Hg19 conservation alignment: Difference between revisions
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<UL> | <UL> | ||
<LI>[[Hg19 Genome size statistics]]</LI> | <LI>46-way [[Hg19 Genome size statistics]]</LI> | ||
<LI>[[Hg19 conservation lastz parameters]]</LI> | <LI>46-way [[Hg19 conservation lastz parameters]]</LI> | ||
<LI>[[ | <LI>all other [[UCSC Multiple Alignments]]</LI> | ||
</UL> | </UL> | ||
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<TD>Scientific<BR>name</TD> | <TD>Scientific<BR>name</TD> | ||
<TD>Common<BR>name</TD> | <TD>Common<BR>name</TD> | ||
<TD>assembly<BR>date</TD> | <TD>assembly<BR>date</TD> | ||
<TD>source<BR>version</TD> | <TD>source<BR>version</TD> | ||
| Line 25: | Line 24: | ||
<TD>Window<BR>Masker</TD> | <TD>Window<BR>Masker</TD> | ||
<TD>chain<BR>on hg19</TD> | <TD>chain<BR>on hg19</TD> | ||
<TD>% of hg19<BR>matched<BR>(chainLink table)</TD> | <TD>% of hg19<BR>matched<BR>(chainLink table)</TD> | ||
</TR> | </TR> | ||
<TR> | <TR> | ||
<TH>01</TH><TH>hg19</TH><TD>Homo<BR>sapiens</TD><TD>Human</TD> | <TH>01</TH><TH>hg19</TH><TD>Homo<BR>sapiens</TD><TD>Human</TD> | ||
<TD> | |||
<TD>GRCh37</TD> | |||
<TD>GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1)</TD> | <TD>GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1)</TD> | ||
<TD ALIGN=RIGHT>2009-04-24</TD> | <TD ALIGN=RIGHT>2009-04-24</TD> | ||
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</TR><TR> | </TR><TR> | ||
<TH>02</TH><TH>panTro2</TH><TD>Pan<BR>troglodytes</TD><TD>Chimp</TD> | <TH>02</TH><TH>panTro2</TH><TD>Pan<BR>troglodytes</TD><TD>Chimp</TD> | ||
<TD>Mar. 2006</TD> | <TD>Mar. 2006</TD> | ||
<TD>Washington University Build 2 Version 1</TD> | <TD>Washington University Build 2 Version 1</TD> | ||
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</TR><TR> | </TR><TR> | ||
<TH>03</TH><TH>gorGor1</TH><TD>Gorilla<BR>gorilla<BR>gorilla</TD><TD>Gorilla</TD> | <TH>03</TH><TH>gorGor1</TH><TD>Gorilla<BR>gorilla<BR>gorilla</TD><TD>Gorilla</TD> | ||
<TD>Oct. 2008</TD> | <TD>Oct. 2008</TD> | ||
<TD>Sanger Institute Oct 2008 (NCBI project 31265, CABD01000000)</TD> | <TD>Sanger Institute Oct 2008 (NCBI project 31265, CABD01000000)</TD> | ||
| Line 47: | Line 50: | ||
</TR><TR> | </TR><TR> | ||
<TH>04</TH><TH>ponAbe2</TH><TD>Pongo<BR>pygmaeus<BR>abelii</TD><TD>Orangutan</TD> | <TH>04</TH><TH>ponAbe2</TH><TD>Pongo<BR>pygmaeus<BR>abelii</TD><TD>Orangutan</TD> | ||
<TD>July 2007</TD> | <TD>July 2007</TD> | ||
<TD>WUSTL 3.0</TD> | <TD>WUSTL 3.0</TD> | ||
<TD ALIGN=RIGHT>2007-09-15</TD> | <TD ALIGN=RIGHT>2007-09-15</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-14</TD><TD ALIGN=RIGHT>91.350%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>05</TH><TH>rheMac2</TH><TD>Macaca<BR>mulatta</TD><TD>Rhesus</TD> | <TH>05</TH><TH>rheMac2</TH><TD>Macaca<BR>mulatta</TD><TD>Rhesus</TD> | ||
<TD>Jan. 2006</TD> | <TD>Jan. 2006</TD> | ||
<TD>Venter Inst./Baylor/WashU Merged assembly Jan 2006 v1 edit4</TD> | <TD>Venter Inst./Baylor/WashU Merged assembly Jan 2006 v1 edit4</TD> | ||
<TD ALIGN=RIGHT>2006-01-30</TD> | <TD ALIGN=RIGHT>2006-01-30</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-14</TD><TD ALIGN=RIGHT>82.744%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>06</TH><TH>papHam1</TH><TD>Papio<BR>hamadryas</TD><TD>Baboon</TD> | <TH>06</TH><TH>papHam1</TH><TD>Papio<BR>hamadryas</TD><TD>Baboon</TD> | ||
