Hg18 44way alignment: Difference between revisions

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==see also==
==see also==


[[Genome size statistics]]
<UL>
 
<LI>Human 44-way [[Genome size statistics|Hg18 Genome size statistics]]</LI>
==sanity==
<LI>Human 44-way [[Hg18 44way blastz parameters|Hg18 conservation lastz parameters]]</LI>
The table below needs to be examined for sanity.  The "chain on hg18" date should be <em>after</em> the masking date.  It appears some do not match that criteria.  When all the chain tables exist, that is a good sign that the multiple alignment can be done.
<LI>all other [[UCSC Multiple Alignments]]</LI>
</UL>


==do not edit==
==do not edit==
Line 19: Line 20:
   <TD>assembly<BR>date</TD>
   <TD>assembly<BR>date</TD>
   <TD>source<BR>version</TD>
   <TD>source<BR>version</TD>
   <TD>RepeatMasker</TD>
   <TD>Repeat<BR>Masker</TD>
   <TD>WindowMasker</TD>
   <TD>Window<BR>Masker</TD>
   <TD>chain<BR>on&nbsp;hg18</TD>
   <TD>chain<BR>on&nbsp;hg18</TD>
  <TD>%&nbsp;of&nbsp;hg18<BR>matched<BR>(chainLink&nbsp;table)</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>01</TH>
   <TH>01</TH><TH>hg18</TH><TD>Homo<BR>sapiens</TD><TD>Human</TD>
  <TH>hg18</TH>
   <TD>Mar.&nbsp;2006</TD><TD>NCBI Build 36.1</TD><TD ALIGN=RIGHT>2005-12-09</TD>
  <TD>Homo<BR>sapiens</TD>
   <TD ALIGN=RIGHT>2006-12-05</TD><TD>N/A</TD><TD ALIGN=RIGHT>N/A</TD>
  <TD>Human</TD>
   <TD>Mar.&nbsp;2006</TD>
  <TD>NCBI&nbsp;Build&nbsp;36.1</TD>
  <TD>2005-12-09</TD>
   <TD>2006-12-05</TD>
  <TD>N/A</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>02</TH>
   <TH>02</TH><TH>panTro2</TH><TD>Pan<BR>troglodytes</TD><TD>Chimp</TD>
  <TH>panTro2</TH>
   <TD>Mar.&nbsp;2006</TD><TD>Washington University Build 2 Version 1</TD><TD ALIGN=RIGHT>2006-03-24</TD>
  <TD>Pan<BR>troglodytes</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2006-07-15</TD><TD ALIGN=RIGHT>94.888%</TD>
  <TD>Chimp</TD>
   <TD>Mar.&nbsp;2006</TD>
  <TD>Washington&nbsp;University&nbsp;Build&nbsp;2&nbsp;Version&nbsp;1</TD>
  <TD>2006-03-24</TD>
   <TD>N/A</TD>
  <TD>2006-07-15</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>03</TH>
   <TH>03</TH><TH>gorGor1</TH><TD>Gorilla<BR>gorilla<BR>gorilla</TD><TD>Gorilla</TD>
  <TH>gorGor1</TH>
   <TD>Oct.&nbsp;2008</TD><TD>Sanger Institute Oct 2008 (NCBI project 31265, CABD01000000)</TD><TD ALIGN=RIGHT>2008-11-03</TD>
  <TD>N/A</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2008-11-05</TD><TD ALIGN=RIGHT>61.731%</TD>
   <TD>N/A</TD>
  <TD>N/A</TD>
  <TD>N/A</TD>
   <TD>N/A</TD>
  <TD>N/A</TD>
  <TD>N/A</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>04</TH>
   <TH>04</TH><TH>ponAbe2</TH><TD>Pongo<BR>pygmaeus<BR>abelii</TD><TD>Orangutan</TD>
  <TH>ponAbe2</TH>
   <TD>July&nbsp;2007</TD><TD>WUSTL 3.0</TD><TD ALIGN=RIGHT>2007-09-15</TD>
  <TD>Pongo<BR>pygmaeus<BR>abelii</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2007-10-03</TD><TD ALIGN=RIGHT>92.892%</TD>
  <TD>Orangutan</TD>
   <TD>July&nbsp;2007</TD>
  <TD>WUSTL&nbsp;3.0</TD>
  <TD>2007-09-15</TD>
   <TD>N/A</TD>
  <TD>2007-10-03</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>05</TH>
   <TH>05</TH><TH>rheMac2</TH><TD>Macaca<BR>mulatta</TD><TD>Rhesus</TD>
  <TH>rheMac2</TH>
   <TD>Jan.&nbsp;2006</TD><TD>Venter Inst./Baylor/WashU Merged assembly Jan 2006 v1 edit4</TD><TD ALIGN=RIGHT>2006-01-30</TD>
  <TD>Macaca<BR>mulatta</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2006-03-17</TD><TD ALIGN=RIGHT>85.552%</TD>
  <TD>Rhesus</TD>
   <TD>Jan.&nbsp;2006</TD>
  <TD>Venter&nbsp;Inst./Baylor/WashU&nbsp;Merged&nbsp;assembly&nbsp;Jan&nbsp;2006&nbsp;v1&nbsp;edit4</TD>
  <TD>2006-01-30</TD>
   <TD>N/A</TD>
  <TD>2006-03-17</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>06</TH>
