg18:panTro2 / +ponAbe2 4 hg18:-----CTGCTGTTGTTGTT,ponAbe2:tgttgttgttgttgttgtt,calJac1:-----CTGTTGCTGTTGTC,panTro2:---tgctgctgttgttgtt,rheMac2:-----gtgttgtcattgtt HCORM -hg18.chr22 16199994 16200001 A 1 +O ins=,imot:0:tt;dels=,dnon:3:G NA +ponAbe2 2 hg18:--tgttttt,ponAbe2:ttttttttt,calJac1:--TATTTTT,panTro2:--tgttttt,rheMac2:--TGTTTTT HCORM -hg18.chr22 16228275 16228287 A 1 -O ins=,imotf:2:ttttttt;dels=,dmotf:11:tttttttt NA -ponAbe2 2 hg18:AC------ttttttttttt,ponAbe2:AC-------tt--------,calJac1:-------------------,panTro2:AC-------tttttttttt,rheMac2:ACttttttttttttttttt HCORM -hg18.chr22 16233338 16233346 A 1 +HC ins=,imot:0:a,imotf:2:a;dels=,dnon:2:C ,1:A>G +hg18:panTro2 2 hg18:aaaaaaaaa,ponAbe2:-acaaaaaa,calJac1:-acaaaaaa,panTro2:aaaaaaaaa,rheMac2:-GCAAAAAA HCORM -hg18.chr22 16251172 16251183 AACC 4 +HC NA ,12:T>G +hg18:panTro2 2 hg18:T--GGTTGGTTGGT,ponAbe2:T--GGTTGGTTGTT,calJac1:TGCGTTCGGTTGTT,panTro2:T--GGTTGGTTGGT,rheMac2:T--GATTGGTTGTT HCORM -hg18.chr22 16284864 16284875 ACC 3 +C NA ,11:g>a,0:t>a,2:g>a,5:ac>gt +hg18:panTro2,-hg18 / +panTro2 4 hg18:tgatggtggtga,ponAbe2:aggtgacggtgg,calJac1:TGGGGACGGTGG,panTro2:tggtggtggtgg,rheMac2:tggtgacggtgg HCORM -hg18.chr22 16297576 16297589 ACCC 4 -HC NA ,7:ca>tg,12:g>a -hg18:panTro2 2 hg18:acccacctgcccgc,ponAbe2:acccacccacccac,calJac1:gcccacc-acctgc,panTro2:acccacctgcccgc,rheMac2:acccacccacccgc HCORM -hg18.chr22 16300660 16300676 AATG 4 +HCO ins=,imot:14:AA;dels= ,7:G>A +hg18:panTro2:ponAbe2 2 hg18:TGAATGAATGAATGAAT,ponAbe2:TGAATGAATGAATGAAT,calJac1:TGAATGAGTGAATG--T,panTro2:TGAATGAATGAATGAAT,rheMac2:TGAATGAGTGAATG--T HCORM -hg18.chr22 16352085 16352096 AGG 3 +HC NA ,11:c>t +hg18:panTro2 2 hg18:cctcctcctcct,ponAbe2:cctcctcctccc,calJac1:cctctgcctcct,panTro2:cctcctcctcct,rheMac2:cctcctcctccc HCORM -hg18.chr22 16354599 16354613 A 1 -O ins=,imot:0:taaaaaa;dels=,dmot:7:a ,8:a>t,15:a>g -ponAbe2 2 hg18:-------aaaaaaaaaaaaaa,ponAbe2:--------taaaaaagaaaaa,calJac1:--------aaaaaaaaaaaaa,panTro2:------aaaaaaaaaaaaaaa,rheMac2:taaaaaaaaaaaaaaaaaaaa HCORM -hg18.chr22 16358663 16358672 A 1 -O ins=,imot:0:TTTT;dels= ,8:T>C -ponAbe2 2 hg18:----TTTTTTTTT,ponAbe2:----TTTTCTTTT,calJac1:----TTTCTTTTT,panTro2:--TTTTTTTTTTT,rheMac2:TTTTTTTTTTTTT HCORM -hg18.chr22 16396341 16396352 AC 2 -HC NA ,9:G>A,2:T>C -hg18:panTro2 2 hg18:TGTGTGTGTATG,ponAbe2:TGTGTGTGTGTG,calJac1:GGTGTGTGTTTG,panTro2:TGCGTGTGTATG,rheMac2:TGTGTGTGTGTG HCORM -hg18.chr22 16396592 16396600 AACT 4 +O ins=;dels=,dmotf:0:AGTT ,5:G>A +hg18:panTro2:ponAbe2,-hg18:panTro2 / +ponAbe2 1 hg18:----AATTAGTT,ponAbe2:AGTTAGTTAGTT,calJac1:----AGTTAGGT,panTro2:----AATTAGTT,rheMac2:AATTAGTTAGTT HCORM -hg18.chr22 16408653 16408666 AGCC 4 +O NA ,8:T>C +ponAbe2 2 hg18:CCAGCCAGTCAGCC,ponAbe2:CCAGCCAGCCAGCC,calJac1:CCCGCCAGTCAGCC,panTro2:CCAGCCAGTCAGCC,rheMac2:CCAGCCAGTCAGCC HCORM -hg18.chr22 16412284 16412295 ATG 3 +HC NA ,6:G>C +hg18:panTro2 2 hg18:CATCATCATCAT,ponAbe2:CATCATGATCAT,calJac1:CGTCATGAGCAT,panTro2:CATCATCATCAT,rheMac2:CATCATGATCAT HCORM -hg18.chr22 16415043 16415060 AGC 3 +HC ins=;dels=,dmot:5:CAG ,1:G>A,12:A>C N:U:L:L -1 