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>[[ | <LI>all other [[UCSC Multiple Alignments]]</LI> | ||
</UL> | </UL> | ||
<TABLE BORDER=0> | |||
<TR><TD>The default<BR>scoring matrix is:</TD><TD WIDTH=42> </TD> | |||
<TD>The HoxD55<BR>scoring matrix is:</TD><TD WIDTH=42> </TD><TD>The human-chimp.v2<BR>scoring matrix is:</TD></TR> | |||
<TR><TD> | |||
<TABLE BORDER=1> | |||
<TR><TH> </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> </TD><TD><TABLE BORDER=1> | |||
<TR><TH> </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> </TD><TD><TABLE BORDER=1> | |||
<TR><TH> </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== | ||
| Line 17: | Line 47: | ||
<TH>L(3000)</TH><TH>Q</TH><TH>Y(9400)</TH> | <TH>L(3000)</TH><TH>Q</TH><TH>Y(9400)</TH> | ||
<TH>program<BR>run</TH><TH>E(30)</TH><TH>H(0)</TH> | <TH>program<BR>run</TH><TH>E(30)</TH><TH>H(0)</TH> | ||
<TH>O(400)</TH><TH>T(1)</TH> | <TH>O(400)</TH><TH>T(1)</TH> | ||
<TH>chain table<BR>date</TH> | <TH>chain table<BR>date</TH> | ||
<TH>% of hg19<BR>matched<BR>(chainLink table)</TH> | <TH>% of hg19<BR>matched<BR>(chainLink table)</TH> | ||
<TH>% of query<BR>matched<BR>(chainLinkHg19)</TH> | |||
</TR> | </TR> | ||
<TR> | <TR> | ||
<TH>Chimp panTro2</TH> | <TH>Chimp panTro2</TH> | ||
<TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | ||
<TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD> | <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD> | ||
<TD>2009-03-20</TD><TD ALIGN=RIGHT>94.846%</TD> | <TD>2009-03-20</TD><TD ALIGN=RIGHT>94.846%</TD> | ||
</TR><TR> | <TD ALIGN=RIGHT>94.908%</TD></TR> | ||
<TR> | |||
<TH>Gorilla gorGor1</TH> | <TH>Gorilla gorGor1</TH> | ||
<TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | ||
<TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD> | <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD> | ||
<TD>2009-03-22</TD><TD ALIGN=RIGHT>59.484%</TD> | <TD>2009-03-22</TD><TD ALIGN=RIGHT>59.484%</TD> | ||
</TR><TR> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Orangutan ponAbe2</TH> | <TH>Orangutan ponAbe2</TH> | ||
<TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | ||
<TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD> | <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD> | ||
<TD>2009-05-14</TD><TD ALIGN=RIGHT>91.350%</TD> | <TD>2009-05-14</TD><TD ALIGN=RIGHT>91.350%</TD> | ||
</TR><TR> | <TD ALIGN=RIGHT>89.617%</TD></TR> | ||
<TR> | |||
<TH>Rhesus rheMac2</TH> | <TH>Rhesus rheMac2</TH> | ||
<TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | ||
<TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD> | <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD> | ||
<TD> | <TD>2009-05-14</TD><TD ALIGN=RIGHT>82.744%</TD> | ||
</TR><TR> | <TD ALIGN=RIGHT>87.422%</TD></TR> | ||
<TR> | |||
<TH>Baboon papHam1</TH> | <TH>Baboon papHam1</TH> | ||
<TD | |||
</TR><TR> | <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | ||
<TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD> | |||
<TD>2009-05-20</TD><TD ALIGN=RIGHT>82.810%</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Marmoset calJac1</TH> | <TH>Marmoset calJac1</TH> | ||
<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> | ||
<TD>2009-05-14</TD><TD ALIGN=RIGHT>70.860%</TD> | |||
<TD ALIGN=RIGHT>71.897%</TD></TR> | |||
<TR> | |||
<TH>Tarsier tarSyr1</TH> | |||
<TD>no</TD><TD>40M</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>2009-05-15</TD><TD ALIGN=RIGHT>47.830%</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Mouse lemur micMur1</TH> | |||
<TD>no</TD><TD>40M</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>2009-05-22</TD><TD ALIGN=RIGHT>46.519%</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Bushbaby otoGar1</TH> | <TH>Bushbaby otoGar1</TH> | ||
<TD | <TD>no</TD><TD>40M</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 | <TD>2009-05-15</TD><TD ALIGN=RIGHT>43.644%</TD> | ||
</TR><TR> | <TD ALIGN=RIGHT>N/A</TD></TR> | ||
<TH> | <TR> | ||
<TD | <TH>Horse equCab2</TH> | ||
</ | <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD> | ||
< | |||
<TD | <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD> | ||
</TR><TR> | <TD>2009-06-04</TD><TD ALIGN=RIGHT>57.050%</TD> | ||
<TH> | <TD ALIGN=RIGHT>66.774%</TD></TR> | ||
<TD> | <TR> | ||
<TH>Tree shrew tupBel1</TH> | |||