   <TH>06</TH><TH>calJac1</TH><TD>Callithrix<BR>jacchus</TD><TD>Marmoset</TD>
  <TH>calJac1</TH>
   <TD>June&nbsp;2007</TD><TD>WUSTL 2.0.2</TD><TD ALIGN=RIGHT>2007-08-23</TD>
  <TD>Callithrix<BR>jacchus</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2007-11-13</TD><TD ALIGN=RIGHT>78.351%</TD>
  <TD>Marmoset</TD>
   <TD>June&nbsp;2007</TD>
  <TD>WUSTL&nbsp;2.0.2</TD>
  <TD>2007-08-23</TD>
   <TD>N/A</TD>
  <TD>2007-11-13</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>07</TH>
   <TH>07</TH><TH>tarSyr1</TH><TD>Tarsier<BR>syrichta</TD><TD>Tarsier</TD>
  <TH>tarSyr1</TH>
   <TD>Aug.&nbsp;2008</TD><TD>Broad Institute tarSyr1 (NCBI project 20335, ABRT000000000)</TD><TD ALIGN=RIGHT>2008-10-15</TD>
  <TD>Tarsier<BR>syrichta</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2008-10-27</TD><TD ALIGN=RIGHT>47.999%</TD>
  <TD>Tarsier</TD>
   <TD>Aug.&nbsp;2008</TD>
  <TD>Broad&nbsp;Institute&nbsp;tarSyr1</TD>
  <TD>N/A</TD>
   <TD>N/A</TD>
  <TD>2008-07-28</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>08</TH>
   <TH>08</TH><TH>otoGar1</TH><TD>Otolemur<BR>garnettii</TD><TD>Bushbaby</TD>
  <TH>otoGar1</TH>
   <TD>Dec.&nbsp;2006</TD><TD>Broad version 1 (NCBI project 16955, AAQR00000000)</TD><TD ALIGN=RIGHT>2006-12-20</TD>
  <TD>Otolemur<BR>garnettii</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2007-02-27</TD><TD ALIGN=RIGHT>44.638%</TD>
  <TD>Bushbaby</TD>
   <TD>Dec.&nbsp;2006</TD>
  <TD>Broad&nbsp;version&nbsp;1</TD>
  <TD>2006-12-20</TD>
   <TD>N/A</TD>
  <TD>2007-02-27</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>09</TH>
   <TH>09</TH><TH>micMur1</TH><TD>Microcebus<BR>murinus</TD><TD>Mouse&nbsp;lemur</TD>
  <TH>micMur1</TH>
   <TD>Jun.&nbsp;2003</TD><TD>Broad Institute micMur1 (NCBI project 19967, ABDC00000000)</TD><TD ALIGN=RIGHT>2008-08-03</TD>
  <TD>Microcebus<BR>murinus</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2008-08-04</TD><TD ALIGN=RIGHT>46.445%</TD>
  <TD>Mouse&nbsp;lemur</TD>
   <TD>Jun.&nbsp;2003</TD>
  <TD>Broad&nbsp;Institute&nbsp;micMur1</TD>
  <TD>2008-08-03</TD>
   <TD>N/A</TD>
  <TD>2008-08-04</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>10</TH>
   <TH>10</TH><TH>tupBel1</TH><TD>Tupaia<BR>belangeri</TD><TD>TreeShrew</TD>
  <TH>tupBel1</TH>
   <TD>Dec.&nbsp;2006</TD><TD>Broad Institute tupBel1 (NCBI project 13971, AAPY01000000)</TD><TD ALIGN=RIGHT>2008-10-15</TD>
  <TD>Tupaia<BR>belangeri</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2006-12-20</TD><TD ALIGN=RIGHT>37.348%</TD>
  <TD>TreeShrew</TD>
   <TD>Dec.&nbsp;2006</TD>
  <TD>Broad&nbsp;version&nbsp;1</TD>
  <TD>N/A</TD>
   <TD>N/A</TD>
  <TD>2006-12-20</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>11</TH>
   <TH>11</TH><TH>mm9</TH><TD>Mus<BR>musculus</TD><TD>Mouse</TD>
  <TH>mm9</TH>
   <TD>July&nbsp;2007</TD><TD>NCBI Build 37</TD><TD ALIGN=RIGHT>2007-07-20</TD>
  <TD>Mus<BR>musculus</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2007-08-14</TD><TD ALIGN=RIGHT>35.201%</TD>
  <TD>Mouse</TD>
   <TD>July&nbsp;2007</TD>
  <TD>NCBI&nbsp;Build&nbsp;37</TD>
  <TD>2007-07-20</TD>
   <TD>N/A</TD>
  <TD>2007-08-14</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>12</TH>
   <TH>12</TH><TH>rn4</TH><TD>Rattus<BR>norvegicus</TD><TD>Rat</TD>
  <TH>rn4</TH>
   <TD>Nov.&nbsp;2004</TD><TD>Baylor HGSC v. 3.4</TD><TD ALIGN=RIGHT>2006-03-16</TD>
  <TD>Rattus<BR>norvegicus</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2006-02-17</TD><TD ALIGN=RIGHT>32.893%</TD>
  <TD>Rat</TD>
   <TD>Nov.&nbsp;2004</TD>
  <TD>Baylor&nbsp;HGSC&nbsp;v.&nbsp;3.4</TD>
  <TD>2006-03-16</TD>
   <TD>N/A</TD>
  <TD>2006-02-17</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>13</TH>