hg18:AACATCAGCAGCAGCAGA,ponAbe2:AACAA---CAGCAGCAGA,calJac1:AG------CAGCAGCAGC,panTro2:AACAACAGCAGCAGCAGA,rheMac2:AGCAACAGCAGCCGCAGA HCORM -hg18.chr22 16472890 16472900 A 1 -C ins=,imot:0:taaa;dels=,dmot:35:aa,dnon:27:AAA,dnon:40:T,dmotf:15:aa,dmotf:14:A,dmotf:18:aaaaaaaa,dmot:10:a,dmotf:31:AA ,36:a>t -panTro2 2 hg18:----aaaaaa---------------------------aaaT,ponAbe2:----aaaaaaa------------------------aaaaaT,calJac1:----aaaaaaataataataaaaaaaaTAAATAATTAAAAAT,panTro2:----aaaaaaa------------------------ataaaT,rheMac2:taaaaaaaaaa------------------------aaaaaa HCORM -hg18.chr22 16504297 16504305 A 1 -HC ins=;dels=,dmotf:0:T NA -hg18:panTro2 2 hg18:-TTtttttt,ponAbe2:TTTtttttt,calJac1:--TTGtttt,panTro2:-TTtttttt,rheMac2:TTTtttttt HCORM -hg18.chr22 16570421 16570431 AT 2 +HCO NA ,3:G>T,0:A>G,10:A>G +hg18:panTro2:ponAbe2 2 hg18:ATATATATATA,ponAbe2:ATATATATATA,calJac1:ATAGGTATAGA,panTro2:ATATATATATA,rheMac2:GTAGATATATG HCORM -hg18.chr22 16594984 16594991 AT 2 +O ins=,imot:0:ATAT;dels= ,6:A>C +ponAbe2 2 hg18:----ATATATA,ponAbe2:ATATATATATA,calJac1:----ATATATA,panTro2:----ATATATA,rheMac2:----ATCTATA HCORM +hg18.chr22 16119035 16119047 AGGG 4 NA ,1:G>A +ponAbe2 hg18:GGGGGAGGGAGGG,ponAbe2:GAGGGAGGGAGGG,calJac1:GGGGAAGGGAGGG,panTro2:GGGGGAGGGAGGG,rheMac2:GGGGGAGGGAGGG diff -r c802de6bf0ba697d9a5038ab41dfa1425f0c296f -r 753130def2f89698bb95a554ce76c7ea8c5102d7 test-data/regVariation/microsatellite/Galaxy17_unmasked_short.maf.gz Binary file test-data/regVariation/microsatellite/Galaxy17_unmasked_short.maf.gz has changed diff -r c802de6bf0ba697d9a5038ab41dfa1425f0c296f -r 753130def2f89698bb95a554ce76c7ea8c5102d7 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -194,8 +194,8 @@ <tool file="regVariation/compute_motif_frequencies_for_all_motifs.xml" /><tool file="regVariation/categorize_elements_satisfying_criteria.xml" />s <tool file="regVariation/draw_stacked_barplots.xml" /> -  + <tool file="regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml" /> + <tool file="regVariation/microsatellite_birthdeath.xml" /></section><section name="Multiple regression" id="multReg"><tool file="regVariation/linear_regression.xml" /> diff -r c802de6bf0ba697d9a5038ab41dfa1425f0c296f -r 753130def2f89698bb95a554ce76c7ea8c5102d7 tools/regVariation/microsatellite_birthdeath.pl --- a/tools/regVariation/microsatellite_birthdeath.pl +++ b/tools/regVariation/microsatellite_birthdeath.pl @@ -8,7 +8,7 @@ use Cwd; use File::Path qw(make_path remove_tree); use File::Temp qw/ tempfile tempdir /; -my $tdir = tempdir( CLEANUP => 0 ); +my $tdir = tempdir( CLEANUP => 1 ); chdir $tdir; my $dir = getcwd; # print "current dit=$dir\n"; @@ -20,6 +20,8 @@ use FileHandle; use IO::Handle; # 5.004 or higher + + #my @ar = ("/Users/ydk/work/rhesus_microsat/results/galay/chr22_5sp.maf.txt", "/Users/ydk/work/rhesus_microsat/results/galay/dataset_11.dat", #"/Users/ydk/work/rhesus_microsat/results/galay/chr22_5spec.maf.summ","hg18,panTro2,ponAbe2,rheMac2,calJac1","((((hg18, panTro2), ponAbe2), rheMac2), calJac1)","9,10,12,12", #"10","0.8"); @@ -47,6 +49,7 @@ my %replacementArrTag= (); my %backReplacementArr= (); my %backReplacementArrTag= (); +$tree_definition=~s/\s+//g; my $tree_definition_split = $tree_definition; $tree_definition_split =~ s/[]//g; @@ -211,7 +214,7 @@ my $rh = load_revHash(1); #print "inputs are : \n"; foreach(@ARGV){print $_,"\n";} -open (SELECT, ">$selected") or die "Cannot open selected file: $selected: $!"; +#open (SELECT, ">$selected") or die "Cannot open selected file: $selected: $!"; open (SUMMARY, ">$summout") or die "Cannot open summout file: $summout: $!"; #open (RUN, ">$runtime") or die "Cannot open orth file: $runtime: $!"; #my $ctlfile = "baseml\.ctl"; #$ARGV[4]; @@ -678,10 +681,8 @@ last; } } - foreach my $seqfile (@filterseqfiles){ my $fullpath = $seqfile; - #print "opening file: $fullpath\n"; <STDIN>; open (MATCH, "<$fullpath") or die "Cannot open MATCH file $fullpath: $!"; my $matchlines = 0; @@ -699,7 +700,7 @@ $matchlines++; print MEGAM $line; $line = <MATCH>; - print MEGAM "\n" if $line !~/[0-9a-zA-Z]/; + print MEGAM "\n" if $line !~ /[0-9a-zA-Z]/; last if $line !~/[0-9a-zA-Z]/; } } @@ -902,7 +903,7 @@ my $upstream_gaps = (substr($sequences{$tag}, 0, $extreme_start) =~ s/\-/-/g); #1 NOW MEASURING THE NUMBER OF GAPS IN THE UPSTEAM #2 AND DOWNSTREAM SEQUENCES OF THE MICROSATs IN THIS #3 CLUSTER. - +# print "seq length $tag = $sequences{$tag} = ",length($sequences{$tag})," extreme_end=$extreme_end\n" ; my $downstream_gaps = (substr($sequences{$tag}, $extreme_end) =~ s/\-/-/g); if (($extreme_start - $upstream_gaps )< $EDGE_DISTANCE || (length($sequences{$tag}) - $extreme_end - $downstream_gaps) < $EDGE_DISTANCE){ $edge_microsat=1; @@ -994,7 +995,7 @@ # print "tree_analysis = $tree_analysis .. conformation=$conformation\n"; #<STDIN>; - print SELECT "\"$conformation\"\t$tree_analysis\n"; +# print SELECT "\"$conformation\"\t$tree_analysis\n"; next if $tree_analysis =~ /DISCARD/; if (exists $treesToReject{$tree_analysis}){ @@ -1270,7 +1271,6 @@ } - close SUMMARY; my @summarizarr = ("+C=+C +R.+C -HCOR,+C", @@ -1303,6 +1303,12 @@ } # print "$fields[0] : $count\n"; } +my $rootdir = $dir; +$rootdir =~ s/\/[A-Za-z0-9\-_]+$//; +chdir $rootdir; +remove_tree($dir); + + #-------------------------------------------------------------------------------------------------------- #-------------------------------------------------------------------------------------------------------- #-------------------------------------------------------------------------------------------------------- @@ -2066,7 +2072,7 @@ # print "template DEFINED.. received: @_\n" if defined %template; # print "only received = @_" if !defined %template; my $stopper = 0; - if (!defined %template){ +# if (!defined %template){ TEMP MASKED OCT 18 2012 $stopper = 1; %template=(); # print "tree decipherer = $tree_decipherer\n" if $printer == 1; @@ -2076,7 +2082,7 @@ # print "addding : $template_ref->{$key} for $key\n" if $printer == 1; $template{$key} = $template_ref->{$key}; } - } +# } TEMP MASK OCT 18 2012 END # <STDIN>; for my $templet ( keys %template ) { # print "$templet => @{$template{$templet}}\n"; @@ -4175,6 +4181,8 @@ } } + close IN; + close OUT; # print "countermatch = $countermatch\n"; # <STDIN>; } diff -r c802de6bf0ba697d9a5038ab41dfa1425f0c296f -r 753130def2f89698bb95a554ce76c7ea8c5102d7 tools/regVariation/microsatellite_birthdeath.xml --- a/tools/regVariation/microsatellite_birthdeath.xml +++ b/tools/regVariation/microsatellite_birthdeath.xml @@ -1,4 +1,4 @@ -<tool id="microsatellite_birthdeath" name="Identify microsatellite births and deaths" version="1.0.2"> +<tool id="microsatellite_birthdeath" name="Identify microsatellite births and deaths" version="1.0.0"><description> and causal mutational mechanisms from previously identified orthologous microsatellite sets</description><command interpreter="perl"> microsatellite_birthdeath.pl diff -r c802de6bf0ba697d9a5038ab41dfa1425f0c296f -r 753130def2f89698bb95a554ce76c7ea8c5102d7 tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl --- a/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl +++ b/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl @@ -6,18 +6,27 @@ use IO::Handle; use Cwd; use File::Path; -#use File::Temp qw/ tempfile tempdir /; use vars qw($distance @thresholds @tags $species_set @allspecies $printer $treeSpeciesNum $focalspec $mergestarts $mergeends $mergemicros $interrtypecord $microscanned $interrcord $interr_poscord $no_of_interruptionscord $infocord $typecord $startcord $strandcord $endcord $microsatcord $motifcord $sequencepos $no_of_species $gapcord $prinkter); +use File::Path qw(make_path remove_tree); +use File::Temp qw/ tempfile tempdir /; +my $tdir = tempdir( CLEANUP => 1 ); +chdir $tdir; +my $dir = getcwd; +#print "dir = $dir\n"; #$ENV{'PATH'} .= ':' . dirname($0); my $date = `date`; my ($mafile, $mafile_sputt, $orthfile, $threshold_array, $allspeciesin, $tree_definition_all, $separation) = @ARGV; if (!$mafile or !$mafile_sputt or !$orthfile or !$threshold_array or !$separation or !$tree_definition_all or !$allspeciesin) { die "missing arguments\n"; } + +$tree_definition_all =~ s/\s+//g; +$threshold_array =~ s/\s+//g; +$allspeciesin =~ s/\s+//g; #------------------------------------------------------------------------------- # WHICH SPUTNIK USED? my $sputnikpath = (); -$sputnikpath = "bx-sputnik" ; +$sputnikpath = "sputnik_lowthresh_MATCH_MIN_SCORE3" ; #$sputnikpath = "/Users/ydk/work/rhesus_microsat/codes/./sputnik_Mac-PowerPC"; #print "sputnik_Mac-PowerPC non-existant\n" if !-e $sputnikpath; #exit if !-e $sputnikpath; @@ -38,7 +47,6 @@ my $round = 0; #my $tdir = tempdir( CLEANUP => 0 ); #chdir $tdir; -my $dir = getcwd; foreach my $tree_definition (@tree_definitions){ my @commas = ($tree_definition =~ /,/g) ; @@ -113,8 +121,6 @@ my @sp_tags = (); # print "$ptag _ orthfile\n"; <STDIN>; - - #print "orgs=@orgs, pchr=$pchr, hence, ptag = $ptag\n"; foreach my $sp (@tag){ push(@sp_tags, ($sp.".".$ptag)); @@ -191,7 +197,7 @@ my $sputnikinput = $pipedir.$sp."_nogap_op_unrand"; push(@sput_filelist, $sputnikinput); my $sputnikcommand = $sputnikpath." ".$sputnikinput." > ".