<TD>Nov. 2008</TD> | <TD>Nov. 2008</TD> | ||
<TD>Baylor BCM HGSC Pham_1.0</TD> | <TD>Baylor BCM HGSC Pham_1.0</TD> | ||
<TD ALIGN=RIGHT>2009-05-13</TD> | <TD ALIGN=RIGHT>2009-05-13</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-20</TD><TD ALIGN=RIGHT>82.810%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>07</TH><TH>calJac1</TH><TD>Callithrix<BR>jacchus</TD><TD>Marmoset</TD> | <TH>07</TH><TH>calJac1</TH><TD>Callithrix<BR>jacchus</TD><TD>Marmoset</TD> | ||
<TD>June 2007</TD> | <TD>June 2007</TD> | ||
<TD>WUSTL 2.0.2</TD> | <TD>WUSTL 2.0.2</TD> | ||
<TD ALIGN=RIGHT>2007-08-23</TD> | <TD ALIGN=RIGHT>2007-08-23</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD>N/A</TD><TD ALIGN=RIGHT>N/A</TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-14</TD><TD ALIGN=RIGHT>70.860%</TD> | ||
</TR><TR> | |||
<TH>08</TH><TH>tarSyr1</TH><TD>Tarsius<BR>syrichta</TD><TD>Tarsier</TD> | |||
<TD>Aug. 2008</TD> | |||
<TD>Broad Institute tarSyr1 (NCBI project 20335, ABRT000000000)</TD> | |||
<TD ALIGN=RIGHT>2008-10-15</TD> | |||
<TD ALIGN=RIGHT>N/A</TD><TD>2009-05-15</TD><TD ALIGN=RIGHT>47.830%</TD> | |||
</TR><TR> | |||
<TH>09</TH><TH>micMur1</TH><TD>Microcebus<BR>murinus</TD><TD>Mouse lemur</TD> | |||
<TD>Jul. 2007</TD> | |||
<TD>Broad Institute micMur1 (NCBI project 19967, ABDC00000000)</TD> | |||
<TD ALIGN=RIGHT>2008-08-03</TD> | |||
<TD ALIGN=RIGHT>N/A</TD><TD>2009-05-22</TD><TD ALIGN=RIGHT>46.519%</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>10</TH><TH>otoGar1</TH><TD>Otolemur<BR>garnettii</TD><TD>Bushbaby</TD> | ||
<TD>Dec. 2006</TD> | <TD>Dec. 2006</TD> | ||
<TD>Broad version 1 (NCBI project 16955, AAQR00000000)</TD> | <TD>Broad version 1 (NCBI project 16955, AAQR00000000)</TD> | ||
<TD ALIGN=RIGHT>2006-12-20</TD> | <TD ALIGN=RIGHT>2006-12-20</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-15</TD><TD ALIGN=RIGHT>43.644%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>11</TH><TH>equCab2</TH><TD>Equus<BR>caballus</TD><TD>Horse</TD> | ||
<TD> | |||
<TD>Broad Institute | <TD>Sep. 2007</TD> | ||
<TD ALIGN=RIGHT>2008- | <TD>Broad Institute EquCab2</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>2008-04-03</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD>2009-06-04</TD><TD ALIGN=RIGHT>57.050%</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>12</TH><TH>tupBel1</TH><TD>Tupaia<BR>belangeri</TD><TD>Tree shrew</TD> | ||
<TD>Dec. 2006</TD> | <TD>Dec. 2006</TD> | ||
<TD>Broad Institute tupBel1 (NCBI project 13971, AAPY01000000)</TD> | <TD>Broad Institute tupBel1 (NCBI project 13971, AAPY01000000)</TD> | ||
<TD ALIGN=RIGHT>2008-10-15</TD> | <TD ALIGN=RIGHT>2008-10-15</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-06-01</TD><TD ALIGN=RIGHT>36.156%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>13</TH><TH>turTru1</TH><TD>Tursiops<BR>truncatus</TD><TD>Dolphin</TD> | ||
<TD> | |||
<TD>Broad Institute | <TD>Feb. 2008</TD> | ||
<TD ALIGN=RIGHT>2008-10- | <TD>Broad Institute turTru1 (NCBI project 20367, ABRN01000000)</TD> | ||
<TD ALIGN=RIGHT>2008-10-15</TD> | |||
<TD ALIGN=RIGHT>N/A</TD><TD>2009-06-04</TD><TD ALIGN=RIGHT>48.398%</TD> | |||
<TD ALIGN=RIGHT>N/A</TD><TD>2009- | |||
</TR><TR> | </TR><TR> | ||
<TH>14</TH><TH>speTri1</TH><TD>Spermophilus<BR>tridecemlineatus</TD><TD>Squirrel</TD> | <TH>14</TH><TH>speTri1</TH><TD>Spermophilus<BR>tridecemlineatus</TD><TD>Squirrel</TD> | ||
