Hg38 4-way conservation alignment: Difference between revisions

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==See Also==
==see also==


<UL>
<UL>
<LI>Human 4-way [[Hg38 4-way Genome size statistics]]</LI>
<LI>Human 4-way [[Hg38 4-way Genome size statistics]]</LI>
<LI>Human 4-way [[Hg38 4-way conservation alignment]]</LI>
<LI>Human 4-way [[Hg38 4-way conservation lastz parameters]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
</UL>
</UL>


==do not edit==


<TABLE BORDER=0>
This table is automatically generated off-line from the UCSC databases.  Please do not edit it.
<TR><TD>The default<BR>scoring matrix is:</TD><TD WIDTH=42>&nbsp;</TD>
<TD>The HoxD55<BR>scoring matrix is:</TD><TD WIDTH=42>&nbsp;</TD><TD>The human-chimp.v2<BR>scoring matrix is:</TD></TR>


<TR><TD>
<TABLE BORDER=1>
<TABLE BORDER=1>
<TR><TH>&nbsp;</TH><TH>A</TH><TH>C</TH><TH>G</TH><TH>T</TH></TR>
<TR>
<TR><TH>A</TH><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>
  <TH>URL&nbsp;to<BR>assembly<BR>sequence</TH>
<TR><TH>C</TH><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>
  <TH>UCSC&nbsp;db&nbsp;name/<BR>genome-preview<BR>browser</TH>
<TR><TH>G</TH><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>
  <TD>Scientific&nbsp;name/<BR>assembly&nbsp;information</TD>
<TR><TH>T</TH><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>
  <TD>Common<BR>name</TD>
</TABLE>
  <TD>assembly&nbsp;date&nbsp;(version)</TD>
O=400 E=30
  <TD>source<BR>version</TD>
</TD><TD WIDTH=42>&nbsp;</TD><TD><TABLE BORDER=1>
  <TD>Repeat<BR>Masker</TD>
<TR><TH>&nbsp;</TH><TH>A</TH><TH>C</TH><TH>G</TH><TH>T</TH></TR>
  <TD>Window<BR>Masker</TD>
<TR><TH>A</TH><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>
  <TD>chain<BR>on&nbsp;hg38</TD>
<TR><TH>C</TH><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>
   <TD>%&nbsp;of&nbsp;hg38<BR>matched<BR>(chainLink&nbsp;table)</TD>
<TR><TH>G</TH><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>
<TR><TH>T</TH><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>
</TABLE>
O=400 E=30
</TD><TD WIDTH=42>&nbsp;</TD><TD><TABLE BORDER=1>
<TR><TH>&nbsp;</TH><TH>A</TH><TH>C</TH><TH>G</TH><TH>T</TH></TR>
<TR><TH>A</TH><TD>90</TD><TD>-330</TD><TD>-236</TD><TD>-356</TD></TR>
<TR><TH>C</TH><TD>-330</TD><TD>100</TD><TD>-318</TD><TD>-236</TD></TR>
<TR><TH>G</TH><TD>-236</TD><TD>-318</TD><TD>100</TD><TD>-330</TD></TR>
<TR><TH>T</TH><TD>-356</TD><TD>-236</TD><TD>-330</TD><TD>90</TD></TR>
</TABLE>
O=600 E=150
</TD>
</TR></TABLE>
 
