Ce10 conservation alignment: Difference between revisions

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(updated with chain link measurements)
(fix broken links to sanger wormbase)
 
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<UL>
<UL>
<LI>June 2011 C. elegans 9-way [[Ce10 Genome size statistics]]</LI>
<LI>June 2011 C. elegans 9-way [[Ce10 Genome size statistics]]</LI>
<LI>June 2011 C. elegans 9-way [[Ce10_conservation_lastz_parameters]]<LI>
<LI>June 2011 C. elegans 9-way [[Ce10_conservation_lastz_parameters]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
</UL>
</UL>
==UCSC and external download locations==
<TABLE BORDER=1>
<TR><TH>UCSC download locations</TH><TH>external source locations</TH></TR>
<TR><TD>[http://hgdownload-test.cse.ucsc.edu/goldenPath/ce10/ elegans]</TD><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS220/genomes/c_elegans/ WormBase WS220]</TD></TR>
<TR><TD>[http://hgdownload-test.cse.ucsc.edu/goldenPath/cb4/ briggsae]</TD><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS220/genomes/c_briggsae/ WormBase WS225]</TD></TR>
<TR><TD>[http://hgdownload-test.cse.ucsc.edu/goldenPath/caePb3/ brenneri]</TD><TD>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_brenneri/C_brenneri-6.0.1b/ Genbank 6.0.1b]</TD></TR>
<TR><TD>[http://hgdownload-test.cse.ucsc.edu/goldenPath/caeJap4/ japonica]</TD><TD>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_japonica/C_japonica-7.0.1/ Genbank 7.0.1]</TD></TR>
<TR><TD>[http://hgdownload-test.cse.ucsc.edu/goldenPath/caeAng1/ angaria]</TD><TD>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_PS1010/ps1010rel4/ Genbank ps1010rel4]</TD></TR>
<TR><TD>[http://hgdownload-test.cse.ucsc.edu/goldenPath/caeRem4/ remanei]</TD><TD>[ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS220/genomes/c_remanei/ WormBase WS220]</TD></TR>
<TR><TD>[http://hgdownload-test.cse.ucsc.edu/goldenPath/caeSp71/ C. sp. 7 JU1286]</TD><TD>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_7_MAF_2007/Caenorhabditis_sp7_JU1286-4.0.1/ Genbank 4.0.1]</TD></TR>
<TR><TD>[http://hgdownload-test.cse.ucsc.edu/goldenPath/caeSp91/ C. sp. 9 JU1422]</TD><TD>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_9_MAF_2010/Caenorhabditis_sp9_JU1422-3.0.1/ Genbank 3.0.1]</TD></TR>
<TR><TD>[http://hgdownload-test.cse.ucsc.edu/goldenPath/caeSp111/ C. sp. 11 JU1373]</TD><TD>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_11_MAF_2010/Caenorhabditis_sp11_JU1373-3.0.1/ Genbank 3.0.1]</TD></TR>
</TABLE>
Please note, the external sources often provide several different types of names for contigs and scaffolds.  When these sequences are placed in the UCSC genome browser a choice is made for the format of the names.  If you want to display custom tracks on the UCSC genome browser, you will need to use the UCSC contig/scaffold/chromosome naming scheme.