$sputnikoutput; - #print "$sputnikcommand\n"; + # print "$sputnikcommand\n"; my @sputnikcommand_system = $sputnikcommand; system(@sputnikcommand_system); } @@ -473,6 +479,11 @@ `cat @outputfiles > $orthfile`; +my $rootdir = $dir; +$rootdir =~ s/\/[A-Za-z0-9\-_]+$//; +chdir $rootdir; +remove_tree($dir); + #print "date = $date\n"; #remove_tree($tdir); #------------------------------------------------------------------------------------------------ diff -r c802de6bf0ba697d9a5038ab41dfa1425f0c296f -r 753130def2f89698bb95a554ce76c7ea8c5102d7 tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml --- a/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml +++ b/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml @@ -1,4 +1,4 @@ -<tool id="multispecies_orthologous_microsats" name="Extract orthologous microsatellites" version="1.0.2"> +<tool id="multispecies_orthologous_microsats" name="Extract orthologous microsatellites" version="1.0.0"><description> for multiple (>2) species alignments</description><command interpreter="perl"> multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl @@ -40,7 +40,7 @@ <param name="input2" value="regVariation/microsatellite/Galaxy17_masked_short.maf.gz"/><param name="thresholds" value="9,10,12,12"/><param name="species" value="hg18,panTro2,ponAbe2,rheMac2,calJac1"/> - <param name="treedefinition" value="((((hg18, panTro2), ponAbe2), rheMac2), calJac1)"/> + <param name="treedefinition" value="((((hg18,panTro2),ponAbe2),rheMac2),calJac1)"/><param name="separation" value="10"/><output name="out_file1" file="regVariation/microsatellite/Galaxy17_short_raw.txt"/></test> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Fixes for loading embedded grids in Trackster.
by Bitbucket 11 Jan '13

11 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c802de6bf0ba/ changeset: c802de6bf0ba user: jgoecks date: 2013-01-11 15:14:21 summary: Fixes for loading embedded grids in Trackster. affected #: 1 file diff -r 790d86fdc5a5fd7b5de2683ca07c0665094bb73e -r c802de6bf0ba697d9a5038ab41dfa1425f0c296f templates/tracks/history_select_grid.mako --- a/templates/tracks/history_select_grid.mako +++ b/templates/tracks/history_select_grid.mako @@ -10,21 +10,20 @@ <%def name="select_header()"><script type="text/javascript"> - // Handle all label clicks. - var f = function() { + // Load all grid URLs into modal-body element so that + // grid + links stays embedded. + var load_urls_into_modal_body = function() { $(".addtracktab, #grid-table a").click(function() { - var parent_body = $(".divider").parent(); - if (parent_body.length !== 0) { - parent_body.load($(this).attr("href")); - f(); + var modal_body = $(".modal-body"); + if (modal_body.length !== 0) { + modal_body.load($(this).attr("href")); return false; } }); }; // Need to process label URLs when document loaded and when grid changes. $(document).ready(function() { - f(); - // $('#grid-table-body').bind('update', f); + load_urls_into_modal_body(); }); </script><style> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: clements: Updated default text at bottom of welcome page that comes up when you first launch your own Galaxy.