<TD>no</TD><TD>40M</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- | <TD>2009-06-01</TD><TD ALIGN=RIGHT>36.156%</TD> | ||
</TR><TR> | |||
<TH> | <TD ALIGN=RIGHT>N/A</TD></TR> | ||
<TD> | <TR> | ||
<TH>Dolphin turTru1</TH> | |||
<TD>no</TD><TD>40M</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- | |||
</TR><TR> | <TD>2009-06-04</TD><TD ALIGN=RIGHT>48.398%</TD> | ||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Squirrel speTri1</TH> | <TH>Squirrel speTri1</TH> | ||
<TD | <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD> | ||
</TR><TR> | |||
<TH> | <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD> | ||
<TD | <TD>2009-06-04</TD><TD ALIGN=RIGHT>35.713%</TD> | ||
</TR><TR> | <TD ALIGN=RIGHT>N/A</TD></TR> | ||
<TH> | <TR> | ||
<TD | <TH>Alpaca vicPac1</TH> | ||
</TR><TR> | |||
<TH> | <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD> | ||
<TD | <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD> | ||
</TR><TR> | <TD>2009-06-04</TD><TD ALIGN=RIGHT>39.399%</TD> | ||
<TH> | |||
<TD | <TD ALIGN=RIGHT>N/A</TD></TR> | ||
</TR><TR> | <TR> | ||
<TH>Sloth choHof1</TH> | |||
<TD>no</TD><TD>40M</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>2009-06-05</TD><TD ALIGN=RIGHT>34.377%</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Megabat pteVam1</TH> | |||
<TD>no</TD><TD>40M</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>2009-06-04</TD><TD ALIGN=RIGHT>45.414%</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Elephant loxAfr3</TH> | |||
<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>2009-07-22</TD><TD ALIGN=RIGHT>46.636%</TD> | |||
<TD ALIGN=RIGHT>42.430%</TD></TR> | |||
<TR> | |||
<TH>Cat felCat3</TH> | <TH>Cat felCat3</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> | ||
<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> | |||
</TR><TR> | <TD>2009-06-04</TD><TD ALIGN=RIGHT>35.713%</TD> | ||
<TD ALIGN=RIGHT>61.104%</TD></TR> | |||
<TR> | |||
<TH>Dog canFam2</TH> | <TH>Dog canFam2</TH> | ||
<TD>yes</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD> | <TD>yes</TD><TD>40M</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>2009-05-14</TD><TD ALIGN=RIGHT>52.879%</TD> | <TD>2009-05-14</TD><TD ALIGN=RIGHT>52.879%</TD> | ||
</TR><TR> | <TD ALIGN=RIGHT>62.055%</TD></TR> | ||
<TH> | <TR> | ||
<TD | <TH>Armadillo dasNov2</TH> | ||
</TR><TR> | |||
<TH> | <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD> | ||
<TD | <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD> | ||
</ | <TD>2009-05-27</TD><TD ALIGN=RIGHT>33.543%</TD> | ||
< | |||
<TD | <TD ALIGN=RIGHT>N/A</TD></TR> | ||
</TR><TR> | <TR> | ||
<TH>Rabbit oryCun2</TH> | |||
<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>2009-08-12</TD><TD ALIGN=RIGHT>44.317%</TD> | |||
<TD ALIGN=RIGHT>48.405%</TD></TR> | |||
<TR> | |||
<TH>Microbat myoLuc1</TH> | <TH>Microbat myoLuc1</TH> | ||
<TD | <TD>no</TD><TD>40M</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 | <TD>2009-06-04</TD><TD ALIGN=RIGHT>33.174%</TD> | ||
</TR><TR> | <TD ALIGN=RIGHT>N/A</TD></TR> | ||
<TR> | |||
<TH>Cow bosTau4</TH> | <TH>Cow bosTau4</TH> | ||
<TD | |||
</TR><TR> | <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD> | ||
<TH> | <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD> | ||
<TD | <TD>2009-06-04</TD><TD ALIGN=RIGHT>46.506%</TD> | ||
</TR><TR> | |||
<TH> | <TD ALIGN=RIGHT>50.297%</TD></TR> | ||
<TD | <TR> | ||
</TR><TR> | <TH>Guinea Pig cavPor3</TH> | ||
<TD>no</TD><TD>40M</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>2009-06-06</TD><TD ALIGN=RIGHT>43.680%</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Rock hyrax proCap1</TH> | |||
<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>2009-05-26</TD><TD ALIGN=RIGHT>30.864%</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Kangaroo rat dipOrd1</TH> | <TH>Kangaroo rat dipOrd1</TH> | ||
<TD | |||
</TR><TR> | <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD> | ||
<TH> | <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD> | ||
<TD | <TD>2009-05-29</TD><TD ALIGN=RIGHT>27.161%</TD> | ||
</TR><TR> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Pika ochPri2</TH> | |||
<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>2009-05-30</TD><TD ALIGN=RIGHT>27.768%</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Hedgehog eriEur1</TH> | |||