   <TH>13</TH><TH>dipOrd1</TH><TD>Dipodomys<BR>ordii</TD><TD>Kangaroo&nbsp;rat</TD>
  <TH>dipOrd1</TH>
   <TD>Jul.&nbsp;2008</TD><TD>Broad Institute dipOrd1 (NCBI project 20385, ABRO01000000)</TD><TD ALIGN=RIGHT>2008-10-15</TD>
  <TD>Dipodomys<BR>ordii</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2008-10-22</TD><TD ALIGN=RIGHT>27.282%</TD>
  <TD>Kangaroo&nbsp;rat</TD>
   <TD>Jul.&nbsp;2008</TD>
  <TD>Broad&nbsp;Institute</TD>
  <TD>N/A</TD>
   <TD>N/A</TD>
  <TD>2008-07-28</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>14</TH>
   <TH>14</TH><TH>cavPor3</TH><TD>Cavia<BR>porcellus</TD><TD>Guinea&nbsp;Pig</TD>
  <TH>cavPor3</TH>
   <TD>Feb.&nbsp;2008</TD><TD>Broad Institute cavPor3</TD><TD ALIGN=RIGHT>2008-04-05</TD>
  <TD>Cavia<BR>porcellus</TD>
   <TD ALIGN=RIGHT>2008-04-08</TD><TD>2008-04-11</TD><TD ALIGN=RIGHT>43.971%</TD>
  <TD>Guinea&nbsp;Pig</TD>
   <TD>Feb.&nbsp;2008</TD>
  <TD>Broad&nbsp;Institute&nbsp;cavPor3</TD>
  <TD>2008-04-05</TD>
   <TD>2008-04-08</TD>
  <TD>2008-04-11</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>15</TH>
   <TH>15</TH><TH>speTri1</TH><TD>Spermophilus<BR>tridecemlineatus</TD><TD>Squirrel</TD>
  <TH>speTri1</TH>
   <TD>Feb.&nbsp;2008</TD><TD>Broad Institute speTri1</TD><TD ALIGN=RIGHT>2008-08-03</TD>
  <TD>Spermophilus<BR>tridecemlineatus</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2008-08-05</TD><TD ALIGN=RIGHT>35.828%</TD>
  <TD>Squirrel</TD>
   <TD>Feb.&nbsp;2008</TD>
  <TD>Broad&nbsp;Institute&nbsp;speTri1</TD>
  <TD>2008-08-03</TD>
   <TD>N/A</TD>
  <TD>2008-08-05</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>16</TH>
   <TH>16</TH><TH>oryCun1</TH><TD>Oryctolagus<BR>cuniculus</TD><TD>Rabbit</TD>
  <TH>oryCun1</TH>
   <TD>May&nbsp;2005</TD><TD>Broad May 2005</TD><TD ALIGN=RIGHT>2005-05-22</TD>
  <TD>Oryctolagus<BR>cuniculus</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2007-04-17</TD><TD ALIGN=RIGHT>34.015%</TD>
  <TD>Rabbit</TD>
   <TD>May&nbsp;2005</TD>
  <TD>Broad&nbsp;May&nbsp;2005</TD>
  <TD>2005-05-22</TD>
   <TD>N/A</TD>
  <TD>2007-04-17</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>17</TH>
   <TH>17</TH><TH>ochPri2</TH><TD>Ochotona<BR>princeps</TD><TD>Pika</TD>
  <TH>ochPri2</TH>
   <TD>Jul.&nbsp;2008</TD><TD>Broad Institute ochPri2</TD><TD ALIGN=RIGHT>2008-07-28</TD>
  <TD>Ochotona<BR>princeps</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2008-07-30</TD><TD ALIGN=RIGHT>27.974%</TD>
  <TD>Pika</TD>
   <TD>Jul.&nbsp;2008</TD>
  <TD>Broad&nbsp;Institute&nbsp;ochPri2</TD>
  <TD>2008-07-28</TD>
   <TD>N/A</TD>
  <TD>2008-07-30</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>18</TH>
   <TH>18</TH><TH>sorAra1</TH><TD>Sorex<BR>araneus</TD><TD>Shrew</TD>
  <TH>sorAra1</TH>
   <TD>June&nbsp;2006</TD><TD>Broad Institute sorAra1 (Draft_v2)</TD><TD ALIGN=RIGHT>2008-10-20</TD>
  <TD>Sorex<BR>araneus</TD>
   <TD ALIGN=RIGHT>2008-10-21</TD><TD>2007-03-10</TD><TD ALIGN=RIGHT>20.056%</TD>
  <TD>Shrew</TD>
   <TD>June&nbsp;2006</TD>
  <TD>Broad&nbsp;Institute&nbsp;sorAra&nbsp;(Draft_v2)</TD>
  <TD>N/A</TD>
   <TD>N/A</TD>
  <TD>2007-03-10</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>19</TH>
   <TH>19</TH><TH>eriEur1</TH><TD>Erinaceus<BR>europaeus</TD><TD>hedgehog</TD>
  <TH>eriEur1</TH>
   <TD>June&nbsp;2006</TD><TD>Broad Institute eriEur1 (Draft_v1)</TD><TD ALIGN=RIGHT>2008-10-21</TD>
  <TD>Erinaceus<BR>europaeus</TD>
   <TD ALIGN=RIGHT>2008-10-21</TD><TD>2007-03-11</TD><TD ALIGN=RIGHT>19.622%</TD>
  <TD>Hedgehog</TD>
   <TD>June&nbsp;2006</TD>
  <TD>Broad&nbsp;Institute&nbsp;eriEur1&nbsp;(Draft_v1)</TD>
  <TD>N/A</TD>
   <TD>N/A</TD>
  <TD>2007-03-11</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>20</TH>