<TD>Feb. 2008</TD> | <TD>Feb. 2008</TD> | ||
<TD>Broad Institute speTri1</TD> | <TD>Broad Institute speTri1</TD> | ||
<TD ALIGN=RIGHT>2008-08-03</TD> | <TD ALIGN=RIGHT>2008-08-03</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-06-04</TD><TD ALIGN=RIGHT>35.713%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>15</TH><TH> | <TH>15</TH><TH>vicPac1</TH><TD>Vicugna<BR>pacos</TD><TD>Alpaca</TD> | ||
<TD> | |||
<TD>Broad Institute | <TD>Jul. 2008</TD> | ||
<TD ALIGN=RIGHT>2008- | <TD>Broad Institute vicPac1</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>2008-10-17</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD>2009-06-04</TD><TD ALIGN=RIGHT>39.399%</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH>16</TH><TH> | <TH>16</TH><TH>choHof1</TH><TD>Choloepus<BR>hoffmanni</TD><TD>Sloth</TD> | ||
<TD> | |||
<TD>Broad | <TD>Jul. 2008</TD> | ||
<TD ALIGN=RIGHT> | <TD>Broad Institute choHof1</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>2008-10-16</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD>2009-06-05</TD><TD ALIGN=RIGHT>34.377%</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH>17</TH><TH> | <TH>17</TH><TH>pteVam1</TH><TD>Pteropus<BR>vampyrus</TD><TD>Megabat</TD> | ||
<TD>Jul. 2008</TD> | <TD>Jul. 2008</TD> | ||
<TD>Broad Institute | <TD>Broad Institute pteVam1 (NCBI project 20325, ABRP01000000)</TD> | ||
<TD ALIGN=RIGHT>2008- | <TD ALIGN=RIGHT>2008-10-15</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-06-04</TD><TD ALIGN=RIGHT>45.414%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>18</TH><TH> | <TH>18</TH><TH>loxAfr3</TH><TD>Loxodonta<BR>africana</TD><TD>Elephant</TD> | ||
<TD> | |||
<TD>Broad Institute | <TD>Jul. 2009</TD> | ||
<TD ALIGN=RIGHT> | <TD>Broad Institute loxAfr3 (NCBI project 12569, AAGU03000000)</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>2009-07-15</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD>2009-07-22</TD><TD ALIGN=RIGHT>46.636%</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH>19</TH><TH>felCat3</TH><TD>Felis<BR>catus</TD><TD>Cat</TD> | <TH>19</TH><TH>felCat3</TH><TD>Felis<BR>catus</TD><TD>Cat</TD> | ||
<TD>Mar. 2006</TD> | <TD>Mar. 2006</TD> | ||
<TD>Broad Release 3</TD> | <TD>Broad Release 3</TD> | ||
<TD ALIGN=RIGHT>2006-10-16</TD> | <TD ALIGN=RIGHT>2006-10-16</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-06-04</TD><TD ALIGN=RIGHT>35.713%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>20</TH><TH>canFam2</TH><TD>Canis<BR>lupus<BR>familiaris</TD><TD>Dog</TD> | <TH>20</TH><TH>canFam2</TH><TD>Canis<BR>lupus<BR>familiaris</TD><TD>Dog</TD> | ||
<TD>May 2005</TD> | <TD>May 2005</TD> | ||
<TD>Broad Institute v. 2.0</TD> | <TD>Broad Institute v. 2.0</TD> | ||
<TD ALIGN=RIGHT>2005-07-10</TD> | <TD ALIGN=RIGHT>2005-07-10</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-14</TD><TD ALIGN=RIGHT>52.879%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>21</TH><TH> | <TH>21</TH><TH>dasNov2</TH><TD>Dasypus<BR>novemcinctus</TD><TD>Armadillo</TD> | ||
<TD>Jul. 2008</TD> | <TD>Jul. 2008</TD> | ||
<TD>Broad Institute | <TD>Broad Institute dasNov2 (NCBI project 12594, AAGV020000000)</TD> | ||
<TD ALIGN=RIGHT>2008-10- | <TD ALIGN=RIGHT>2008-10-07</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-27</TD><TD ALIGN=RIGHT>33.543%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>22</TH><TH>oryCun2</TH><TD>Oryctolagus<BR>cuniculus</TD><TD>Rabbit</TD> | ||
