View source for Ce10 conservation alignment

==see also==

<UL>
<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>all other [[UCSC Multiple Alignments]]</LI>
</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==

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

<TABLE BORDER=1>
<TR>
  <TH>URL&nbsp;to<BR>assembly<BR>sequence</TH>
  <TH>UCSC&nbsp;db&nbsp;name/<BR>genome-preview<BR>browser</TH>
  <TD>Scientific&nbsp;name/<BR>assembly&nbsp;information</TD>
  <TD>Common<BR>name</TD>
  <TD>assembly&nbsp;date</TD>
  <TD>source<BR>version</TD>
  <TD>Repeat<BR>Masker</TD>
  <TD>Window<BR>Masker</TD>
  <TD>chain<BR>on&nbsp;ce10</TD>
  <TD>%&nbsp;of&nbsp;ce10<BR>matched<BR>(chainLink&nbsp;table)</TD>
</TR>
<TR>
  <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>Washington University School of Medicine GSC and Sanger Institute WS220</TD>
  <TD ALIGN=RIGHT>2011-05-23</TD>
  <TD ALIGN=RIGHT>N/A</TD>
  <TD>N/A</TD><TD ALIGN=RIGHT>N/A</TD>
</TR><TR>
  <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>Washington University School of Medicine GSC and Sanger Institute cb4 </TD>
  <TD ALIGN=RIGHT>2011-05-24</TD>
  <TD ALIGN=RIGHT>2011-05-24</TD>
  <TD>2011-06-07</TD><TD ALIGN=RIGHT>39.386%</TD>
</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-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>Washington University School of Medicine GSC Caenorhabditis sp. 9 JU1422 MAF-2010 3.0.1 (GCA_000186805.1)</TD>
  <TD ALIGN=RIGHT>2011-05-27</TD>
  <TD ALIGN=RIGHT>2011-05-31</TD>
  <TD>2011-06-07</TD><TD ALIGN=RIGHT>42.169%</TD>
</TR><TR>
  <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>Washington University School of Medicine GSC C. remanei 15.0.1</TD>
  <TD ALIGN=RIGHT>2011-05-25</TD>
  <TD ALIGN=RIGHT>2011-05-25</TD>
  <TD>2011-06-07</TD><TD ALIGN=RIGHT>41.722%</TD>
</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-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>Washington University School of Medicine GSC Caenorhabditis sp. 9 JU1422 MAF-2010 3.0.1 (GCA_000186765.1)</TD>
  <TD ALIGN=RIGHT>2011-05-31</TD>
  <TD ALIGN=RIGHT>2011-05-31</TD>
  <TD>2011-06-07</TD><TD ALIGN=RIGHT>37.876%</TD>
</TR><TR>
  <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>The Caenorhabditis brenneri Sequencing and Analysis Consortium (GCA_000143925.2)</TD>
  <TD ALIGN=RIGHT>2011-06-08</TD>
  <TD ALIGN=RIGHT>2011-06-08</TD>
  <TD>2011-06-08</TD><TD ALIGN=RIGHT>40.644%</TD>
</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-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>Washington University School of Medicine GSC Caenorhabditis sp. 7 JU1286 MAF-2007 4.0.1 (GCA_000186785.1)</TD>
  <TD ALIGN=RIGHT>2011-05-27</TD>
  <TD ALIGN=RIGHT>2011-05-27</TD>
  <TD>2011-06-07</TD><TD ALIGN=RIGHT>40.236%</TD>
</TR><TR>
  <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>Washington University School of Medicine GSC C. japonica 7.0.1 (GCA_000147155.1)</TD>
  <TD ALIGN=RIGHT>2011-06-03</TD>
  <TD ALIGN=RIGHT>2011-06-03</TD>
  <TD>2011-06-07</TD><TD ALIGN=RIGHT>27.737%</TD>
</TR><TR>
  <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>Division of Biology, California Institute of Technology(PS1010) ps10rel4 (GCA_000165025.1)</TD>
  <TD ALIGN=RIGHT>2011-05-31</TD>
  <TD ALIGN=RIGHT>2011-05-31</TD>
  <TD>2011-06-08</TD><TD ALIGN=RIGHT>17.625%</TD>
</TR>
</TABLE>