   <TH>20</TH><TH>felCat3</TH><TD>Felis<BR>catus</TD><TD>Cat</TD>
  <TH>felCat3</TH>
   <TD>Mar.&nbsp;2006</TD><TD>Broad Release 3</TD><TD ALIGN=RIGHT>2006-10-16</TD>
  <TD>Felis<BR>catus</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2006-11-10</TD><TD ALIGN=RIGHT>35.888%</TD>
  <TD>Cat</TD>
   <TD>Mar.&nbsp;2006</TD>
  <TD>Broad&nbsp;Release&nbsp;3</TD>
  <TD>2006-10-16</TD>
   <TD>N/A</TD>
  <TD>2006-11-10</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>21</TH>
   <TH>21</TH><TH>canFam2</TH><TD>Canis<BR>lupus<BR>familiaris</TD><TD>Dog</TD>
  <TH>canFam2</TH>
   <TD>May&nbsp;2005</TD><TD>Broad Institute v. 2.0</TD><TD ALIGN=RIGHT>2005-07-10</TD>
  <TD>Canis<BR>lupus<BR>familiaris</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2005-12-29</TD><TD ALIGN=RIGHT>52.915%</TD>
  <TD>Dog</TD>
   <TD>May&nbsp;2005</TD>
  <TD>Broad&nbsp;Institute&nbsp;v.&nbsp;2.0</TD>
  <TD>2005-07-10</TD>
   <TD>N/A</TD>
  <TD>2005-12-29</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>22</TH>
   <TH>22</TH><TH>equCab2</TH><TD>Equus<BR>caballus</TD><TD>Horse</TD>
  <TH>equCab2</TH>
   <TD>Sep.&nbsp;2007</TD><TD>Broad Institute EquCab2</TD><TD ALIGN=RIGHT>2008-04-03</TD>
  <TD>Equus<BR>caballus</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2008-04-11</TD><TD ALIGN=RIGHT>57.162%</TD>
  <TD>Horse</TD>
   <TD>Sep.&nbsp;2007</TD>
  <TD>Broad&nbsp;Institute&nbsp;EquCab2</TD>
  <TD>2008-04-03</TD>
   <TD>N/A</TD>
  <TD>2008-04-11</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>23</TH>
   <TH>23</TH><TH>pteVam1</TH><TD>Pteropus<BR>vampyrus</TD><TD>Megabat</TD>
  <TH>pteVam1</TH>
   <TD>Jul.&nbsp;2008</TD><TD>Broad Institute pteVam1 (NCBI project 20325, ABRP01000000)</TD><TD ALIGN=RIGHT>2008-10-15</TD>
  <TD>Pteropus<BR>vampyrus</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2008-10-22</TD><TD ALIGN=RIGHT>45.502%</TD>
  <TD>Megabat</TD>
   <TD>Jul.&nbsp;2008</TD>
  <TD>Broad&nbsp;Institute&nbsp;pteVam1</TD>
  <TD>N/A</TD>
   <TD>N/A</TD>
  <TD>2008-07-13</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>24</TH>
   <TH>24</TH><TH>myoLuc1</TH><TD>Myotis<BR>lucifugus</TD><TD>Microbat</TD>
  <TH>myoLuc1</TH>
   <TD>Mar.&nbsp;2006</TD><TD>Broad Institute myoLuc1</TD><TD ALIGN=RIGHT>2008-07-29</TD>
  <TD>Myotis<BR>lucifugus</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2008-08-02</TD><TD ALIGN=RIGHT>33.044%</TD>
  <TD>Microbat</TD>
   <TD>Mar.&nbsp;2006</TD>
  <TD>Broad&nbsp;Institute&nbsp;myoLuc1</TD>
  <TD>2008-07-29</TD>
   <TD>N/A</TD>
  <TD>2008-08-02</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>25</TH>
   <TH>25</TH><TH>turTru1</TH><TD>Tursiops<BR>truncatus</TD><TD>Dolphin</TD>
  <TH>turTru1</TH>
   <TD>Feb.&nbsp;2008</TD><TD>Broad Institute turTru1 (NCBI project 20367, ABRN01000000)</TD><TD ALIGN=RIGHT>2008-10-15</TD>
  <TD>Tursiops<BR>truncatus</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2008-10-22</TD><TD ALIGN=RIGHT>48.537%</TD>
  <TD>Dolphin</TD>
   <TD>Feb.&nbsp;2008</TD>
  <TD>Broad&nbsp;Institute&nbsp;turTru1</TD>
  <TD>N/A</TD>
   <TD>N/A</TD>
  <TD>2008-07-12</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>26</TH>
   <TH>26</TH><TH>bosTau4</TH><TD>Bos<BR>taurus</TD><TD>Cow</TD>
  <TH>bosTau4</TH>
   <TD>Oct.&nbsp;2007</TD><TD>Baylor Release 4.0</TD><TD ALIGN=RIGHT>2008-03-10</TD>
  <TD>Bos<BR>taurus</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2008-03-11</TD><TD ALIGN=RIGHT>46.689%</TD>
  <TD>Cow</TD>
   <TD>Oct.&nbsp;2007</TD>
  <TD>Baylor&nbsp;Release&nbsp;4.0</TD>
  <TD>2008-03-10</TD>
   <TD>N/A</TD>
  <TD>2008-03-11</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>27</TH>
   <TH>27</TH><TH>vicPac1</TH><TD>Vicugna<BR>pacos</TD><TD>Alpaca</TD>
  <TH>vicPac1</TH>