<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>2009-05-30</TD><TD ALIGN=RIGHT>19.362%</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Tenrec echTel1</TH> | |||
<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>2009-05-28</TD><TD ALIGN=RIGHT>23.120%</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Mouse mm9</TH> | |||
<TD>yes</TD><TD>40M</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>2009-05-13</TD><TD ALIGN=RIGHT>35.299%</TD> | |||
<TD ALIGN=RIGHT>38.693%</TD></TR> | |||
<TR> | |||
<TH>Rat rn4</TH> | |||
<TD>yes</TD><TD>40M</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>2009-05-13</TD><TD ALIGN=RIGHT>32.879%</TD> | |||
<TD ALIGN=RIGHT>36.860%</TD></TR> | |||
<TR> | |||
<TH>Shrew sorAra1</TH> | |||
<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>2009-05-29</TD><TD ALIGN=RIGHT>19.760%</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Wallaby macEug1</TH> | <TH>Wallaby macEug1</TH> | ||
<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>2009-05-31</TD><TD ALIGN=RIGHT>6.011%</TD> | |||
< | <TD ALIGN=RIGHT>N/A</TD></TR> | ||
< | <TR> | ||
</ | |||
< | |||
<TD | |||
</TR><TR> | |||
<TH>Opossum monDom5</TH> | <TH>Opossum monDom5</TH> | ||
<TD | <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD> | ||
</TR><TR> | |||
<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 ALIGN=RIGHT>11.615%</TD></TR> | |||
<TR> | |||
<TH>Platypus ornAna1</TH> | <TH>Platypus ornAna1</TH> | ||
<TD | |||
</TR><TR> | <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>7.627%</TD> | |||
<TD ALIGN=RIGHT>11.259%</TD></TR> | |||
<TR> | |||
<TH>Chicken galGal3</TH> | <TH>Chicken galGal3</TH> | ||
<TD>yes</TD><TD>40M</TD><TD>2200</TD><TD>10000</TD><TD>HoxD55.q</TD> | <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>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> | |||
</TR><TR> | <TD>2009-05-14</TD><TD ALIGN=RIGHT>3.591%</TD> | ||
<TD ALIGN=RIGHT>8.786%</TD></TR> | |||
<TR> | |||
<TH>Zebra finch taeGut1</TH> | <TH>Zebra finch taeGut1</TH> | ||
<TD | <TD>no</TD><TD>40M</TD><TD>2200</TD><TD>10000</TD><TD>HoxD55.q</TD> | ||
</TR><TR> | |||
<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 anoCar1</TH> | <TH>Lizard anoCar1</TH> | ||
<TD | |||
</TR><TR> | <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 xenTro2</TH> | <TH>X. tropicalis xenTro2</TH> | ||
<TD | <TD>no</TD><TD>40M</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD> | ||
</TR><TR> | <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TH> | |||
<TD | <TD>2009-05-27</TD><TD ALIGN=RIGHT>3.176%</TD> | ||
</ | <TD ALIGN=RIGHT>6.773%</TD></TR> | ||
< | <TR> | ||
<TD | <TH>Stickleback gasAcu1</TH> | ||
</TR><TR> | <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 fr2</TH> | <TH>Fugu fr2</TH> | ||
<TD | |||
</TR><TR> | <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD> | ||
<TH> | <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD> | ||
<TD | <TD>2009-05-20</TD><TD ALIGN=RIGHT>1.702%</TD> | ||
</TR><TR> | |||
<TD ALIGN=RIGHT>10.929%</TD></TR> | |||
<TR> | |||
<TH>Zebrafish 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 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 oryLat2</TH> | <TH>Medaka oryLat2</TH> | ||
<TD | <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD> | ||
</TR><TR> | <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 petMar1</TH> | <TH>Lamprey petMar1</TH> | ||
<TD | <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD> | ||
</TR> | <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:
- 46-way Hg19 Genome size statistics
- 46-way Hg19 conservation alignment
- all other UCSC Multiple Alignments
| The default scoring matrix is: | The HoxD55 scoring matrix is: | The human-chimp.v2 scoring matrix is: | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
O=400 E=30 |
O=400 E=30 |
O=600 E=150 |
do not edit, automatically generated table
| query | abridged repeats(no) |
M(40M) | K(3000) | L(3000) | Q | Y(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 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 0 | 600 | 2 | 2009-03-20 | 94.846% | 94.908% |
| Gorilla gorGor1 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 0 | 600 | 2 | 2009-03-22 | 59.484% | N/A |
| Orangutan ponAbe2 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 0 | 600 | 2 | 2009-05-14 | 91.350% | 89.617% |
| Rhesus rheMac2 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 0 | 600 | 2 | 2009-05-14 | 82.744% | 87.422% |