==do not edit==
==do not edit==
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<TR>
<TR>
   <TH>URL&nbsp;to<BR>assembly<BR>sequence</TH>
   <TH>URL&nbsp;to<BR>assembly<BR>sequence</TH>
   <TH>UCSC&nbsp;db&nbsp;name/<BR>genome-test<BR>browser</TH>
   <TH>UCSC&nbsp;db&nbsp;name/<BR>genome-preview<BR>browser</TH>
   <TD>Scientific&nbsp;name/<BR>assembly&nbsp;information</TD>
   <TD>Scientific&nbsp;name/<BR>assembly&nbsp;information</TD>
   <TD>Common<BR>name</TD>
   <TD>Common<BR>name</TD>
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</TR>
</TR>
<TR>
<TR>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_elegans/ 01]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ce10 ce10]</TH><TD>[http://wiki.wormbase.org/index.php/Caenorhabditis_elegans Caenorhabditis<BR>elegans]</TD><TD>C.&nbsp;elegans</TD>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_elegans/ 01]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=ce10 ce10]</TH><TD>[http://wiki.wormbase.org/index.php/Caenorhabditis_elegans Caenorhabditis<BR>elegans]</TD><TD>C.&nbsp;elegans</TD>
   <TD>Oct.&nbsp;2010&nbsp;(WS220/ce10)</TD>
   <TD>Oct.&nbsp;2010&nbsp;(WS220/ce10)</TD>
   <TD>Washington University School of Medicine GSC and Sanger Institute WS220</TD>
   <TD>Washington University School of Medicine GSC and Sanger Institute WS220</TD>
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   <TD>N/A</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD>N/A</TD><TD ALIGN=RIGHT>N/A</TD>
</TR><TR>
</TR><TR>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS225/genomes/c_briggsae/ 02]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=cb4 cb4]</TH><TD>[http://www.sanger.ac.uk/Projects/C_briggsae/ Caenorhabditis<BR>briggsae]</TD><TD>C.&nbsp;briggsae</TD>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS225/genomes/c_briggsae/ 02]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=cb4 cb4]</TH><TD>[http://www.sanger.ac.uk/Projects/C_briggsae/ Caenorhabditis<BR>briggsae]</TD><TD>C.&nbsp;briggsae</TD>
   <TD>Apr.&nbsp;2011&nbsp;(WS225/cb4)</TD>
   <TD>Apr.&nbsp;2011&nbsp;(WS225/cb4)</TD>
   <TD>Washington University School of Medicine GSC and Sanger Institute cb4 </TD>
   <TD>Washington University School of Medicine GSC and Sanger Institute cb4 </TD>
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   <TD>2011-06-07</TD><TD ALIGN=RIGHT>39.386%</TD>
   <TD>2011-06-07</TD><TD ALIGN=RIGHT>39.386%</TD>
</TR><TR>
</TR><TR>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_9_MAF_2010/Caenorhabditis_sp9_JU1422-3.0.1/ 03]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp91 caeSp91]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AENM01 Caenorhabditis<BR>sp9.<BR>JU1422]</TD><TD>C.&nbsp;sp.&nbsp;9&nbsp;ju1422</TD>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_9_MAF_2010/Caenorhabditis_sp9_JU1422-3.0.1/ 03]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp91 caeSp91]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AENM01 Caenorhabditis<BR>sp9.<BR>JU1422]</TD><TD>C.&nbsp;sp.&nbsp;9&nbsp;ju1422</TD>
   <TD>Nov.&nbsp;2010&nbsp;(WUSTL&nbsp;3.0.1/caeSp91)</TD>
   <TD>Nov.&nbsp;2010&nbsp;(WUSTL&nbsp;3.0.1/caeSp91)</TD>
   <TD>Washington University School of Medicine GSC Caenorhabditis sp. 9 JU1422 MAF-2010 3.0.1 (GCA_000186805.1)</TD>
   <TD>Washington University School of Medicine GSC Caenorhabditis sp. 9 JU1422 MAF-2010 3.0.1 (GCA_000186805.1)</TD>
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   <TD>2011-06-07</TD><TD ALIGN=RIGHT>42.169%</TD>
   <TD>2011-06-07</TD><TD ALIGN=RIGHT>42.169%</TD>
</TR><TR>
</TR><TR>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_remanei/ 04]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caeRem4 caeRem4]</TH><TD>[http://genome.wustl.edu/genomes/view/caenorhabditis_remanei/ Caenorhabditis<BR>remanei]</TD><TD>C.&nbsp;remanei</TD>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_remanei/ 04]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeRem4 caeRem4]</TH><TD>[http://genome.wustl.edu/genomes/view/caenorhabditis_remanei/ Caenorhabditis<BR>remanei]</TD><TD>C.&nbsp;remanei</TD>
   <TD>Jul.&nbsp;2007&nbsp;(WS220/caeRem4)</TD>
   <TD>Jul.&nbsp;2007&nbsp;(WS220/caeRem4)</TD>
   <TD>Washington University School of Medicine GSC C. remanei 15.0.1</TD>
   <TD>Washington University School of Medicine GSC C. remanei 15.0.1</TD>
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   <TD>2011-06-07</TD><TD ALIGN=RIGHT>41.722%</TD>
   <TD>2011-06-07</TD><TD ALIGN=RIGHT>41.722%</TD>
</TR><TR>
</TR><TR>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_9_MAF_2010/Caenorhabditis_sp9_JU1422-3.0.1/ 05]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp111 caeSp111]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AEKS01 Caenorhabditis<BR>sp.<BR>11<BR>JU1373]</TD><TD>C.&nbsp;sp.&nbsp;11&nbsp;ju1373</TD>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_9_MAF_2010/Caenorhabditis_sp9_JU1422-3.0.1/ 05]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp111 caeSp111]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AEKS01 Caenorhabditis<BR>sp.<BR>11<BR>JU1373]</TD><TD>C.&nbsp;sp.&nbsp;11&nbsp;ju1373</TD>