   <TD>Jul.&nbsp;2008</TD><TD>Broad Institute vicPac1</TD><TD ALIGN=RIGHT>2008-10-17</TD>
  <TD>Vicugna<BR>vicugna</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2008-10-28</TD><TD ALIGN=RIGHT>39.531%</TD>
  <TD>Alpaca</TD>
   <TD>Jul.&nbsp;2008</TD>
  <TD>Broad&nbsp;Institute&nbsp;vicPac1</TD>
  <TD>N/A</TD>
   <TD>N/A</TD>
  <TD>N/A</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>28</TH>
   <TH>28</TH><TH>dasNov2</TH><TD>Dasypus<BR>novemcinctus</TD><TD>Armadillo</TD>
  <TH>dasNov2</TH>
   <TD>Jul.&nbsp;2008</TD><TD>Broad Institute dasNov2 (NCBI project 12594, AAGV020000000)</TD><TD ALIGN=RIGHT>2008-10-07</TD>
  <TD>Dasypus<BR>novemcinctus</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2008-10-27</TD><TD ALIGN=RIGHT>33.663%</TD>
  <TD>Armadillo</TD>
   <TD>Jul.&nbsp;2008</TD>
  <TD>Broad&nbsp;Institute&nbsp;dasNov2</TD>
  <TD>2008-10-07</TD>
   <TD>N/A</TD>
  <TD>2008-08-03</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>29</TH>
   <TH>29</TH><TH>choHof1</TH><TD>Choloepus<BR>hoffmanni</TD><TD>Sloth</TD>
  <TH>choHof1</TH>
   <TD>Jul.&nbsp;2008</TD><TD>Broad Institute choHof1</TD><TD ALIGN=RIGHT>2008-10-16</TD>
  <TD>Choloepus<BR>hoffmanni</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2008-10-24</TD><TD ALIGN=RIGHT>34.463%</TD>
  <TD>Sloth</TD>
   <TD>Jul.&nbsp;2008</TD>
  <TD>Broad&nbsp;Institute&nbsp;choHof1</TD>
  <TD>N/A</TD>
   <TD>N/A</TD>
  <TD>2008-08-05</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>30</TH>
   <TH>30</TH><TH>echTel1</TH><TD>Echinops<BR>telfairi</TD><TD>Tenrec</TD>
  <TH>echTel1</TH>
   <TD>July&nbsp;2005</TD><TD>Broad July 2005</TD><TD ALIGN=RIGHT>2005-08-04</TD>
  <TD>Echinops<BR>telfairi</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2007-04-17</TD><TD ALIGN=RIGHT>23.645%</TD>
  <TD>Tenrec</TD>
   <TD>July&nbsp;2005</TD>
  <TD>Broad&nbsp;July&nbsp;2005</TD>
  <TD>2005-08-04</TD>
   <TD>N/A</TD>
  <TD>2007-04-17</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>31</TH>
   <TH>31</TH><TH>loxAfr2</TH><TD>Loxodonta<BR>africana</TD><TD>Elephant</TD>
  <TH>loxAfr2</TH>
   <TD>Jul.&nbsp;2008</TD><TD>Broad Institute loxAfr2 (NCBI project 12569, AAGU02000000)</TD><TD ALIGN=RIGHT>2008-10-07</TD>
  <TD>Loxodonta<BR>africana</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2008-10-27</TD><TD ALIGN=RIGHT>35.204%</TD>
  <TD>Elephant</TD>
   <TD>Jul.&nbsp;2008</TD>
  <TD>Broad&nbsp;Institute&nbsp;loxAfr2</TD>
  <TD>2008-10-07</TD>
   <TD>N/A</TD>
  <TD>2008-08-02</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>32</TH>
   <TH>32</TH><TH>proCap1</TH><TD>Procavia<BR>capensis</TD><TD>Rock&nbsp;hyrax</TD>
  <TH>proCap1</TH>
   <TD>Jul.&nbsp;2008</TD><TD>Broad Institute proCap1 (NCBI project 13972, ABRQ01000000)</TD><TD ALIGN=RIGHT>2008-10-16</TD>
  <TD>Procavia<BR>capensis</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2008-10-24</TD><TD ALIGN=RIGHT>30.935%</TD>
  <TD>Rock&nbsp;hyrax</TD>
   <TD>Jul.&nbsp;2008</TD>
  <TD>Broad&nbsp;Institute&nbsp;proCap1</TD>
  <TD>N/A</TD>
   <TD>N/A</TD>
  <TD>2008-08-01</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>33</TH>
   <TH>33</TH><TH>monDom4</TH><TD>Monodelphis<BR>domestica</TD><TD>Opossum</TD>
  <TH>monDom4</TH>
   <TD>Jan.&nbsp;2006</TD><TD>Broad Inst. monDom4 Jan06</TD><TD ALIGN=RIGHT>2006-02-10</TD>
  <TD>Monodelphis<BR>domestica</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2006-02-13</TD><TD ALIGN=RIGHT>12.385%</TD>
  <TD>Opossum</TD>
   <TD>Jan.&nbsp;2006</TD>
  <TD>Broad&nbsp;Inst.&nbsp;monDom4&nbsp;Jan06</TD>
  <TD>2006-02-10</TD>
   <TD>N/A</TD>
  <TD>2006-02-13</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>34</TH>
   <TH>34</TH><TH>ornAna1</TH><TD>Ornithorhynchus<BR>anatinus</TD><TD>Platypus</TD>
