Hg19 conservation lastz parameters: 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 alignment]]</LI>
<LI>46-way [[Hg19 conservation alignment]]</LI>
<LI>[[Hg19 Andy's alignment notes]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
<LI>[[Hg18 44way blastz parameters]]</LI>
<LI>[[Genome size statistics|Hg18 Genome size statistics]]</LI>
<LI>[[Hg18 44way alignment]]</LI>
</UL>
</UL>
<TABLE BORDER=0>
<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>
<TR><TH>&nbsp;</TH><TH>A</TH><TH>C</TH><TH>G</TH><TH>T</TH></TR>
<TR><TH>A</TH><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>
<TR><TH>C</TH><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>
<TR><TH>G</TH><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>
<TR><TH>T</TH><TD>-123</TD><TD>-31</TD><TD>-114</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>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>
<TR><TH>C</TH><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>
<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==
==do not edit, automatically generated table==


<TABLE BORDER=1>
<TABLE BORDER=1>
<TR>
<TR><TH>query</TH>
   <TH>&nbsp;</TH>
   <TH>abridged<BR>repeats(no)</TH>
   <TH>UCSC<BR>db&nbsp;name</TH>
   <TH>M(40M)</TH><TH>K(3000)</TH>
   <TD>Scientific<BR>name</TD>
   <TH>L(3000)</TH><TH>Q</TH><TH>Y(9400)</TH>
   <TD>Common<BR>name</TD>
   <TH>program<BR>run</TH><TH>E(30)</TH><TH>H(0)</TH>


   <TD>assembly<BR>date</TD>
   <TH>O(400)</TH><TH>T(1)</TH>
  <TD>source<BR>version</TD>
   <TH>chain&nbsp;table<BR>date</TH>
   <TD>Repeat<BR>Masker</TD>
   <TH>%&nbsp;of&nbsp;hg19<BR>matched<BR>(chainLink&nbsp;table)</TH>
   <TD>Window<BR>Masker</TD>
  <TD>chain<BR>on&nbsp;hg19</TD>


   <TD>%&nbsp;of&nbsp;hg19<BR>matched<BR>(chainLink&nbsp;table)</TD>
   <TH>%&nbsp;of&nbsp;query<BR>matched<BR>(chainLinkHg19)</TH>
</TR>
</TR>
<TR>
<TR>
   <TH>01</TH><TH>hg19</TH><TD>Homo<BR>sapiens</TD><TD>Human</TD>
   <TH>Chimp&nbsp;panTro2</TH>
  <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD>


   <TD>Feb.&nbsp;2009</TD>
   <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD>
  <TD>GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1)</TD>
  <TD>2009-03-20</TD><TD ALIGN=RIGHT>94.846%</TD>
  <TD ALIGN=RIGHT>2009-04-24</TD>
  <TD ALIGN=RIGHT>94.908%</TD></TR>
  <TD ALIGN=RIGHT>N/A</TD><TD>N/A</TD><TD ALIGN=RIGHT>N/A</TD>
<TR>
</TR><TR>
  <TH>Gorilla&nbsp;gorGor1</TH>
  <TH>02</TH><TH>panTro2</TH><TD>Pan<BR>troglodytes</TD><TD>Chimp</TD>


   <TD>Mar.&nbsp;2006</TD>
   <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD>
  <TD>Washington University Build 2 Version 1</TD>
  <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD>
  <TD ALIGN=RIGHT>2006-03-24</TD>
  <TD>2009-03-22</TD><TD ALIGN=RIGHT>59.484%</TD>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-03-20</TD><TD ALIGN=RIGHT>94.846%</TD>
</TR><TR>
  <TH>03</TH><TH>gorGor1</TH><TD>Gorilla<BR>gorilla<BR>gorilla</TD><TD>Gorilla</TD>


   <TD>Oct.&nbsp;2008</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD>Sanger Institute Oct 2008 (NCBI project 31265, CABD01000000)</TD>
<TR>
  <TD ALIGN=RIGHT>2008-11-03</TD>
  <TH>Orangutan&nbsp;ponAbe2</TH>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-03-22</TD><TD ALIGN=RIGHT>59.484%</TD>
   <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD>
</TR><TR>
  <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD>
  <TH>04</TH><TH>ponAbe2</TH><TD>Pongo<BR>pygmaeus<BR>abelii</TD><TD>Orangutan</TD>


   <TD>July&nbsp;2007</TD>
   <TD>2009-05-14</TD><TD ALIGN=RIGHT>91.350%</TD>
  <TD>WUSTL 3.0</TD>
   <TD ALIGN=RIGHT>89.617%</TD></TR>
  <TD ALIGN=RIGHT>2007-09-15</TD>
<TR>
   <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-14</TD><TD ALIGN=RIGHT>91.350%</TD>
   <TH>Rhesus&nbsp;rheMac2</TH>
</TR><TR>
  <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD>
   <TH>05</TH><TH>rheMac2</TH><TD>Macaca<BR>mulatta</TD><TD>Rhesus</TD>