   <TD>Nov.&nbsp;2010&nbsp;(WUSTL&nbsp;3.0.1/caeSp111)</TD>
   <TD>Nov.&nbsp;2010&nbsp;(WUSTL&nbsp;3.0.1/caeSp111)</TD>
   <TD>Washington University School of Medicine GSC Caenorhabditis sp. 9 JU1422 MAF-2010 3.0.1 (GCA_000186765.1)</TD>
   <TD>Washington University School of Medicine GSC Caenorhabditis sp. 9 JU1422 MAF-2010 3.0.1 (GCA_000186765.1)</TD>
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   <TD>2011-06-07</TD><TD ALIGN=RIGHT>37.876%</TD>
   <TD>2011-06-07</TD><TD ALIGN=RIGHT>37.876%</TD>
</TR><TR>
</TR><TR>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_brenneri/ 06]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caePb3 caePb3]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABEG02 Caenorhabditis<BR>brenneri]</TD><TD>C.&nbsp;brenneri</TD>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_brenneri/C_brenneri-6.0.1b/ 06]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caePb3 caePb3]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABEG02 Caenorhabditis<BR>brenneri]</TD><TD>C.&nbsp;brenneri</TD>
   <TD>Nov.&nbsp;2010&nbsp;(C.&nbsp;brenneri&nbsp;6.0.1b/caePb3)</TD>
   <TD>Nov.&nbsp;2010&nbsp;(C.&nbsp;brenneri&nbsp;6.0.1b/caePb3)</TD>
   <TD>The Caenorhabditis brenneri Sequencing and Analysis Consortium (GCA_000143925.2)</TD>
   <TD>The Caenorhabditis brenneri Sequencing and Analysis Consortium (GCA_000143925.2)</TD>
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   <TD>2011-06-08</TD><TD ALIGN=RIGHT>40.644%</TD>
   <TD>2011-06-08</TD><TD ALIGN=RIGHT>40.644%</TD>
</TR><TR>
</TR><TR>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_7_MAF_2007/Caenorhabditis_sp7_JU1286-4.0.1/ 07]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp71 caeSp71]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AENL01 Caenorhabditis<BR>sp7.<BR>JU1286]</TD><TD>C.&nbsp;sp.&nbsp;7&nbsp;ju1286</TD>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_7_MAF_2007/Caenorhabditis_sp7_JU1286-4.0.1/ 07]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeSp71 caeSp71]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AENL01 Caenorhabditis<BR>sp7.<BR>JU1286]</TD><TD>C.&nbsp;sp.&nbsp;7&nbsp;ju1286</TD>
   <TD>Nov.&nbsp;2010&nbsp;(WUSTL&nbsp;4.0.1/caeSp71)</TD>
   <TD>Nov.&nbsp;2010&nbsp;(WUSTL&nbsp;4.0.1/caeSp71)</TD>
   <TD>Washington University School of Medicine GSC Caenorhabditis sp. 7 JU1286 MAF-2007 4.0.1 (GCA_000186785.1)</TD>
   <TD>Washington University School of Medicine GSC Caenorhabditis sp. 7 JU1286 MAF-2007 4.0.1 (GCA_000186785.1)</TD>
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   <TD>2011-06-07</TD><TD ALIGN=RIGHT>40.236%</TD>
   <TD>2011-06-07</TD><TD ALIGN=RIGHT>40.236%</TD>
</TR><TR>
</TR><TR>
   <TH>[ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_japonica/ 08]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caeJap4 caeJap4]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABLE03 Caenorhabditis<BR>japonica]</TD><TD>C.&nbsp;japonica</TD>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_japonica/C_japonica-7.0.1/ 08]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeJap4 caeJap4]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABLE03 Caenorhabditis<BR>japonica]</TD><TD>C.&nbsp;japonica</TD>
   <TD>Aug.&nbsp;2010&nbsp;(WUSTL&nbsp;7.0.1/caeJap4)</TD>
   <TD>Aug.&nbsp;2010&nbsp;(WUSTL&nbsp;7.0.1/caeJap4)</TD>
   <TD>Washington University School of Medicine GSC C. japonica 7.0.1 (GCA_000147155.1)</TD>
   <TD>Washington University School of Medicine GSC C. japonica 7.0.1 (GCA_000147155.1)</TD>
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   <TD>2011-06-07</TD><TD ALIGN=RIGHT>27.737%</TD>
   <TD>2011-06-07</TD><TD ALIGN=RIGHT>27.737%</TD>
</TR><TR>
</TR><TR>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_PS1010/ps1010rel4/ 09]</TH><TH>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=caeAng1 caeAng1]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AEHI01 Caenorhabditis<BR>angaria]</TD><TD>C.&nbsp;angaria</TD>
   <TH>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_PS1010/ps1010rel4/ 09]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=caeAng1 caeAng1]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AEHI01 Caenorhabditis<BR>angaria]</TD><TD>C.&nbsp;angaria</TD>
   <TD>Oct.&nbsp;2010&nbsp;(WS225/caeAng1)</TD>
   <TD>Oct.&nbsp;2010&nbsp;(WS225/caeAng1)</TD>
   <TD>Division of Biology, California Institute of Technology(PS1010) ps10rel4 (GCA_000165025.1)</TD>
   <TD>Division of Biology, California Institute of Technology(PS1010) ps10rel4 (GCA_000165025.1)</TD>