| Baboon papHam1 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 0 | 600 | 2 | 2009-05-20 | 82.810% | N/A |
| Marmoset calJac1 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 0 | 600 | 2 | 2009-05-14 | 70.860% | 71.897% |
| Tarsier tarSyr1 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-15 | 47.830% | N/A |
| Mouse lemur micMur1 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-22 | 46.519% | N/A |
| Bushbaby otoGar1 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-15 | 43.644% | N/A |
| Horse equCab2 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-06-04 | 57.050% | 66.774% |
| Tree shrew tupBel1 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-06-01 | 36.156% | N/A |
| Dolphin turTru1 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-06-04 | 48.398% | N/A |
| Squirrel speTri1 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-06-04 | 35.713% | N/A |
| Alpaca vicPac1 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-06-04 | 39.399% | N/A |
| Sloth choHof1 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-06-05 | 34.377% | N/A |
| Megabat pteVam1 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-06-04 | 45.414% | N/A |
| Elephant loxAfr3 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-07-22 | 46.636% | 42.430% |
| Cat felCat3 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-06-04 | 35.713% | 61.104% |
| Dog canFam2 | yes | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-14 | 52.879% | 62.055% |
| Armadillo dasNov2 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-27 | 33.543% | N/A |
| Rabbit oryCun2 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-08-12 | 44.317% | 48.405% |
| Microbat myoLuc1 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-06-04 | 33.174% | N/A |
| Cow bosTau4 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-06-04 | 46.506% | 50.297% |
| Guinea Pig cavPor3 | no | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-06-06 | 43.680% | N/A |
| Rock hyrax proCap1 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-26 | 30.864% | N/A |
| Kangaroo rat dipOrd1 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-29 | 27.161% | N/A |
| Pika ochPri2 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-30 | 27.768% | N/A |
| Hedgehog eriEur1 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-30 | 19.362% | N/A |
| Tenrec echTel1 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-28 | 23.120% | N/A |
| Mouse mm9 | yes | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-13 | 35.299% | 38.693% |
| Rat rn4 | yes | 40M | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-13 | 32.879% | 36.860% |
| Shrew sorAra1 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-29 | 19.760% | N/A |
| Wallaby macEug1 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 0 | 400 | 1 | 2009-05-31 | 6.011% | N/A |
| Opossum monDom5 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 0 | 400 | 1 | 2009-05-29 | 14.358% | 11.615% |
| Platypus ornAna1 | no | 40M | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2009-05-27 | 7.627% | 11.259% |
| Chicken galGal3 | yes | 40M | 2200 | 10000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2009-05-14 | 3.591% | 8.786% |
| Zebra finch taeGut1 | no | 40M | 2200 | 10000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2009-05-26 | 3.496% | 7.795% |
| Lizard anoCar1 | no | 40M | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2009-05-30 | 3.591% | 5.146% |
| X. tropicalis xenTro2 | no | 40M | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2009-05-27 | 3.176% | 6.773% |
| Stickleback gasAcu1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 0 | 400 | 1 | 2009-05-14 | 1.916% | 11.175% |
| Fugu fr2 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 0 | 400 | 1 | 2009-05-20 | 1.702% | 10.929% |
| Zebrafish danRer6 | no | 40M | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2009-07-10 | 3.051% | 6.399% |
| Tetraodon tetNig2 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 0 | 400 | 1 | 2009-08-10 | 1.712% | 14.194% |
| Medaka oryLat2 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 0 | 400 | 1 | 2009-05-22 | 1.849% | 6.705% |
| Lamprey petMar1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 0 | 400 | 1 | 2009-05-14 | 1.082% | 3.200% |