<TD> | |||
<TD>Broad Institute | <TD>Apr. 2009</TD> | ||
<TD ALIGN=RIGHT> | <TD>Broad Institute oryCun2 (NCBI project 12819, AAGW00000000)</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>2009-08-11</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD>2009-08-12</TD><TD ALIGN=RIGHT>44.317%</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>23</TH><TH>myoLuc1</TH><TD>Myotis<BR>lucifugus</TD><TD>Microbat</TD> | ||
<TD>Mar. 2006</TD> | <TD>Mar. 2006</TD> | ||
<TD>Broad Institute myoLuc1</TD> | <TD>Broad Institute myoLuc1</TD> | ||
<TD ALIGN=RIGHT>2008-07-29</TD> | <TD ALIGN=RIGHT>2008-07-29</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-06-04</TD><TD ALIGN=RIGHT>33.174%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>24</TH><TH>bosTau4</TH><TD>Bos<BR>taurus</TD><TD>Cow</TD> | ||
<TD>Oct. 2007</TD> | <TD>Oct. 2007</TD> | ||
<TD>Baylor Release 4.0</TD> | <TD>Baylor Release 4.0</TD> | ||
<TD ALIGN=RIGHT>2008-03-10</TD> | <TD ALIGN=RIGHT>2008-03-10</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-06-04</TD><TD ALIGN=RIGHT>46.506%</TD> | ||
</TR><TR> | |||
<TH>25</TH><TH>cavPor3</TH><TD>Cavia<BR>porcellus</TD><TD>Guinea Pig</TD> | |||
<TD>Feb. 2008</TD> | |||
<TD>Broad Institute cavPor3</TD> | |||
<TD ALIGN=RIGHT>2008-04-05</TD> | |||
<TD ALIGN=RIGHT>2008-04-08</TD><TD>2009-06-06</TD><TD ALIGN=RIGHT>43.680%</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>26</TH><TH>proCap1</TH><TD>Procavia<BR>capensis</TD><TD>Rock hyrax</TD> | ||
<TD>Jul. 2008</TD> | <TD>Jul. 2008</TD> | ||
<TD>Broad Institute | <TD>Broad Institute proCap1 (NCBI project 13972, ABRQ01000000)</TD> | ||
<TD ALIGN=RIGHT>2008-10-16</TD> | <TD ALIGN=RIGHT>2008-10-16</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-26</TD><TD ALIGN=RIGHT>30.864%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>27</TH><TH>dipOrd1</TH><TD>Dipodomys<BR>ordii</TD><TD>Kangaroo rat</TD> | ||
<TD>Jul. 2008</TD> | <TD>Jul. 2008</TD> | ||
<TD>Broad Institute dipOrd1 (NCBI project 20385, ABRO01000000)</TD> | <TD>Broad Institute dipOrd1 (NCBI project 20385, ABRO01000000)</TD> | ||
<TD ALIGN=RIGHT>2008-10-15</TD> | <TD ALIGN=RIGHT>2008-10-15</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-29</TD><TD ALIGN=RIGHT>27.161%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>28</TH><TH>ochPri2</TH><TD>Ochotona<BR>princeps</TD><TD>Pika</TD> | ||
<TD>Jul. 2008</TD> | <TD>Jul. 2008</TD> | ||
<TD>Broad Institute | <TD>Broad Institute ochPri2</TD> | ||
<TD ALIGN=RIGHT>2008- | <TD ALIGN=RIGHT>2008-07-28</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-30</TD><TD ALIGN=RIGHT>27.768%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>29</TH><TH>eriEur1</TH><TD>Erinaceus<BR>europaeus</TD><TD>Hedgehog</TD> | ||
<TD> | |||
<TD> | <TD>June 2006</TD> | ||
<TD ALIGN=RIGHT> | <TD>Broad Institute eriEur1 (Draft_v1, NCBI project 12575)</TD> | ||
<TD ALIGN=RIGHT>2008- | <TD ALIGN=RIGHT>2008-10-21</TD> | ||
<TD ALIGN=RIGHT>2008-10-21</TD><TD>2009-05-30</TD><TD ALIGN=RIGHT>19.362%</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>30</TH><TH>echTel1</TH><TD>Echinops<BR>telfairi</TD><TD>Tenrec</TD> | ||
<TD>July 2005</TD> | <TD>July 2005</TD> | ||
<TD>Broad July 2005</TD> | <TD>Broad July 2005</TD> | ||
<TD ALIGN=RIGHT>2005-08-04</TD> | <TD ALIGN=RIGHT>2005-08-04</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD>N/A</TD><TD ALIGN=RIGHT>N/A</TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-28</TD><TD ALIGN=RIGHT>23.120%</TD> | ||
