Hg19 conservation lastz parameters: Difference between revisions

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m (update loxAfr2 to loxAfr3)
(updated table contents)
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   <TD ALIGN=RIGHT>66.774%</TD></TR>
   <TD ALIGN=RIGHT>66.774%</TD></TR>
<TR>
<TR>
   <TH>TreeShrew&nbsp;tupBel1</TH>
   <TH>Tree shrew&nbsp;tupBel1</TH>


   <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
Line 144: Line 144:
<TR>
<TR>
   <TH>Elephant&nbsp;loxAfr3</TH>
   <TH>Elephant&nbsp;loxAfr3</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>2009-07-22</TD><TD ALIGN=RIGHT>46.636%</TD>
   <TD>2009-07-22</TD><TD ALIGN=RIGHT>46.636%</TD>
   <TD ALIGN=RIGHT>42.430</TD></TR>
 
   <TD ALIGN=RIGHT>42.430%</TD></TR>
<TR>
<TR>
   <TH>Cat&nbsp;felCat3</TH>
   <TH>Cat&nbsp;felCat3</TH>
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   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>N/A</TD></TR>
<TR>
<TR>
   <TH>Rabbit&nbsp;oryCun1</TH>
   <TH>Rabbit&nbsp;oryCun2</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>


   <TD>2009-05-29</TD><TD ALIGN=RIGHT>33.676%</TD>
   <TD>2009-08-12</TD><TD ALIGN=RIGHT>44.317%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>48.405%</TD></TR>
<TR>
<TR>
   <TH>Microbat&nbsp;myoLuc1</TH>
   <TH>Microbat&nbsp;myoLuc1</TH>
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   <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>2009-05-29</TD><TD ALIGN=RIGHT>14.358%</TD>
   <TD>2009-05-29</TD><TD ALIGN=RIGHT>14.358%</TD>
   <TD ALIGN=RIGHT>11.615</TD></TR>
   <TD ALIGN=RIGHT>11.615%</TD></TR>
<TR>
<TR>
   <TH>Platypus&nbsp;ornAna1</TH>
   <TH>Platypus&nbsp;ornAna1</TH>
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   <TD ALIGN=RIGHT>6.399%</TD></TR>
   <TD ALIGN=RIGHT>6.399%</TD></TR>
<TR>
<TR>
   <TH>Tetraodon&nbsp;tetNig1</TH>
   <TH>Tetraodon&nbsp;tetNig2</TH>
   <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
   <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>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>2.003%</TD>
   <TD>2009-08-10</TD><TD ALIGN=RIGHT>1.712%</TD>
   <TD ALIGN=RIGHT>14.443%</TD></TR>
   <TD ALIGN=RIGHT>14.194%</TD></TR>
<TR>
<TR>
   <TH>Medaka&nbsp;oryLat2</TH>
   <TH>Medaka&nbsp;oryLat2</TH>
   <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
   <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>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>2009-05-22</TD><TD ALIGN=RIGHT>1.849%</TD>
   <TD ALIGN=RIGHT>6.705%</TD></TR>
   <TD ALIGN=RIGHT>6.705%</TD></TR>
<TR>
<TR>
Line 350: Line 349:
   <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
   <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>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>2009-05-14</TD><TD ALIGN=RIGHT>1.082%</TD>
   <TD ALIGN=RIGHT>3.200%</TD></TR>
   <TD ALIGN=RIGHT>3.200%</TD></TR>
</TABLE>
</TABLE>


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

Revision as of 17:58, 27 August 2009

See Also:

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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