   <TD>Jan.&nbsp;2006</TD>
   <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD>
  <TD>Venter Inst./Baylor/WashU Merged assembly Jan 2006 v1 edit4</TD>
  <TD>2009-05-14</TD><TD ALIGN=RIGHT>82.744%</TD>
  <TD ALIGN=RIGHT>2006-01-30</TD>
  <TD ALIGN=RIGHT>87.422%</TD></TR>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-14</TD><TD ALIGN=RIGHT>82.744%</TD>
<TR>
</TR><TR>
   <TH>Baboon&nbsp;papHam1</TH>
   <TH>06</TH><TH>papHam1</TH><TD>Papio<BR>hamadryas</TD><TD>Baboon</TD>


   <TD>Nov.&nbsp;2008</TD>
   <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD>
  <TD>Baylor BCM HGSC Pham_1.0</TD>
  <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD>
  <TD ALIGN=RIGHT>2009-05-13</TD>
  <TD>2009-05-20</TD><TD ALIGN=RIGHT>82.810%</TD>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-20</TD><TD ALIGN=RIGHT>82.810%</TD>
</TR><TR>
  <TH>07</TH><TH>calJac1</TH><TD>Callithrix<BR>jacchus</TD><TD>Marmoset</TD>


   <TD>June&nbsp;2007</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD>WUSTL 2.0.2</TD>
<TR>
  <TD ALIGN=RIGHT>2007-08-23</TD>
  <TH>Marmoset&nbsp;calJac1</TH>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-14</TD><TD ALIGN=RIGHT>70.860%</TD>
   <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD>
</TR><TR>
  <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD>
  <TH>08</TH><TH>tarSyr1</TH><TD>Tarsius<BR>syrichta</TD><TD>Tarsier</TD>


   <TD>Aug.&nbsp;2008</TD>
   <TD>2009-05-14</TD><TD ALIGN=RIGHT>70.860%</TD>
  <TD>Broad Institute tarSyr1 (NCBI project 20335, ABRT000000000)</TD>
   <TD ALIGN=RIGHT>71.897%</TD></TR>
  <TD ALIGN=RIGHT>2008-10-15</TD>
<TR>
   <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-15</TD><TD ALIGN=RIGHT>47.830%</TD>
   <TH>Tarsier&nbsp;tarSyr1</TH>
</TR><TR>
  <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <TH>09</TH><TH>micMur1</TH><TD>Microcebus<BR>murinus</TD><TD>Mouse&nbsp;lemur</TD>


   <TD>Jun.&nbsp;2003</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>Broad Institute micMur1 (NCBI project 19967, ABDC00000000)</TD>
  <TD>2009-05-15</TD><TD ALIGN=RIGHT>47.830%</TD>
  <TD ALIGN=RIGHT>2008-08-03</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-22</TD><TD ALIGN=RIGHT>46.519%</TD>
<TR>
</TR><TR>
  <TH>Mouse lemur&nbsp;micMur1</TH>
   <TH>10</TH><TH>otoGar1</TH><TD>Otolemur<BR>garnettii</TD><TD>Bushbaby</TD>


   <TD>Dec.&nbsp;2006</TD>
   <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>Broad version 1 (NCBI project 16955, AAQR00000000)</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD ALIGN=RIGHT>2006-12-20</TD>
  <TD>2009-05-22</TD><TD ALIGN=RIGHT>46.519%</TD>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-15</TD><TD ALIGN=RIGHT>43.644%</TD>
</TR><TR>
  <TH>11</TH><TH>equCab2</TH><TD>Equus<BR>caballus</TD><TD>Horse</TD>


   <TD>Sep.&nbsp;2007</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD>Broad Institute EquCab2</TD>
<TR>
  <TD ALIGN=RIGHT>2008-04-03</TD>
  <TH>Bushbaby&nbsp;otoGar1</TH>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-22</TD><TD ALIGN=RIGHT>57.051%</TD>
   <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
</TR><TR>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TH>12</TH><TH>tupBel1</TH><TD>Tupaia<BR>belangeri</TD><TD>TreeShrew</TD>


   <TD>Dec.&nbsp;2006</TD>
   <TD>2009-05-15</TD><TD ALIGN=RIGHT>43.644%</TD>
  <TD>Broad Institute tupBel1 (NCBI project 13971, AAPY01000000)</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
  <TD ALIGN=RIGHT>2008-10-15</TD>
<TR>
   <TD ALIGN=RIGHT>N/A</TD><TD>N/A</TD><TD ALIGN=RIGHT>N/A</TD>
  <TH>Horse&nbsp;equCab2</TH>
</TR><TR>
  <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TH>13</TH><TH>turTru1</TH><TD>Tursiops<BR>truncatus</TD><TD>Dolphin</TD>