  <TH>ornAna1</TH>
   <TD>Mar.&nbsp;2007</TD><TD>WUSTL version 5.0.1</TD><TD ALIGN=RIGHT>2007-07-20</TD>
  <TD>Ornithorhynchus<BR>anatinus</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2007-04-04</TD><TD ALIGN=RIGHT>7.870%</TD>
  <TD>Platypus</TD>
   <TD>Mar.&nbsp;2007</TD>
  <TD>WUSTL&nbsp;version&nbsp;5.0.1</TD>
  <TD>2007-07-20</TD>
   <TD>N/A</TD>
  <TD>2007-04-04</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>35</TH>
   <TH>35</TH><TH>galGal3</TH><TD>Gallus<BR>gallus</TD><TD>Chicken</TD>
  <TH>galGal3</TH>
   <TD>May&nbsp;2006</TD><TD>Chicken Genome Sequencing Consortium May 2006 release</TD><TD ALIGN=RIGHT>2006-05-18</TD>
  <TD>Gallus<BR>gallus</TD>
   <TD ALIGN=RIGHT>2007-01-02</TD><TD>2006-05-23</TD><TD ALIGN=RIGHT>3.589%</TD>
  <TD>Chicken</TD>
   <TD>May&nbsp;2006</TD>
  <TD>Chicken&nbsp;Genome&nbsp;Sequencing&nbsp;Consortium&nbsp;May&nbsp;2006&nbsp;release</TD>
  <TD>2006-05-18</TD>
   <TD>2007-01-02</TD>
  <TD>2006-05-23</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>36</TH>
   <TH>36</TH><TH>taeGut1</TH><TD>Taeniopygia<BR>guttata</TD><TD>Zebra&nbsp;finch</TD>
  <TH>taeGut1</TH>
   <TD>Jul.&nbsp;2008</TD><TD>Washington University taeGut1</TD><TD ALIGN=RIGHT>N/A</TD>
  <TD>Taeniopygia<BR>guttata</TD>
   <TD ALIGN=RIGHT>2008-08-05</TD><TD>2008-09-09</TD><TD ALIGN=RIGHT>3.503%</TD>
  <TD>Zebra&nbsp;finch</TD>
   <TD>Jul.&nbsp;2008</TD>
  <TD>Washington&nbsp;University&nbsp;taeGut1</TD>
  <TD>N/A</TD>
   <TD>2008-08-05</TD>
  <TD>2008-09-09</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>37</TH>
   <TH>37</TH><TH>anoCar1</TH><TD>Anolis<BR>carolinensis</TD><TD>Lizard</TD>
  <TH>anoCar1</TH>
   <TD>Feb.&nbsp;2007</TD><TD>Broad Institute AnoCar (1.0)</TD><TD ALIGN=RIGHT>2007-03-07</TD>
  <TD>Anolis<BR>carolinensis</TD>
   <TD ALIGN=RIGHT>2007-02-16</TD><TD>2007-02-18</TD><TD ALIGN=RIGHT>4.774%</TD>
  <TD>Lizard</TD>
   <TD>Feb.&nbsp;2007</TD>
  <TD>Broad&nbsp;Institute&nbsp;AnoCar&nbsp;(1.0)</TD>
  <TD>2007-03-07</TD>
   <TD>2007-02-16</TD>
  <TD>2007-02-18</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>38</TH>
   <TH>38</TH><TH>xenTro2</TH><TD>Xenopus<BR>tropicalis</TD><TD>X.&nbsp;tropicalis</TD>
  <TH>xenTro2</TH>
   <TD>Aug.&nbsp;2005</TD><TD>JGI v4.1</TD><TD ALIGN=RIGHT>2006-04-17</TD>
  <TD>Xenopus<BR>tropicalis</TD>
   <TD ALIGN=RIGHT>2007-02-20</TD><TD>2006-04-20</TD><TD ALIGN=RIGHT>2.623%</TD>
  <TD>X.&nbsp;tropicalis</TD>
   <TD>Aug.&nbsp;2005</TD>
  <TD>JGI&nbsp;v4.1</TD>
  <TD>2006-04-17</TD>
   <TD>2007-02-20</TD>
  <TD>2006-04-20</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>39</TH>
   <TH>39</TH><TH>danRer5</TH><TD>Danio<BR>rerio</TD><TD>Zebrafish</TD>
  <TH>danRer5</TH>
   <TD>July&nbsp;2007</TD><TD>Wellcome Trust Sanger Institute, Zv7 assembly</TD><TD ALIGN=RIGHT>2007-09-05</TD>
  <TD>Danio<BR>rerio</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2007-10-17</TD><TD ALIGN=RIGHT>2.565%</TD>
  <TD>Zebrafish</TD>
   <TD>July&nbsp;2007</TD>
  <TD>Wellcome&nbsp;Trust&nbsp;Sanger&nbsp;Institute,&nbsp;Zv7&nbsp;assembly</TD>
  <TD>2007-09-05</TD>
   <TD>N/A</TD>
  <TD>2007-10-17</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>40</TH>
   <TH>40</TH><TH>tetNig1</TH><TD>Tetraodon<BR>nigroviridis</TD><TD>Tetraodon</TD>
  <TH>tetNig1</TH>
   <TD>Feb.&nbsp;2004</TD><TD>Genoscope and Broad Institute V7 (NCBI project 12350, CAAE01000000)</TD><TD ALIGN=RIGHT>2004-08-17</TD>
  <TD>Tetraodon<BR>nigroviridis</TD>
   <TD ALIGN=RIGHT>2006-12-05</TD><TD>2006-01-07</TD><TD ALIGN=RIGHT>2.001%</TD>
  <TD>Tetraodon</TD>
   <TD>Feb.&nbsp;2004</TD>
  <TD>Genoscope&nbsp;and&nbsp;Broad&nbsp;Institute,&nbsp;V7</TD>
  <TD>2004-08-17</TD>
   <TD>2006-12-05</TD>
  <TD>2006-01-07</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>41</TH>