</TR><TR> | |||
<TH>31</TH><TH>mm9</TH><TD>Mus<BR>musculus</TD><TD>Mouse</TD> | |||
<TD>July 2007</TD> | |||
<TD>NCBI Build 37</TD> | |||
<TD ALIGN=RIGHT>2007-07-20</TD> | |||
<TD ALIGN=RIGHT>N/A</TD><TD>2009-05-13</TD><TD ALIGN=RIGHT>35.299%</TD> | |||
</TR><TR> | |||
<TH>32</TH><TH>rn4</TH><TD>Rattus<BR>norvegicus</TD><TD>Rat</TD> | |||
<TD>Nov. 2004</TD> | |||
<TD>Baylor HGSC v. 3.4</TD> | |||
<TD ALIGN=RIGHT>2006-03-16</TD> | |||
<TD ALIGN=RIGHT>N/A</TD><TD>2009-05-13</TD><TD ALIGN=RIGHT>32.879%</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>33</TH><TH>sorAra1</TH><TD>Sorex<BR>araneus</TD><TD>Shrew</TD> | ||
<TD> | |||
<TD>Broad Institute | <TD>June 2006</TD> | ||
<TD ALIGN=RIGHT>2008-10- | <TD>Broad Institute sorAra1 (Draft_v2)</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>2008-10-20</TD> | ||
<TD ALIGN=RIGHT>2008-10-21</TD><TD>2009-05-29</TD><TD ALIGN=RIGHT>19.760%</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>34</TH><TH>macEug1</TH><TD>Macropus<BR>eugenii</TD><TD>Wallaby</TD> | ||
<TD> | |||
<TD> | <TD>Nov. 2007</TD> | ||
<TD ALIGN=RIGHT> | <TD>Baylor Release 1.0</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>N/A</TD> | ||
<TD ALIGN=RIGHT>2008-12-26</TD><TD>2009-05-31</TD><TD ALIGN=RIGHT>6.011%</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>35</TH><TH>monDom5</TH><TD>Monodelphis<BR>domestica</TD><TD>Opossum</TD> | ||
<TD>Oct. 2006</TD> | <TD>Oct. 2006</TD> | ||
<TD>Broad Institute monDom5 (NCBI project 12561, accession AAFR03000000)</TD> | <TD>Broad Institute monDom5 (NCBI project 12561, accession AAFR03000000)</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>2009-07-06</TD> | ||
<TD ALIGN=RIGHT>2008-12-02</TD><TD> | <TD ALIGN=RIGHT>2008-12-02</TD><TD>2009-05-29</TD><TD ALIGN=RIGHT>14.358%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>36</TH><TH>ornAna1</TH><TD>Ornithorhynchus<BR>anatinus</TD><TD>Platypus</TD> | ||
<TD>Mar. 2007</TD> | <TD>Mar. 2007</TD> | ||
<TD>WUSTL version 5.0.1</TD> | <TD>WUSTL version 5.0.1</TD> | ||
<TD ALIGN=RIGHT>2007-07-20</TD> | <TD ALIGN=RIGHT>2007-07-20</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD> | <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-27</TD><TD ALIGN=RIGHT>7.627%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>37</TH><TH>galGal3</TH><TD>Gallus<BR>gallus</TD><TD>Chicken</TD> | ||
<TD>May 2006</TD> | <TD>May 2006</TD> | ||
<TD>Chicken Genome Sequencing Consortium May 2006 release</TD> | <TD>Chicken Genome Sequencing Consortium May 2006 release</TD> | ||
<TD ALIGN=RIGHT>2006-05-18</TD> | <TD ALIGN=RIGHT>2006-05-18</TD> | ||
<TD ALIGN=RIGHT>2007-01-02</TD><TD> | <TD ALIGN=RIGHT>2007-01-02</TD><TD>2009-05-14</TD><TD ALIGN=RIGHT>3.591%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>38</TH><TH>taeGut1</TH><TD>Taeniopygia<BR>guttata</TD><TD>Zebra finch</TD> | ||
<TD>Jul. 2008</TD> | <TD>Jul. 2008</TD> | ||
<TD>Washington University taeGut1</TD> | <TD>Washington University taeGut1</TD> | ||
<TD ALIGN=RIGHT>2009-02-04</TD> | <TD ALIGN=RIGHT>2009-02-04</TD> | ||
<TD ALIGN=RIGHT>2008-08-05</TD><TD> | <TD ALIGN=RIGHT>2008-08-05</TD><TD>2009-05-26</TD><TD ALIGN=RIGHT>3.496%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>39</TH><TH>anoCar1</TH><TD>Anolis<BR>carolinensis</TD><TD>Lizard</TD> | ||