Latest revision as of 15:34, 13 June 2011

see also

UCSC and external download locations

UCSC download locationsexternal source locations
elegansWormBase WS220
briggsaeWormBase WS225
brenneriGenbank 6.0.1b
japonicaGenbank 7.0.1
angariaGenbank ps1010rel4
remaneiWormBase WS220
C. sp. 7 JU1286Genbank 4.0.1
C. sp. 9 JU1422Genbank 3.0.1
C. sp. 11 JU1373Genbank 3.0.1

Please note, the external sources often provide several different types of names for contigs and scaffolds. When these sequences are placed in the UCSC genome browser a choice is made for the format of the names. If you want to display custom tracks on the UCSC genome browser, you will need to use the UCSC contig/scaffold/chromosome naming scheme.

do not edit

This table is automatically generated off-line from the UCSC databases. Please do not edit it.

URL to
assembly
sequence		 UCSC db name/
genome-preview
browser		 Scientific name/
assembly information		 Common
name		 assembly date source
version		 Repeat
Masker		 Window
Masker		 chain
on ce10		 % of ce10
matched
(chainLink table)
01ce10Caenorhabditis
elegans		C. elegans Oct. 2010 (WS220/ce10) Washington University School of Medicine GSC and Sanger Institute WS220 2011-05-23 N/A N/AN/A
02cb4Caenorhabditis
briggsae		C. briggsae Apr. 2011 (WS225/cb4) Washington University School of Medicine GSC and Sanger Institute cb4 2011-05-24 2011-05-24 2011-06-0739.386%
03caeSp91Caenorhabditis
sp9.
JU1422		C. sp. 9 ju1422 Nov. 2010 (WUSTL 3.0.1/caeSp91) Washington University School of Medicine GSC Caenorhabditis sp. 9 JU1422 MAF-2010 3.0.1 (GCA_000186805.1) 2011-05-27 2011-05-31 2011-06-0742.169%
04caeRem4Caenorhabditis
remanei		C. remanei Jul. 2007 (WS220/caeRem4) Washington University School of Medicine GSC C. remanei 15.0.1 2011-05-25 2011-05-25 2011-06-0741.722%
05caeSp111Caenorhabditis
sp.
11
JU1373		C. sp. 11 ju1373 Nov. 2010 (WUSTL 3.0.1/caeSp111) Washington University School of Medicine GSC Caenorhabditis sp. 9 JU1422 MAF-2010 3.0.1 (GCA_000186765.1) 2011-05-31 2011-05-31 2011-06-0737.876%
06caePb3Caenorhabditis
brenneri		C. brenneri Nov. 2010 (C. brenneri 6.0.1b/caePb3) The Caenorhabditis brenneri Sequencing and Analysis Consortium (GCA_000143925.2) 2011-06-08 2011-06-08 2011-06-0840.644%
07caeSp71Caenorhabditis
sp7.
JU1286		C. sp. 7 ju1286 Nov. 2010 (WUSTL 4.0.1/caeSp71) Washington University School of Medicine GSC Caenorhabditis sp. 7 JU1286 MAF-2007 4.0.1 (GCA_000186785.1) 2011-05-27 2011-05-27 2011-06-0740.236%
08caeJap4Caenorhabditis
japonica		C. japonica Aug. 2010 (WUSTL 7.0.1/caeJap4) Washington University School of Medicine GSC C. japonica 7.0.1 (GCA_000147155.1) 2011-06-03 2011-06-03 2011-06-0727.737%
09caeAng1Caenorhabditis
angaria		C. angaria Oct. 2010 (WS225/caeAng1) Division of Biology, California Institute of Technology(PS1010) ps10rel4 (GCA_000165025.1) 2011-05-31 2011-05-31 2011-06-0817.625%
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