by Bitbucket 10 Jan '13

10 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/790d86fdc5a5/ changeset: 790d86fdc5a5 user: clements date: 2013-01-10 23:01:02 summary: Updated default text at bottom of welcome page that comes up when you first launch your own Galaxy. affected #: 2 files diff -r 674273be9a1ffba71ce15462a9f5efd5569503a7 -r 790d86fdc5a5fd7b5de2683ca07c0665094bb73e static/welcome.html.sample --- a/static/welcome.html.sample +++ b/static/welcome.html.sample @@ -15,7 +15,8 @@ <br/><img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" /><hr/> - This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. + <a target="_blank" class="reference" href="http://galaxyproject.org/">Galaxy</a> is an open, web-based platform for data intensive biomedical research. The <a target="_blank" class="reference" href="http://wiki.galaxyproject.org/GalaxyTeam">Galaxy team</a> is a part of <a target="_blank" class="reference" href="http://www.bx.psu.edu">BX</a> at <a target="_blank" class="reference" href="http://www.psu.edu">Penn State</a>, and the <a target="_blank" class="reference" href="http://www.biology.emory.edu/">Biology</a> and <a target="_blank" class="reference" href="http://www.mathcs.emory.edu/">Mathematics and Computer Science</a> departments at <a target="_blank" class="reference" href="http://www.emory.edu/">Emory University</a>. The <a target="_blank" class="reference" href="http://galaxyproject.org/">Galaxy Project</a> is supported in part by <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.huck.psu.edu">The Huck Institutes of the Life Sciences</a>, <a target="_blank" class="reference" href="http://www.ics.psu.edu">The Institute for CyberScience at Penn State</a>, and <a target="_blank" class="reference" href="http://www.emory.edu/">Emory University</a>.</p> + </div></body></html> diff -r 674273be9a1ffba71ce15462a9f5efd5569503a7 -r 790d86fdc5a5fd7b5de2683ca07c0665094bb73e static/welcome.rst --- a/static/welcome.rst +++ b/static/welcome.rst @@ -24,24 +24,35 @@ ========== * `Galaxy documentation`__ -* `Galaxy wiki page`__ -* `People and Technology behind Galaxy`__ -* Report bugs and problems to Galaxy mailing list: `galaxy(a)bx.psu.edu`__ +* `Galaxy wiki`__ +* Report bugs and problems to Galaxy mailing list: `galaxy-dev(a)bx.psu.edu`__ .. __: /static/help.html -.. __: http://www.bx.psu.edu/cgi-bin/trac.cgi -.. __: http://wiki.g2.bx.psu.edu/Galaxy%20Team -.. __: mailto:galaxy@bx.psu.edu +.. __: http://wiki.galaxyproject.org/ +.. __: mailto:galaxy-dev@bx.psu.edu Version: <b>2.1</b> Revision: <b>$Rev$</b> ----- -The Galaxy team is a part of the `Center for Comparative Genomics and Bioinformatics`__ at `Penn State`__. +`Galaxy`__ is an open, web-based platform for data intensive biomedical research on which you can perform, reproduce, and share complete analyses. The `Galaxy team`__ is a part of the `Center for Comparative Genomics and Bioinformatics`__ at `Penn State`__, and the `Biology`__ and `Mathematics and Computer Science`__ departments at `Emory University`__. The `Galaxy Project`__ is supported in part by `NHGRI`__, `NSF`__, `The Huck Institutes of the Life Sciences`__, `The Institute for CyberScience at Penn State`__, and `Emory University`__. +The Galaxy team is a part of the + +.. __: http://galaxyproject.org/ +.. __: http://wiki.galaxyproject.org/GalaxyTeam .. __: http://www.bx.psu.edu .. __: http://www.psu.edu +.. __: http://www.biology.emory.edu/ +.. __: http://www.mathcs.emory.edu/ +.. __: http://www.emory.edu/ +.. __: http://galaxyproject.org/ +.. __: http://www.genome.gov/ +.. __: http://www.nsf.gov/ +.. __: http://www.huck.psu.edu/ +.. __: http://www.ics.psu.edu/ +.. __: http://www.emory.edu/ ----- -Galaxy build 502 \ No newline at end of file +Galaxy build 502 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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