   <TD>Feb.&nbsp;2008</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>Broad Institute turTru1 (NCBI project 20367, ABRN01000000)</TD>
  <TD>2009-06-04</TD><TD ALIGN=RIGHT>57.050%</TD>
  <TD ALIGN=RIGHT>2008-10-15</TD>
  <TD ALIGN=RIGHT>66.774%</TD></TR>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-29</TD><TD ALIGN=RIGHT>48.400%</TD>
<TR>
</TR><TR>
   <TH>Tree shrew&nbsp;tupBel1</TH>
   <TH>14</TH><TH>speTri1</TH><TD>Spermophilus<BR>tridecemlineatus</TD><TD>Squirrel</TD>


   <TD>Feb.&nbsp;2008</TD>
   <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>Broad Institute speTri1</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD ALIGN=RIGHT>2008-08-03</TD>
  <TD>2009-06-01</TD><TD ALIGN=RIGHT>36.156%</TD>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-15</TD><TD ALIGN=RIGHT>35.712%</TD>
</TR><TR>
  <TH>15</TH><TH>vicPac1</TH><TD>Vicugna<BR>pacos</TD><TD>Alpaca</TD>


   <TD>Jul.&nbsp;2008</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD>Broad Institute vicPac1</TD>
<TR>
  <TD ALIGN=RIGHT>2008-10-17</TD>
  <TH>Dolphin&nbsp;turTru1</TH>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-29</TD><TD ALIGN=RIGHT>39.399%</TD>
   <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
</TR><TR>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TH>16</TH><TH>choHof1</TH><TD>Choloepus<BR>hoffmanni</TD><TD>Sloth</TD>


   <TD>Jul.&nbsp;2008</TD>
   <TD>2009-06-04</TD><TD ALIGN=RIGHT>48.398%</TD>
  <TD>Broad Institute choHof1</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
  <TD ALIGN=RIGHT>2008-10-16</TD>
<TR>
   <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-26</TD><TD ALIGN=RIGHT>34.376%</TD>
  <TH>Squirrel&nbsp;speTri1</TH>
</TR><TR>
  <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TH>17</TH><TH>pteVam1</TH><TD>Pteropus<BR>vampyrus</TD><TD>Megabat</TD>


   <TD>Jul.&nbsp;2008</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>Broad Institute pteVam1 (NCBI project 20325, ABRP01000000)</TD>
  <TD>2009-06-04</TD><TD ALIGN=RIGHT>35.713%</TD>
  <TD ALIGN=RIGHT>2008-10-15</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-21</TD><TD ALIGN=RIGHT>45.416%</TD>
<TR>
</TR><TR>
  <TH>Alpaca&nbsp;vicPac1</TH>
   <TH>18</TH><TH>loxAfr2</TH><TD>Loxodonta<BR>africana</TD><TD>Elephant</TD>


   <TD>Jul.&nbsp;2008</TD>
   <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>Broad Institute loxAfr2 (NCBI project 12569, AAGU02000000)</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD ALIGN=RIGHT>2008-10-07</TD>
  <TD>2009-06-04</TD><TD ALIGN=RIGHT>39.399%</TD>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-28</TD><TD ALIGN=RIGHT>35.153%</TD>
</TR><TR>
  <TH>19</TH><TH>felCat3</TH><TD>Felis<BR>catus</TD><TD>Cat</TD>


   <TD>Mar.&nbsp;2006</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD>Broad Release 3</TD>
<TR>
  <TD ALIGN=RIGHT>2006-10-16</TD>
  <TH>Sloth&nbsp;choHof1</TH>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-14</TD><TD ALIGN=RIGHT>35.717%</TD>
   <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
</TR><TR>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TH>20</TH><TH>canFam2</TH><TD>Canis<BR>lupus<BR>familiaris</TD><TD>Dog</TD>


   <TD>May&nbsp;2005</TD>
   <TD>2009-06-05</TD><TD ALIGN=RIGHT>34.377%</TD>
  <TD>Broad Institute v. 2.0</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
  <TD ALIGN=RIGHT>2005-07-10</TD>
<TR>
   <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-14</TD><TD ALIGN=RIGHT>52.879%</TD>
  <TH>Megabat&nbsp;pteVam1</TH>
</TR><TR>
  <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TH>21</TH><TH>dasNov2</TH><TD>Dasypus<BR>novemcinctus</TD><TD>Armadillo</TD>


   <TD>Jul.&nbsp;2008</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>Broad Institute dasNov2 (NCBI project 12594, AAGV020000000)</TD>
  <TD>2009-06-04</TD><TD ALIGN=RIGHT>45.414%</TD>
  <TD ALIGN=RIGHT>2008-10-07</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-27</TD><TD ALIGN=RIGHT>33.543%</TD>
<TR>
</TR><TR>
  <TH>Elephant&nbsp;loxAfr3</TH>
   <TH>22</TH><TH>oryCun1</TH><TD>Oryctolagus<BR>cuniculus</TD><TD>Rabbit</TD>