<TD>Feb. 2007</TD> | <TD>Feb. 2007</TD> | ||
<TD>Broad Institute AnoCar (1.0)</TD> | <TD>Broad Institute AnoCar (1.0)</TD> | ||
<TD ALIGN=RIGHT>2007-03-07</TD> | <TD ALIGN=RIGHT>2007-03-07</TD> | ||
<TD ALIGN=RIGHT>2007-02-16</TD><TD> | <TD ALIGN=RIGHT>2007-02-16</TD><TD>2009-05-30</TD><TD ALIGN=RIGHT>3.591%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>40</TH><TH>xenTro2</TH><TD>Xenopus<BR>tropicalis</TD><TD>X. tropicalis</TD> | ||
<TD>Aug. 2005</TD> | <TD>Aug. 2005</TD> | ||
<TD>JGI v4.1</TD> | <TD>JGI v4.1</TD> | ||
<TD ALIGN=RIGHT>2006-04-17</TD> | <TD ALIGN=RIGHT>2006-04-17</TD> | ||
<TD ALIGN=RIGHT>2007-02-20</TD><TD> | <TD ALIGN=RIGHT>2007-02-20</TD><TD>2009-05-27</TD><TD ALIGN=RIGHT>3.176%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>41</TH><TH>gasAcu1</TH><TD>Gasterosteus<BR>aculeatus</TD><TD>Stickleback</TD> | ||
<TD> | |||
<TD> | <TD>Feb. 2006</TD> | ||
<TD ALIGN=RIGHT> | <TD>Broad Institute gasAcu1 (1.0) (NCBI project 13579, AANH01000000)</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>2006-10-17</TD> | ||
<TD ALIGN=RIGHT>2006-12-05</TD><TD>2009-05-14</TD><TD ALIGN=RIGHT>1.916%</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>42</TH><TH>fr2</TH><TD>Takifugu<BR>rubripes</TD><TD>Fugu</TD> | ||
<TD>Oct. 2004</TD> | <TD>Oct. 2004</TD> | ||
<TD>JGI V4.0</TD> | <TD>JGI V4.0</TD> | ||
<TD ALIGN=RIGHT>2007-03-07</TD> | <TD ALIGN=RIGHT>2007-03-07</TD> | ||
<TD ALIGN=RIGHT>2007-01-22</TD><TD> | <TD ALIGN=RIGHT>2007-01-22</TD><TD>2009-05-20</TD><TD ALIGN=RIGHT>1.702%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>43</TH><TH>danRer6</TH><TD>Danio<BR>rerio</TD><TD>Zebrafish</TD> | ||
<TD> | |||
<TD> | <TD>Dec. 2008</TD> | ||
<TD ALIGN=RIGHT> | <TD>Wellcome Trust Sanger Institute, Zv8 assembly (CAAK00000000.5)</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>2009-06-29</TD> | ||
<TD ALIGN=RIGHT>N/A</TD><TD>2009-07-10</TD><TD ALIGN=RIGHT>3.051%</TD> | |||
</TR><TR> | |||
<TH>44</TH><TH>tetNig2</TH><TD>Tetraodon<BR>nigroviridis</TD><TD>Tetraodon</TD> | |||
<TD>Mar. 2007</TD> | |||
<TD>Genoscope Tetraodon v8.0 (NCBI project 12350, CAAE01000000)</TD> | |||
<TD ALIGN=RIGHT>N/A</TD> | |||
<TD ALIGN=RIGHT>2009-08-07</TD><TD>2009-08-10</TD><TD ALIGN=RIGHT>1.712%</TD> | |||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>45</TH><TH>oryLat2</TH><TD>Oryzias<BR>latipes</TD><TD>Medaka</TD> | ||
<TD>Oct. 2005</TD> | <TD>Oct. 2005</TD> | ||
<TD>NIG and Tokyo Univ MEDAKA1 (NCBI project 16702, BAAF04000000)</TD> | <TD>NIG and Tokyo Univ MEDAKA1 (NCBI project 16702, BAAF04000000)</TD> | ||
<TD ALIGN=RIGHT>2008-08-12</TD> | <TD ALIGN=RIGHT>2008-08-12</TD> | ||
<TD ALIGN=RIGHT>2008-08-14</TD><TD> | <TD ALIGN=RIGHT>2008-08-14</TD><TD>2009-05-22</TD><TD ALIGN=RIGHT>1.849%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH> | <TH>46</TH><TH>petMar1</TH><TD>Petromyzon<BR>marinus</TD><TD>Lamprey</TD> | ||
<TD>Mar. 2007</TD> | <TD>Mar. 2007</TD> | ||
<TD>WUSTL v.3.0 (March 2007)</TD> | <TD>WUSTL v.3.0 (March 2007)</TD> | ||
<TD ALIGN=RIGHT>N/A</TD> | <TD ALIGN=RIGHT>N/A</TD> | ||
<TD ALIGN=RIGHT>2008-01-28</TD><TD> | <TD ALIGN=RIGHT>2008-01-28</TD><TD>2009-05-14</TD><TD ALIGN=RIGHT>1.082%</TD> | ||
</TR> | </TR> | ||
</TABLE> | </TABLE> | ||
[[Category:Comparative Genomics]] | |||
Latest revision as of 16:16, 8 October 2012
see also
- 46-way Hg19 Genome size statistics
- 46-way Hg19 conservation lastz parameters
