Hg18 44way alignment: Difference between revisions

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(updated status)
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   <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 Build 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 University Build 2 Version 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 genome_31265</TD><TD ALIGN=RIGHT>N/A</TD>
  <TD>N/A</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>N/A</TD><TD ALIGN=RIGHT>N/A</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 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 Inst./Baylor/WashU Merged assembly Jan 2006 v1 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 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 Institute tarSyr1</TD>
  <TD>2008-10-15</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 version 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 Institute 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 version 1</TD>
  <TD>2008-10-15</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 Build 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 HGSC v. 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 Institute</TD>
  <TD>2008-10-15</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 Institute 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 Institute 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 May 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 Institute 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 Institute sorAra (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 Institute eriEur1 (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 Release 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 Institute v. 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 Institute 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 Institute pteVam1</TD>
  <TD>2008-10-15</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 Institute 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 Institute turTru1</TD>
  <TD>2008-10-15</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 Release 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 Institute 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 Institute 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 Institute choHof1</TD>
  <TD>2008-10-16</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 July 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 Institute 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 Institute proCap1</TD>
  <TD>2008-10-16</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 Inst. monDom4 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 version 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 Genome Sequencing Consortium May 2006 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 University 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 Institute AnoCar (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 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 Trust Sanger Institute, Zv7 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 and Broad Institute, 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 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 Institute gasAcu1 (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 v.3.0 (March 2007)</TD>
  <TD>N/A</TD>
   <TD>2008-01-28</TD>
  <TD>2008-01-29</TD>
</TR>
</TR>
</TABLE>
</TABLE>

Revision as of 18:29, 29 October 2008

see also

Genome size statistics

sanity

The table below needs to be examined for sanity. The "chain on hg18" date should be after the masking date. Some of these existing pair-wise alignments need to be re-done since the genomes have been properly repeat masked. When all the chain tables exist, that is a good sign that the multiple alignment can be done.

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 genome_31265N/A N/AN/AN/A
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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