   <TD>May&nbsp;2005</TD>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>Broad May 2005</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD ALIGN=RIGHT>2005-05-22</TD>
  <TD>2009-07-22</TD><TD ALIGN=RIGHT>46.636%</TD>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-29</TD><TD ALIGN=RIGHT>33.676%</TD>
</TR><TR>
  <TH>23</TH><TH>myoLuc1</TH><TD>Myotis<BR>lucifugus</TD><TD>Microbat</TD>


   <TD>Mar.&nbsp;2006</TD>
   <TD ALIGN=RIGHT>42.430%</TD></TR>
   <TD>Broad Institute myoLuc1</TD>
<TR>
  <TD ALIGN=RIGHT>2008-07-29</TD>
  <TH>Cat&nbsp;felCat3</TH>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-31</TD><TD ALIGN=RIGHT>33.173%</TD>
   <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
</TR><TR>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TH>24</TH><TH>bosTau4</TH><TD>Bos<BR>taurus</TD><TD>Cow</TD>


   <TD>Oct.&nbsp;2007</TD>
   <TD>2009-06-04</TD><TD ALIGN=RIGHT>35.713%</TD>
  <TD>Baylor Release 4.0</TD>
   <TD ALIGN=RIGHT>61.104%</TD></TR>
  <TD ALIGN=RIGHT>2008-03-10</TD>
<TR>
   <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-21</TD><TD ALIGN=RIGHT>46.507%</TD>
   <TH>Dog&nbsp;canFam2</TH>
</TR><TR>
  <TD>yes</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <TH>25</TH><TH>cavPor3</TH><TD>Cavia<BR>porcellus</TD><TD>Guinea&nbsp;Pig</TD>


   <TD>Feb.&nbsp;2008</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>Broad Institute cavPor3</TD>
  <TD>2009-05-14</TD><TD ALIGN=RIGHT>52.879%</TD>
  <TD ALIGN=RIGHT>2008-04-05</TD>
  <TD ALIGN=RIGHT>62.055%</TD></TR>
  <TD ALIGN=RIGHT>2008-04-08</TD><TD>2009-05-29</TD><TD ALIGN=RIGHT>-</TD>
<TR>
</TR><TR>
  <TH>Armadillo&nbsp;dasNov2</TH>
  <TH>26</TH><TH>proCap1</TH><TD>Procavia<BR>capensis</TD><TD>Rock&nbsp;hyrax</TD>


   <TD>Jul.&nbsp;2008</TD>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>Broad Institute proCap1 (NCBI project 13972, ABRQ01000000)</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD ALIGN=RIGHT>2008-10-16</TD>
  <TD>2009-05-27</TD><TD ALIGN=RIGHT>33.543%</TD>
   <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-26</TD><TD ALIGN=RIGHT>30.864%</TD>
</TR><TR>
  <TH>27</TH><TH>dipOrd1</TH><TD>Dipodomys<BR>ordii</TD><TD>Kangaroo&nbsp;rat</TD>


   <TD>Jul.&nbsp;2008</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD>Broad Institute dipOrd1 (NCBI project 20385, ABRO01000000)</TD>
<TR>
  <TD ALIGN=RIGHT>2008-10-15</TD>
  <TH>Rabbit&nbsp;oryCun2</TH>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-29</TD><TD ALIGN=RIGHT>27.161%</TD>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
</TR><TR>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TH>28</TH><TH>ochPri2</TH><TD>Ochotona<BR>princeps</TD><TD>Pika</TD>


   <TD>Jul.&nbsp;2008</TD>
   <TD>2009-08-12</TD><TD ALIGN=RIGHT>44.317%</TD>
  <TD>Broad Institute ochPri2</TD>
   <TD ALIGN=RIGHT>48.405%</TD></TR>
  <TD ALIGN=RIGHT>2008-07-28</TD>
<TR>
   <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-30</TD><TD ALIGN=RIGHT>27.768%</TD>
   <TH>Microbat&nbsp;myoLuc1</TH>
</TR><TR>
  <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <TH>29</TH><TH>eriEur1</TH><TD>Erinaceus<BR>europaeus</TD><TD>Hedgehog</TD>


   <TD>June&nbsp;2006</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>Broad Institute eriEur1 (Draft_v1, NCBI project 12575)</TD>
  <TD>2009-06-04</TD><TD ALIGN=RIGHT>33.174%</TD>
  <TD ALIGN=RIGHT>2008-10-21</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
  <TD ALIGN=RIGHT>2008-10-21</TD><TD>2009-05-30</TD><TD ALIGN=RIGHT>19.362%</TD>
<TR>
</TR><TR>
  <TH>Cow&nbsp;bosTau4</TH>
   <TH>30</TH><TH>echTel1</TH><TD>Echinops<BR>telfairi</TD><TD>Tenrec</TD>