==do not edit, automatically generated table==
<TABLE BORDER=1>
<TR><TH>query</TH>
  <TH>abridged<BR>repeats(no)</TH>
  <TH>M(0)</TH><TH>K(3000)</TH>
  <TH>L(3000)</TH><TH>Q</TH><TH>Y(9400)</TH>
  <TH>program<BR>run</TH><TH>E(30)</TH><TH>H(0)</TH>
  <TH>O(400)</TH><TH>T(1)</TH>
  <TH>chain&nbsp;table<BR>date</TH>
   <TH>%&nbsp;of&nbsp;hg38<BR>matched<BR>(chainLink&nbsp;table)</TH>
  <TH>%&nbsp;of&nbsp;query<BR>matched<BR>(chainLinkHg38)</TH>
</TR>
</TR>
<TR>
<TR>
   <TH>Malayan flying lemur&nbsp;galVar1</TH>
   <TH>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000001405.15/ 01]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=hg38 hg38]</TH><TD>[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/index.shtml Homo<BR>sapiens]</TD><TD>Human</TD>
  <TD>no</TD><TD>254</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>Dec.&nbsp;2013&nbsp;(GRCh38/hg38)</TD>
   <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.2)</TD>
  <TD ALIGN=RIGHT>2014-01-10</TD>
   <TD ALIGN=RIGHT>2013-12-25</TD>
  <TD>2015-01-14</TD><TD ALIGN=RIGHT>reference</TD>
</TR><TR>
  <TH>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000696425.1/ 02]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=galVar1 galVar1]</TH><TD>[http://www.ncbi.nlm.nih.gov/assembly/GCF_000696425.1/ Galeopterus<BR>variegatus]</TD><TD>Malayan&nbsp;flying&nbsp;lemur</TD>
  <TD>Jun.&nbsp;2014&nbsp;(G_variegatus-3.0.2/galVar1)</TD>
  <TD>Washington University (WashU)</TD>
  <TD ALIGN=RIGHT>2016-03-02</TD>
  <TD ALIGN=RIGHT>2016-03-04</TD>
   <TD>2016-04-26</TD><TD ALIGN=RIGHT>57.036%</TD>
   <TD>2016-04-26</TD><TD ALIGN=RIGHT>57.036%</TD>
  <TD ALIGN=RIGHT>64.881%</TD></TR>
</TR><TR>
<TR>
   <TH>[http://www.ncbi.nlm.nih.gov/assembly/GCA_000334495.1/ 03]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=tupChi1 tupChi1]</TH><TD>[ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Tupaia_chinensis/TupChi_1.0/ Tupaia<BR>chinensis]</TD><TD>Chinese&nbsp;tree&nbsp;shrew</TD>
   <TH>Chinese tree shrew&nbsp;tupChi1</TH>
   <TD>Jan&nbsp;2013&nbsp;(TupChi_1.0/tupChi1)</TD>
  <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>BGI GCA_000334495.1</TD>
   <TD>9400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD ALIGN=RIGHT>2013-07-05</TD>
  <TD ALIGN=RIGHT>2013-07-05</TD>
   <TD>2015-02-19</TD><TD ALIGN=RIGHT>45.256%</TD>
   <TD>2015-02-19</TD><TD ALIGN=RIGHT>45.256%</TD>
  <TD ALIGN=RIGHT>50.350%</TD></TR>
</TR><TR>
<TR>
   <TH>[http://www.ncbi.nlm.nih.gov/genome/assembly/327618/ 04]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=mm10 mm10]</TH><TD>[http://www.ncbi.nlm.nih.gov/bioproject/51977 Mus<BR>musculus]</TD><TD>Mouse</TD>
   <TH>Mouse&nbsp;mm10</TH>
   <TD>Dec.&nbsp;2011&nbsp;(GRCm38/mm10)</TD>
  <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)</TD>
   <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD ALIGN=RIGHT>2012-02-06</TD>
  <TD ALIGN=RIGHT>2012-02-07</TD>
   <TD>2015-04-09</TD><TD ALIGN=RIGHT>31.653%</TD>
   <TD>2015-04-09</TD><TD ALIGN=RIGHT>31.653%</TD>
  <TD ALIGN=RIGHT>35.372%</TD></TR>
</TR>
</TABLE>
</TABLE>

Latest revision as of 23:41, 21 April 2017

see also

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 (version) source
version		 Repeat
Masker		 Window
Masker		 chain
on hg38		 % of hg38
matched
(chainLink table)
01hg38Homo
sapiens		Human Dec. 2013 (GRCh38/hg38) GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.2) 2014-01-10 2013-12-25 2015-01-14reference
02galVar1Galeopterus
variegatus		Malayan flying lemur Jun. 2014 (G_variegatus-3.0.2/galVar1) Washington University (WashU) 2016-03-02 2016-03-04 2016-04-2657.036%
03tupChi1Tupaia
chinensis		Chinese tree shrew Jan 2013 (TupChi_1.0/tupChi1) BGI GCA_000334495.1 2013-07-05 2013-07-05 2015-02-1945.256%
04mm10Mus
musculus		Mouse Dec. 2011 (GRCm38/mm10) Genome Reference Consortium Mouse Build 38 (GCA_000001635.2) 2012-02-06 2012-02-07 2015-04-0931.653%
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