   <TH>41</TH><TH>fr2</TH><TD>Takifugu<BR>rubripes</TD><TD>Fugu</TD>
  <TH>fr2</TH>
   <TD>Oct.&nbsp;2004</TD><TD>JGI V4.0</TD><TD ALIGN=RIGHT>2007-03-07</TD>
  <TD>Takifugu<BR>rubripes</TD>
   <TD ALIGN=RIGHT>2007-01-22</TD><TD>2007-01-24</TD><TD ALIGN=RIGHT>1.766%</TD>
  <TD>Fugu</TD>
   <TD>Oct.&nbsp;2004</TD>
  <TD>JGI&nbsp;V4.0</TD>
  <TD>2007-03-07</TD>
   <TD>2007-01-22</TD>
  <TD>2007-01-24</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>42</TH>
   <TH>42</TH><TH>gasAcu1</TH><TD>Gasterosteus<BR>aculeatus</TD><TD>Stickleback</TD>
  <TH>gasAcu1</TH>
   <TD>Feb.&nbsp;2006</TD><TD>Broad Institute gasAcu1 (1.0) (NCBI project 13579, AANH01000000)</TD><TD ALIGN=RIGHT>2006-10-17</TD>
  <TD>Gasterosteus<BR>aculeatus</TD>
   <TD ALIGN=RIGHT>2006-12-05</TD><TD>2007-02-08</TD><TD ALIGN=RIGHT>1.923%</TD>
  <TD>Stickleback</TD>
   <TD>Feb.&nbsp;2006</TD>
  <TD>Broad&nbsp;Institute&nbsp;gasAcu1&nbsp;(1.0)</TD>
  <TD>2006-10-17</TD>
   <TD>2006-12-05</TD>
  <TD>2007-02-08</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>43</TH>
   <TH>43</TH><TH>oryLat2</TH><TD>Oryzias<BR>latipes</TD><TD>Medaka</TD>
  <TH>oryLat2</TH>
   <TD>Oct.&nbsp;2005</TD><TD>NIG and Tokyo Univ MEDAKA1 (NCBI project 16702, BAAF04000000)</TD><TD ALIGN=RIGHT>2008-08-12</TD>
  <TD>Oryzias<BR>latipes</TD>
   <TD ALIGN=RIGHT>2008-08-14</TD><TD>2008-08-19</TD><TD ALIGN=RIGHT>1.829%</TD>
  <TD>Medaka</TD>
   <TD>Oct.&nbsp;2005</TD>
  <TD>MEDAKA1</TD>
  <TD>2008-08-12</TD>
   <TD>2008-08-14</TD>
  <TD>2008-08-19</TD>
</TR>
</TR>
<TR>
<TR>
   <TH>44</TH>
   <TH>44</TH><TH>petMar1</TH><TD>Petromyzon<BR>marinus</TD><TD>Lamprey</TD>
  <TH>petMar1</TH>
   <TD>Mar.&nbsp;2007</TD><TD>WUSTL v.3.0 (March 2007)</TD><TD ALIGN=RIGHT>N/A</TD>
  <TD>Petromyzon<BR>marinus</TD>
   <TD ALIGN=RIGHT>2008-01-28</TD><TD>2008-01-29</TD><TD ALIGN=RIGHT>1.251%</TD>
  <TD>Lamprey</TD>
   <TD>Mar.&nbsp;2007</TD>
  <TD>WUSTL&nbsp;v.3.0&nbsp;(March&nbsp;2007)</TD>
  <TD>N/A</TD>
   <TD>2008-01-28</TD>
  <TD>2008-01-29</TD>
</TR>
</TR>
</TABLE>
</TABLE>
[[Category:Comparative Genomics]]

Latest revision as of 22:42, 18 May 2011

see also

do not edit

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

  UCSC
db name		 Scientific
name		 Common
name		 assembly
date		 source
version		 Repeat
Masker		 Window
Masker		 chain
on hg18		 % of hg18
matched
(chainLink table)
01hg18Homo
sapiens		Human Mar. 2006NCBI Build 36.12005-12-09 2006-12-05N/AN/A
02panTro2Pan
troglodytes		Chimp Mar. 2006Washington University Build 2 Version 12006-03-24 N/A2006-07-1594.888%
03gorGor1Gorilla
gorilla
gorilla		Gorilla Oct. 2008Sanger Institute Oct 2008 (NCBI project 31265, CABD01000000)2008-11-03 N/A2008-11-0561.731%
04ponAbe2Pongo
pygmaeus
abelii		Orangutan July 2007WUSTL 3.02007-09-15 N/A2007-10-0392.892%
05rheMac2Macaca
mulatta		Rhesus Jan. 2006Venter Inst./Baylor/WashU Merged assembly Jan 2006 v1 edit42006-01-30 N/A2006-03-1785.552%
06calJac1Callithrix
jacchus		Marmoset June 2007WUSTL 2.0.22007-08-23 N/A2007-11-1378.351%
07tarSyr1Tarsier
syrichta		Tarsier Aug. 2008Broad Institute tarSyr1 (NCBI project 20335, ABRT000000000)2008-10-15 N/A2008-10-2747.999%
08otoGar1Otolemur
garnettii		Bushbaby Dec. 2006Broad version 1 (NCBI project 16955, AAQR00000000)2006-12-20 N/A2007-02-2744.638%
09micMur1Microcebus
murinus		Mouse lemur Jun. 2003Broad Institute micMur1 (NCBI project 19967, ABDC00000000)2008-08-03 N/A2008-08-0446.445%
10tupBel1Tupaia
belangeri		TreeShrew Dec. 2006Broad Institute tupBel1 (NCBI project 13971, AAPY01000000)2008-10-15 N/A2006-12-2037.348%
11mm9Mus
musculus		Mouse July 2007NCBI Build 372007-07-20 N/A2007-08-1435.201%
12rn4Rattus
norvegicus		Rat Nov. 2004Baylor HGSC v. 3.42006-03-16 N/A2006-02-1732.893%