- all other UCSC Multiple Alignments
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 hg19 |
% of hg19 matched (chainLink table) |
|
|---|---|---|---|---|---|---|---|---|---|
| 01 | hg19 | Homo sapiens | Human | GRCh37 | GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1) | 2009-04-24 | N/A | N/A | N/A |
| 02 | panTro2 | Pan troglodytes | Chimp | Mar. 2006 | Washington University Build 2 Version 1 | 2006-03-24 | N/A | 2009-03-20 | 94.846% |
| 03 | gorGor1 | Gorilla gorilla gorilla | Gorilla | Oct. 2008 | Sanger Institute Oct 2008 (NCBI project 31265, CABD01000000) | 2008-11-03 | N/A | 2009-03-22 | 59.484% |
| 04 | ponAbe2 | Pongo pygmaeus abelii | Orangutan | July 2007 | WUSTL 3.0 | 2007-09-15 | N/A | 2009-05-14 | 91.350% |
| 05 | rheMac2 | Macaca mulatta | Rhesus | Jan. 2006 | Venter Inst./Baylor/WashU Merged assembly Jan 2006 v1 edit4 | 2006-01-30 | N/A | 2009-05-14 | 82.744% |
| 06 | papHam1 | Papio hamadryas | Baboon | Nov. 2008 | Baylor BCM HGSC Pham_1.0 | 2009-05-13 | N/A | 2009-05-20 | 82.810% |
| 07 | calJac1 | Callithrix jacchus | Marmoset | June 2007 | WUSTL 2.0.2 | 2007-08-23 | N/A | 2009-05-14 | 70.860% |
| 08 | tarSyr1 | Tarsius syrichta | Tarsier | Aug. 2008 | Broad Institute tarSyr1 (NCBI project 20335, ABRT000000000) | 2008-10-15 | N/A | 2009-05-15 | 47.830% |
| 09 | micMur1 | Microcebus murinus | Mouse lemur | Jul. 2007 | Broad Institute micMur1 (NCBI project 19967, ABDC00000000) | 2008-08-03 | N/A | 2009-05-22 | 46.519% |
| 10 | otoGar1 | Otolemur garnettii | Bushbaby | Dec. 2006 | Broad version 1 (NCBI project 16955, AAQR00000000) | 2006-12-20 | N/A | 2009-05-15 | 43.644% |
| 11 | equCab2 | Equus caballus | Horse | Sep. 2007 | Broad Institute EquCab2 | 2008-04-03 | N/A | 2009-06-04 | 57.050% |
| 12 | tupBel1 | Tupaia belangeri | Tree shrew | Dec. 2006 | Broad Institute tupBel1 (NCBI project 13971, AAPY01000000) | 2008-10-15 | N/A | 2009-06-01 | 36.156% |
| 13 | turTru1 | Tursiops truncatus | Dolphin | Feb. 2008 | Broad Institute turTru1 (NCBI project 20367, ABRN01000000) | 2008-10-15 | N/A | 2009-06-04 | 48.398% |
| 14 | speTri1 | Spermophilus tridecemlineatus | Squirrel | Feb. 2008 | Broad Institute speTri1 | 2008-08-03 | N/A | 2009-06-04 | 35.713% |
| 15 | vicPac1 | Vicugna pacos | Alpaca | Jul. 2008 | Broad Institute vicPac1 | 2008-10-17 | N/A | 2009-06-04 | 39.399% |
| 16 | choHof1 | Choloepus hoffmanni | Sloth | Jul. 2008 | Broad Institute choHof1 | 2008-10-16 | N/A | 2009-06-05 | 34.377% |
| 17 | pteVam1 | Pteropus vampyrus | Megabat | Jul. 2008 | Broad Institute pteVam1 (NCBI project 20325, ABRP01000000) | 2008-10-15 | N/A | 2009-06-04 | 45.414% |
| 18 | loxAfr3 | Loxodonta africana | Elephant | Jul. 2009 | Broad Institute loxAfr3 (NCBI project 12569, AAGU03000000) | 2009-07-15 | N/A | 2009-07-22 | 46.636% |
| 19 | felCat3 | Felis catus | Cat | Mar. 2006 | Broad Release 3 | 2006-10-16 | N/A | 2009-06-04 | 35.713% |
| 20 | canFam2 | Canis lupus familiaris | Dog | May 2005 | Broad Institute v. 2.0 | 2005-07-10 | N/A | 2009-05-14 | 52.879% |
| 21 | dasNov2 | Dasypus novemcinctus | Armadillo | Jul. 2008 | Broad Institute dasNov2 (NCBI project 12594, AAGV020000000) | 2008-10-07 | N/A | 2009-05-27 | 33.543% |
| 22 | oryCun2 | Oryctolagus cuniculus | Rabbit | Apr. 2009 | Broad Institute oryCun2 (NCBI project 12819, AAGW00000000) | 2009-08-11 | N/A | 2009-08-12 | 44.317% |