   <TD>July&nbsp;2005</TD>
   <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>Broad July 2005</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD ALIGN=RIGHT>2005-08-04</TD>
  <TD>2009-06-04</TD><TD ALIGN=RIGHT>46.506%</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&nbsp;2007</TD>
   <TD ALIGN=RIGHT>50.297%</TD></TR>
   <TD>NCBI Build 37</TD>
<TR>
  <TD ALIGN=RIGHT>2007-07-20</TD>
  <TH>Guinea Pig&nbsp;cavPor3</TH>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-13</TD><TD ALIGN=RIGHT>35.299%</TD>
   <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
</TR><TR>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TH>32</TH><TH>rn4</TH><TD>Rattus<BR>norvegicus</TD><TD>Rat</TD>


   <TD>Nov.&nbsp;2004</TD>
   <TD>2009-06-06</TD><TD ALIGN=RIGHT>43.680%</TD>
  <TD>Baylor HGSC v. 3.4</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
  <TD ALIGN=RIGHT>2006-03-16</TD>
<TR>
   <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-13</TD><TD ALIGN=RIGHT>32.879%</TD>
  <TH>Rock hyrax&nbsp;proCap1</TH>
</TR><TR>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TH>33</TH><TH>sorAra1</TH><TD>Sorex<BR>araneus</TD><TD>Shrew</TD>


   <TD>June&nbsp;2006</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>Broad Institute sorAra1 (Draft_v2)</TD>
  <TD>2009-05-26</TD><TD ALIGN=RIGHT>30.864%</TD>
  <TD ALIGN=RIGHT>2008-10-20</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
  <TD ALIGN=RIGHT>2008-10-21</TD><TD>2009-05-29</TD><TD ALIGN=RIGHT>19.760%</TD>
<TR>
</TR><TR>
  <TH>Kangaroo rat&nbsp;dipOrd1</TH>
   <TH>34</TH><TH>macEug1</TH><TD>Macropus<BR>eugenii</TD><TD>Wallaby</TD>


   <TD>Nov.&nbsp;2007</TD>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>Baylor Release 1.0</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD ALIGN=RIGHT>N/A</TD>
  <TD>2009-05-29</TD><TD ALIGN=RIGHT>27.161%</TD>
   <TD ALIGN=RIGHT>2008-12-26</TD><TD>2009-05-31</TD><TD ALIGN=RIGHT>6.011%</TD>
</TR><TR>
  <TH>35</TH><TH>monDom5</TH><TD>Monodelphis<BR>domestica</TD><TD>Opossum</TD>


   <TD>Oct.&nbsp;2006</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD>Broad Institute monDom5 (NCBI project 12561, accession AAFR03000000)</TD>
<TR>
  <TD ALIGN=RIGHT>2008-11-26</TD>
  <TH>Pika&nbsp;ochPri2</TH>
  <TD ALIGN=RIGHT>2008-12-02</TD><TD>2009-05-29</TD><TD ALIGN=RIGHT>14.358%</TD>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
</TR><TR>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TH>36</TH><TH>ornAna1</TH><TD>Ornithorhynchus<BR>anatinus</TD><TD>Platypus</TD>


   <TD>Mar.&nbsp;2007</TD>
   <TD>2009-05-30</TD><TD ALIGN=RIGHT>27.768%</TD>
  <TD>WUSTL version 5.0.1</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
  <TD ALIGN=RIGHT>2007-07-20</TD>
<TR>
   <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-27</TD><TD ALIGN=RIGHT>7.627%</TD>
  <TH>Hedgehog&nbsp;eriEur1</TH>
</TR><TR>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TH>37</TH><TH>galGal3</TH><TD>Gallus<BR>gallus</TD><TD>Chicken</TD>


   <TD>May&nbsp;2006</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>Chicken Genome Sequencing Consortium May 2006 release</TD>
  <TD>2009-05-30</TD><TD ALIGN=RIGHT>19.362%</TD>
  <TD ALIGN=RIGHT>2006-05-18</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
  <TD ALIGN=RIGHT>2007-01-02</TD><TD>2009-05-14</TD><TD ALIGN=RIGHT>3.591%</TD>
<TR>
</TR><TR>
  <TH>Tenrec&nbsp;echTel1</TH>
   <TH>38</TH><TH>taeGut1</TH><TD>Taeniopygia<BR>guttata</TD><TD>Zebra&nbsp;finch</TD>