13dipOrd1Dipodomys
ordii		Kangaroo rat Jul. 2008Broad Institute dipOrd1 (NCBI project 20385, ABRO01000000)2008-10-15 N/A2008-10-2227.282%
14cavPor3Cavia
porcellus		Guinea Pig Feb. 2008Broad Institute cavPor32008-04-05 2008-04-082008-04-1143.971%
15speTri1Spermophilus
tridecemlineatus		Squirrel Feb. 2008Broad Institute speTri12008-08-03 N/A2008-08-0535.828%
16oryCun1Oryctolagus
cuniculus		Rabbit May 2005Broad May 20052005-05-22 N/A2007-04-1734.015%
17ochPri2Ochotona
princeps		Pika Jul. 2008Broad Institute ochPri22008-07-28 N/A2008-07-3027.974%
18sorAra1Sorex
araneus		Shrew June 2006Broad Institute sorAra1 (Draft_v2)2008-10-20 2008-10-212007-03-1020.056%
19eriEur1Erinaceus
europaeus		hedgehog June 2006Broad Institute eriEur1 (Draft_v1)2008-10-21 2008-10-212007-03-1119.622%
20felCat3Felis
catus		Cat Mar. 2006Broad Release 32006-10-16 N/A2006-11-1035.888%
21canFam2Canis
lupus
familiaris		Dog May 2005Broad Institute v. 2.02005-07-10 N/A2005-12-2952.915%
22equCab2Equus
caballus		Horse Sep. 2007Broad Institute EquCab22008-04-03 N/A2008-04-1157.162%
23pteVam1Pteropus
vampyrus		Megabat Jul. 2008Broad Institute pteVam1 (NCBI project 20325, ABRP01000000)2008-10-15 N/A2008-10-2245.502%
24myoLuc1Myotis
lucifugus		Microbat Mar. 2006Broad Institute myoLuc12008-07-29 N/A2008-08-0233.044%
25turTru1Tursiops
truncatus		Dolphin Feb. 2008Broad Institute turTru1 (NCBI project 20367, ABRN01000000)2008-10-15 N/A2008-10-2248.537%
26bosTau4Bos
taurus		Cow Oct. 2007Baylor Release 4.02008-03-10 N/A2008-03-1146.689%
27vicPac1Vicugna
pacos		Alpaca Jul. 2008Broad Institute vicPac12008-10-17 N/A2008-10-2839.531%
28dasNov2Dasypus
novemcinctus		Armadillo Jul. 2008Broad Institute dasNov2 (NCBI project 12594, AAGV020000000)2008-10-07 N/A2008-10-2733.663%
29choHof1Choloepus
hoffmanni		Sloth Jul. 2008Broad Institute choHof12008-10-16 N/A2008-10-2434.463%
30echTel1Echinops
telfairi		Tenrec July 2005Broad July 20052005-08-04 N/A2007-04-1723.645%
31loxAfr2Loxodonta
africana		Elephant Jul. 2008Broad Institute loxAfr2 (NCBI project 12569, AAGU02000000)2008-10-07 N/A2008-10-2735.204%
32proCap1Procavia
capensis		Rock hyrax Jul. 2008Broad Institute proCap1 (NCBI project 13972, ABRQ01000000)2008-10-16 N/A2008-10-2430.935%
33monDom4Monodelphis
domestica		Opossum Jan. 2006Broad Inst. monDom4 Jan062006-02-10 N/A2006-02-1312.385%
34ornAna1Ornithorhynchus
anatinus		Platypus Mar. 2007WUSTL version 5.0.12007-07-20 N/A2007-04-047.870%
35galGal3Gallus
gallus		Chicken May 2006Chicken Genome Sequencing Consortium May 2006 release2006-05-18 2007-01-022006-05-233.589%
36taeGut1Taeniopygia
guttata		Zebra finch Jul. 2008Washington University taeGut1N/A 2008-08-052008-09-093.503%
37anoCar1Anolis
carolinensis		Lizard Feb. 2007Broad Institute AnoCar (1.0)2007-03-07 2007-02-162007-02-184.774%
38xenTro2Xenopus
tropicalis		X. tropicalis Aug. 2005JGI v4.12006-04-17 2007-02-202006-04-202.623%
39danRer5Danio
rerio		Zebrafish July 2007Wellcome Trust Sanger Institute, Zv7 assembly2007-09-05 N/A2007-10-172.565%
40tetNig1Tetraodon
nigroviridis		Tetraodon Feb. 2004Genoscope and Broad Institute V7 (NCBI project 12350, CAAE01000000)2004-08-17 2006-12-052006-01-072.001%
41fr2Takifugu
rubripes		Fugu Oct. 2004JGI V4.02007-03-07 2007-01-222007-01-241.766%
42gasAcu1Gasterosteus
aculeatus		Stickleback Feb. 2006Broad Institute gasAcu1 (1.0) (NCBI project 13579, AANH01000000)2006-10-17 2006-12-052007-02-081.923%
43oryLat2Oryzias
latipes		Medaka Oct. 2005NIG and Tokyo Univ MEDAKA1 (NCBI project 16702, BAAF04000000)2008-08-12 2008-08-142008-08-191.829%
44petMar1Petromyzon
marinus		Lamprey Mar. 2007WUSTL v.3.0 (March 2007)N/A 2008-01-282008-01-291.251%
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