| 23 | myoLuc1 | Myotis lucifugus | Microbat | Mar. 2006 | Broad Institute myoLuc1 | 2008-07-29 | N/A | 2009-06-04 | 33.174% |
| 24 | bosTau4 | Bos taurus | Cow | Oct. 2007 | Baylor Release 4.0 | 2008-03-10 | N/A | 2009-06-04 | 46.506% |
| 25 | cavPor3 | Cavia porcellus | Guinea Pig | Feb. 2008 | Broad Institute cavPor3 | 2008-04-05 | 2008-04-08 | 2009-06-06 | 43.680% |
| 26 | proCap1 | Procavia capensis | Rock hyrax | Jul. 2008 | Broad Institute proCap1 (NCBI project 13972, ABRQ01000000) | 2008-10-16 | N/A | 2009-05-26 | 30.864% |
| 27 | dipOrd1 | Dipodomys ordii | Kangaroo rat | Jul. 2008 | Broad Institute dipOrd1 (NCBI project 20385, ABRO01000000) | 2008-10-15 | N/A | 2009-05-29 | 27.161% |
| 28 | ochPri2 | Ochotona princeps | Pika | Jul. 2008 | Broad Institute ochPri2 | 2008-07-28 | N/A | 2009-05-30 | 27.768% |
| 29 | eriEur1 | Erinaceus europaeus | Hedgehog | June 2006 | Broad Institute eriEur1 (Draft_v1, NCBI project 12575) | 2008-10-21 | 2008-10-21 | 2009-05-30 | 19.362% |
| 30 | echTel1 | Echinops telfairi | Tenrec | July 2005 | Broad July 2005 | 2005-08-04 | N/A | 2009-05-28 | 23.120% |
| 31 | mm9 | Mus musculus | Mouse | July 2007 | NCBI Build 37 | 2007-07-20 | N/A | 2009-05-13 | 35.299% |
| 32 | rn4 | Rattus norvegicus | Rat | Nov. 2004 | Baylor HGSC v. 3.4 | 2006-03-16 | N/A | 2009-05-13 | 32.879% |
| 33 | sorAra1 | Sorex araneus | Shrew | June 2006 | Broad Institute sorAra1 (Draft_v2) | 2008-10-20 | 2008-10-21 | 2009-05-29 | 19.760% |
| 34 | macEug1 | Macropus eugenii | Wallaby | Nov. 2007 | Baylor Release 1.0 | N/A | 2008-12-26 | 2009-05-31 | 6.011% |
| 35 | monDom5 | Monodelphis domestica | Opossum | Oct. 2006 | Broad Institute monDom5 (NCBI project 12561, accession AAFR03000000) | 2009-07-06 | 2008-12-02 | 2009-05-29 | 14.358% |
| 36 | ornAna1 | Ornithorhynchus anatinus | Platypus | Mar. 2007 | WUSTL version 5.0.1 | 2007-07-20 | N/A | 2009-05-27 | 7.627% |
| 37 | galGal3 | Gallus gallus | Chicken | May 2006 | Chicken Genome Sequencing Consortium May 2006 release | 2006-05-18 | 2007-01-02 | 2009-05-14 | 3.591% |
| 38 | taeGut1 | Taeniopygia guttata | Zebra finch | Jul. 2008 | Washington University taeGut1 | 2009-02-04 | 2008-08-05 | 2009-05-26 | 3.496% |
| 39 | anoCar1 | Anolis carolinensis | Lizard | Feb. 2007 | Broad Institute AnoCar (1.0) | 2007-03-07 | 2007-02-16 | 2009-05-30 | 3.591% |
| 40 | xenTro2 | Xenopus tropicalis | X. tropicalis | Aug. 2005 | JGI v4.1 | 2006-04-17 | 2007-02-20 | 2009-05-27 | 3.176% |
| 41 | gasAcu1 | Gasterosteus aculeatus | Stickleback | Feb. 2006 | Broad Institute gasAcu1 (1.0) (NCBI project 13579, AANH01000000) | 2006-10-17 | 2006-12-05 | 2009-05-14 | 1.916% |
| 42 | fr2 | Takifugu rubripes | Fugu | Oct. 2004 | JGI V4.0 | 2007-03-07 | 2007-01-22 | 2009-05-20 | 1.702% |
| 43 | danRer6 | Danio rerio | Zebrafish | Dec. 2008 | Wellcome Trust Sanger Institute, Zv8 assembly (CAAK00000000.5) | 2009-06-29 | N/A | 2009-07-10 | 3.051% |
| 44 | tetNig2 | Tetraodon nigroviridis | Tetraodon | Mar. 2007 | Genoscope Tetraodon v8.0 (NCBI project 12350, CAAE01000000) | N/A | 2009-08-07 | 2009-08-10 | 1.712% |
| 45 | oryLat2 | Oryzias latipes | Medaka | Oct. 2005 | NIG and Tokyo Univ MEDAKA1 (NCBI project 16702, BAAF04000000) | 2008-08-12 | 2008-08-14 | 2009-05-22 | 1.849% |
| 46 | petMar1 | Petromyzon marinus | Lamprey | Mar. 2007 | WUSTL v.3.0 (March 2007) | N/A | 2008-01-28 | 2009-05-14 | 1.082% |