   <TD>Jul.&nbsp;2008</TD>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>Washington University taeGut1</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD ALIGN=RIGHT>2009-02-04</TD>
  <TD>2009-05-28</TD><TD ALIGN=RIGHT>23.120%</TD>
  <TD ALIGN=RIGHT>2008-08-05</TD><TD>2009-05-26</TD><TD ALIGN=RIGHT>3.496%</TD>
</TR><TR>
  <TH>39</TH><TH>anoCar1</TH><TD>Anolis<BR>carolinensis</TD><TD>Lizard</TD>


   <TD>Feb.&nbsp;2007</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD>Broad Institute AnoCar (1.0)</TD>
<TR>
  <TD ALIGN=RIGHT>2007-03-07</TD>
  <TH>Mouse&nbsp;mm9</TH>
  <TD ALIGN=RIGHT>2007-02-16</TD><TD>2009-05-30</TD><TD ALIGN=RIGHT>3.591%</TD>
   <TD>yes</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
</TR><TR>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TH>40</TH><TH>xenTro2</TH><TD>Xenopus<BR>tropicalis</TD><TD>X.&nbsp;tropicalis</TD>


   <TD>Aug.&nbsp;2005</TD>
   <TD>2009-05-13</TD><TD ALIGN=RIGHT>35.299%</TD>
  <TD>JGI v4.1</TD>
   <TD ALIGN=RIGHT>38.693%</TD></TR>
  <TD ALIGN=RIGHT>2006-04-17</TD>
<TR>
   <TD ALIGN=RIGHT>2007-02-20</TD><TD>2009-05-27</TD><TD ALIGN=RIGHT>3.176%</TD>
   <TH>Rat&nbsp;rn4</TH>
</TR><TR>
  <TD>yes</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <TH>41</TH><TH>gasAcu1</TH><TD>Gasterosteus<BR>aculeatus</TD><TD>Stickleback</TD>


   <TD>Feb.&nbsp;2006</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>Broad Institute gasAcu1 (1.0) (NCBI project 13579, AANH01000000)</TD>
  <TD>2009-05-13</TD><TD ALIGN=RIGHT>32.879%</TD>
  <TD ALIGN=RIGHT>2006-10-17</TD>
  <TD ALIGN=RIGHT>36.860%</TD></TR>
  <TD ALIGN=RIGHT>2006-12-05</TD><TD>2009-05-14</TD><TD ALIGN=RIGHT>1.916%</TD>
<TR>
</TR><TR>
   <TH>Shrew&nbsp;sorAra1</TH>
   <TH>42</TH><TH>fr2</TH><TD>Takifugu<BR>rubripes</TD><TD>Fugu</TD>


   <TD>Oct.&nbsp;2004</TD>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>JGI V4.0</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD ALIGN=RIGHT>2007-03-07</TD>
  <TD>2009-05-29</TD><TD ALIGN=RIGHT>19.760%</TD>
  <TD ALIGN=RIGHT>2007-01-22</TD><TD>2009-05-20</TD><TD ALIGN=RIGHT>1.702%</TD>
</TR><TR>
  <TH>43</TH><TH>danRer5</TH><TD>Danio<BR>rerio</TD><TD>Zebrafish</TD>


   <TD>July&nbsp;2007</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD>Wellcome Trust Sanger Institute, Zv7 assembly</TD>
<TR>
  <TD ALIGN=RIGHT>2007-09-05</TD>
  <TH>Wallaby&nbsp;macEug1</TH>
  <TD ALIGN=RIGHT>N/A</TD><TD>2009-05-26</TD><TD ALIGN=RIGHT>2.562%</TD>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
</TR><TR>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TH>44</TH><TH>tetNig1</TH><TD>Tetraodon<BR>nigroviridis</TD><TD>Tetraodon</TD>


   <TD>Feb.&nbsp;2004</TD>
   <TD>2009-05-31</TD><TD ALIGN=RIGHT>6.011%</TD>
  <TD>Genoscope and Broad Institute V7 (NCBI project 12350, CAAE01000000)</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
  <TD ALIGN=RIGHT>2004-08-17</TD>
<TR>
   <TD ALIGN=RIGHT>2006-12-05</TD><TD>2009-05-14</TD><TD ALIGN=RIGHT>2.003%</TD>
  <TH>Opossum&nbsp;monDom5</TH>
</TR><TR>
  <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TH>45</TH><TH>oryLat2</TH><TD>Oryzias<BR>latipes</TD><TD>Medaka</TD>


   <TD>Oct.&nbsp;2005</TD>
   <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>NIG and Tokyo Univ MEDAKA1 (NCBI project 16702, BAAF04000000)</TD>
  <TD>2009-05-29</TD><TD ALIGN=RIGHT>14.358%</TD>
  <TD ALIGN=RIGHT>2008-08-12</TD>
  <TD ALIGN=RIGHT>11.615%</TD></TR>
  <TD ALIGN=RIGHT>2008-08-14</TD><TD>2009-05-22</TD><TD ALIGN=RIGHT>1.849%</TD>
<TR>
</TR><TR>
   <TH>Platypus&nbsp;ornAna1</TH>
   <TH>46</TH><TH>petMar1</TH><TD>Petromyzon<BR>marinus</TD><TD>Lamprey</TD>


   <TD>Mar.&nbsp;2007</TD>
   <TD>no</TD><TD>40M</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
   <TD>WUSTL v.3.0 (March 2007)</TD>
  <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TD ALIGN=RIGHT>N/A</TD>
  <TD>2009-05-27</TD><TD ALIGN=RIGHT>7.627%</TD>
   <TD ALIGN=RIGHT>2008-01-28</TD><TD>2009-05-14</TD><TD ALIGN=RIGHT>1.082%</TD>
 
</TR>
  <TD ALIGN=RIGHT>11.259%</TD></TR>
<TR>
  <TH>Chicken&nbsp;galGal3</TH>
  <TD>yes</TD><TD>40M</TD><TD>2200</TD><TD>10000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
 
  <TD>2009-05-14</TD><TD ALIGN=RIGHT>3.591%</TD>
  <TD ALIGN=RIGHT>8.786%</TD></TR>
<TR>
  <TH>Zebra finch&nbsp;taeGut1</TH>
  <TD>no</TD><TD>40M</TD><TD>2200</TD><TD>10000</TD><TD>HoxD55.q</TD>
 
  <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2009-05-26</TD><TD ALIGN=RIGHT>3.496%</TD>
  <TD ALIGN=RIGHT>7.795%</TD></TR>
<TR>
  <TH>Lizard&nbsp;anoCar1</TH>
 
  <TD>no</TD><TD>40M</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TD>2009-05-30</TD><TD ALIGN=RIGHT>3.591%</TD>
 
  <TD ALIGN=RIGHT>5.146%</TD></TR>
<TR>
  <TH>X. tropicalis&nbsp;xenTro2</TH>
  <TD>no</TD><TD>40M</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
 
  <TD>2009-05-27</TD><TD ALIGN=RIGHT>3.176%</TD>
  <TD ALIGN=RIGHT>6.773%</TD></TR>
<TR>
  <TH>Stickleback&nbsp;gasAcu1</TH>
  <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
 
  <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>2009-05-14</TD><TD ALIGN=RIGHT>1.916%</TD>
  <TD ALIGN=RIGHT>11.175%</TD></TR>
<TR>
  <TH>Fugu&nbsp;fr2</TH>
 
  <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>2009-05-20</TD><TD ALIGN=RIGHT>1.702%</TD>
 
  <TD ALIGN=RIGHT>10.929%</TD></TR>
<TR>
  <TH>Zebrafish&nbsp;danRer6</TH>
  <TD>no</TD><TD>40M</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
 
  <TD>2009-07-10</TD><TD ALIGN=RIGHT>3.051%</TD>
  <TD ALIGN=RIGHT>6.399%</TD></TR>
<TR>
  <TH>Tetraodon&nbsp;tetNig2</TH>
  <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>2009-08-10</TD><TD ALIGN=RIGHT>1.712%</TD>
   <TD ALIGN=RIGHT>14.194%</TD></TR>
<TR>
  <TH>Medaka&nbsp;oryLat2</TH>
  <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>2009-05-22</TD><TD ALIGN=RIGHT>1.849%</TD>
  <TD ALIGN=RIGHT>6.705%</TD></TR>
<TR>
  <TH>Lamprey&nbsp;petMar1</TH>
  <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>2009-05-14</TD><TD ALIGN=RIGHT>1.082%</TD>
  <TD ALIGN=RIGHT>3.200%</TD></TR>
</TABLE>
</TABLE>


[[Category:Comparative Genomics]]
[[Category:Comparative Genomics]]

Latest revision as of 22:29, 18 May 2011

See Also:

The default
scoring matrix is:		  The HoxD55
scoring matrix is:		 The human-chimp.v2
scoring matrix is:
 ACGT
A91-114-31-123
C-114100-125-31
G-31-125100-114
T-123-31-11491

O=400 E=30

 
 ACGT
A91-90-25-100
C-90100-100-25
G-25-100100-90
T-100-25-9091

O=400 E=30

 
 ACGT
A90-330-236-356
C-330100-318-236
G-236-318100-330
T-356-236-33090

O=600 E=150

do not edit, automatically generated table

query abridged
repeats(no)		 M(40M)K(3000) L(3000)QY(9400) program
run		E(30)H(0) O(400)T(1) chain table
date		 % of hg19
matched
(chainLink table)		 % of query
matched
(chainLinkHg19)
Chimp panTro2 no25445003000human_chimp.v2.q 15000lastz15006002 2009-03-2094.846% 94.908%
Gorilla gorGor1 no25445003000human_chimp.v2.q 15000lastz15006002 2009-03-2259.484% N/A
Orangutan ponAbe2 no25445003000human_chimp.v2.q 15000lastz15006002 2009-05-1491.350% 89.617%
Rhesus rheMac2 no25445003000human_chimp.v2.q 15000lastz15006002 2009-05-1482.744% 87.422%
Baboon papHam1 no25445003000human_chimp.v2.q 15000lastz15006002 2009-05-2082.810% N/A
Marmoset calJac1 no25445003000human_chimp.v2.q 15000lastz15006002 2009-05-1470.860% 71.897%
Tarsier tarSyr1 no40M30003000default 9400lastz3004001 2009-05-1547.830% N/A
Mouse lemur micMur1 no40M30003000default 9400lastz3004001 2009-05-2246.519% N/A
Bushbaby otoGar1 no40M30003000default 9400lastz3004001 2009-05-1543.644% N/A
Horse equCab2 no40M30003000default 9400lastz3004001 2009-06-0457.050% 66.774%
Tree shrew tupBel1 no40M30003000default 9400lastz3004001 2009-06-0136.156% N/A
Dolphin turTru1 no40M30003000default 9400lastz3004001 2009-06-0448.398% N/A
Squirrel speTri1 no40M30003000default 9400lastz3004001 2009-06-0435.713% N/A
Alpaca vicPac1 no40M30003000default 9400lastz3004001 2009-06-0439.399% N/A
Sloth choHof1 no40M30003000default 9400lastz3004001 2009-06-0534.377% N/A
Megabat pteVam1 no40M30003000default 9400lastz3004001 2009-06-0445.414% N/A
Elephant loxAfr3 no5030003000default 9400lastz3004001 2009-07-2246.636% 42.430%
Cat felCat3 no40M30003000default 9400lastz3004001 2009-06-0435.713% 61.104%
Dog canFam2 yes40M30003000default 9400lastz3004001 2009-05-1452.879% 62.055%
Armadillo dasNov2 no5030003000default 9400lastz3004001 2009-05-2733.543% N/A
Rabbit oryCun2 no5030003000default 9400lastz3004001 2009-08-1244.317% 48.405%
Microbat myoLuc1 no40M30003000default 9400lastz3004001 2009-06-0433.174% N/A
Cow bosTau4 no40M30003000default 9400lastz3004001 2009-06-0446.506% 50.297%
Guinea Pig cavPor3 no40M30003000default 9400lastz3004001 2009-06-0643.680% N/A
Rock hyrax proCap1 no5030003000default 9400lastz3004001 2009-05-2630.864% N/A
Kangaroo rat dipOrd1 no5030003000default 9400lastz3004001 2009-05-2927.161% N/A
Pika ochPri2 no5030003000default 9400lastz3004001 2009-05-3027.768% N/A
Hedgehog eriEur1 no5030003000default 9400lastz3004001 2009-05-3019.362% N/A
Tenrec echTel1 no5030003000default 9400lastz3004001 2009-05-2823.120% N/A
Mouse mm9 yes40M30003000default 9400lastz3004001 2009-05-1335.299% 38.693%
Rat rn4 yes40M30003000default 9400lastz3004001 2009-05-1332.879% 36.860%
Shrew sorAra1 no5030003000default 9400lastz3004001 2009-05-2919.760% N/A
Wallaby macEug1 no5030003000default 9400lastz3004001 2009-05-316.011% N/A
Opossum monDom5 no5022006000HoxD55.q 3400lastz3004001 2009-05-2914.358% 11.615%
Platypus ornAna1 no40M22006000HoxD55.q 3400lastz3020004001 2009-05-277.627% 11.259%
Chicken galGal3 yes40M220010000HoxD55.q 3400lastz3020004001 2009-05-143.591% 8.786%
Zebra finch taeGut1 no40M220010000HoxD55.q 3400lastz3020004001 2009-05-263.496% 7.795%
Lizard anoCar1 no40M22006000HoxD55.q 3400lastz3020004001 2009-05-303.591% 5.146%
X. tropicalis xenTro2 no40M22006000HoxD55.q 3400lastz3020004001 2009-05-273.176% 6.773%
Stickleback gasAcu1 no5022006000HoxD55.q 3400lastz3004001 2009-05-141.916% 11.175%
Fugu fr2 no5022006000HoxD55.q 3400lastz3004001 2009-05-201.702% 10.929%
Zebrafish danRer6 no40M22006000HoxD55.q 3400lastz3020004001 2009-07-103.051% 6.399%
Tetraodon tetNig2 no5022006000HoxD55.q 3400lastz3004001 2009-08-101.712% 14.194%
Medaka oryLat2 no5022006000HoxD55.q 3400lastz3004001 2009-05-221.849% 6.705%
Lamprey petMar1 no5022006000HoxD55.q 3400lastz3004001 2009-05-141.082% 3.200%
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