Hg38 100-way conservation lastz parameters: Difference between revisions
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<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2015-02-12</TD><TD ALIGN=RIGHT>45.612%</TD> | <TD>2015-02-12</TD><TD ALIGN=RIGHT>45.612%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>67.399%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Pig susScr3</TH> | <TH>Pig susScr3</TH> | ||
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<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2015-02-12</TD><TD ALIGN=RIGHT>41.326%</TD> | <TD>2015-02-12</TD><TD ALIGN=RIGHT>41.326%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>53.005%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Elephant loxAfr3</TH> | <TH>Elephant loxAfr3</TH> | ||
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<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2015-02-12</TD><TD ALIGN=RIGHT>47.700%</TD> | <TD>2015-02-12</TD><TD ALIGN=RIGHT>47.700%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>54.165%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Panda ailMel1</TH> | <TH>Panda ailMel1</TH> | ||
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<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2015-02-12</TD><TD ALIGN=RIGHT>45.782%</TD> | <TD>2015-02-12</TD><TD ALIGN=RIGHT>45.782%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>57.657%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Guinea pig cavPor3</TH> | <TH>Guinea pig cavPor3</TH> | ||
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<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | ||
<TD>2015-02-12</TD><TD ALIGN=RIGHT>34.892%</TD> | <TD>2015-02-12</TD><TD ALIGN=RIGHT>34.892%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>54.580%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Cow bosTau8</TH> | <TH>Cow bosTau8</TH> | ||
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<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | ||
<TD>2015-02-12</TD><TD ALIGN=RIGHT>35.148%</TD> | <TD>2015-02-12</TD><TD ALIGN=RIGHT>35.148%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>54.674%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Cape elephant shrew eleEdw1</TH> | <TH>Cape elephant shrew eleEdw1</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>hg38.eleEdw1.tuning.Q.txt</TD> | <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>hg38.eleEdw1.tuning.Q.txt</TD> | ||
<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD> | <TD>2015-02-12</TD><TD ALIGN=RIGHT>22.161%</TD> | ||
<TD ALIGN=RIGHT>N/A</TD></TR> | <TD ALIGN=RIGHT>N/A</TD></TR> | ||
<TR> | <TR> | ||
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<TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>hg38.triMan1.tuning.Q.txt</TD> | <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>hg38.triMan1.tuning.Q.txt</TD> | ||
<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD> | <TD>2015-02-12</TD><TD ALIGN=RIGHT>41.443%</TD> | ||
<TD ALIGN=RIGHT>N/A</TD></TR> | <TD ALIGN=RIGHT>N/A</TD></TR> | ||
<TR> | <TR> | ||
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<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2015-02-12</TD><TD ALIGN=RIGHT>40.808%</TD> | <TD>2015-02-12</TD><TD ALIGN=RIGHT>40.808%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>52.036%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Star-nosed mole conCri1</TH> | <TH>Star-nosed mole conCri1</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>hg38.conCri1.tuning.Q.txt</TD> | <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>hg38.conCri1.tuning.Q.txt</TD> | ||
<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD> | <TD>2015-02-12</TD><TD ALIGN=RIGHT>33.037%</TD> | ||
<TD ALIGN=RIGHT>N/A</TD></TR> | <TD ALIGN=RIGHT>N/A</TD></TR> | ||
<TR> | <TR> | ||
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<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2015-02-12</TD><TD ALIGN=RIGHT>35.827%</TD> | <TD>2015-02-12</TD><TD ALIGN=RIGHT>35.827%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>42.618%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Pika ochPri3</TH> | <TH>Pika ochPri3</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>hg38.ochPri3.tuning.Q.txt</TD> | <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>hg38.ochPri3.tuning.Q.txt</TD> | ||
<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD> | <TD>2015-02-12</TD><TD ALIGN=RIGHT>30.261%</TD> | ||
<TD ALIGN=RIGHT>N/A</TD></TR> | <TD ALIGN=RIGHT>N/A</TD></TR> | ||
<TR> | <TR> | ||
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<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | ||
<TD>2015-02-12</TD><TD ALIGN=RIGHT>21.643%</TD> | <TD>2015-02-12</TD><TD ALIGN=RIGHT>21.643%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>26.641%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Tenrec echTel2</TH> | <TH>Tenrec echTel2</TH> | ||
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<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | ||
<TD>2015-02-12</TD><TD ALIGN=RIGHT>27.550%</TD> | <TD>2015-02-12</TD><TD ALIGN=RIGHT>27.550%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>30.796%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Mouse mm10</TH> | <TH>Mouse mm10</TH> | ||
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<TH>Rat rn6</TH> | <TH>Rat rn6</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Chinese hamster criGri1</TH> | <TH>Chinese hamster criGri1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Golden hamster mesAur1</TH> | <TH>Golden hamster mesAur1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Prairie vole micOch1</TH> | <TH>Prairie vole micOch1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Shrew sorAra2</TH> | <TH>Shrew sorAra2</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Wallaby macEug2</TH> | <TH>Wallaby macEug2</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Opossum monDom5</TH> | <TH>Opossum monDom5</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> | ||
| Line 391: | Line 397: | ||
<TH>Tasmanian devil sarHar1</TH> | <TH>Tasmanian devil sarHar1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Spiny softshell turtle apaSpi1</TH> | <TH>Spiny softshell turtle apaSpi1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Green seaturtle cheMyd1</TH> | <TH>Green seaturtle cheMyd1</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> | ||
| Line 409: | Line 417: | ||
<TH>Chinese softshell turtle pelSin1</TH> | <TH>Chinese softshell turtle pelSin1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Platypus ornAna1</TH> | <TH>Platypus ornAna1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>American alligator allMis1</TH> | <TH>American alligator allMis1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Rock pigeon colLiv1</TH> | <TH>Rock pigeon colLiv1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Chicken galGal4</TH> | <TH>Chicken galGal4</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Lizard anoCar2</TH> | <TH>Lizard anoCar2</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> | ||
| Line 430: | Line 443: | ||
<TH>Mallard duck anaPla1</TH> | <TH>Mallard duck anaPla1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Turkey melGal1</TH> | <TH>Turkey melGal1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Saker falcon falChe1</TH> | <TH>Saker falcon falChe1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Peregrine falcon falPer1</TH> | <TH>Peregrine falcon falPer1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Parrot amaVit1</TH> | <TH>Parrot amaVit1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Scarlet Macaw araMac1</TH> | <TH>Scarlet Macaw araMac1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Tibetan ground jay pseHum1</TH> | <TH>Tibetan ground jay pseHum1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Budgerigar melUnd1</TH> | <TH>Budgerigar melUnd1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Collared flycatcher ficAlb2</TH> | <TH>Collared flycatcher ficAlb2</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>White-throated sparrow zonAlb1</TH> | <TH>White-throated sparrow zonAlb1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Medium ground finch geoFor1</TH> | <TH>Medium ground finch geoFor1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Zebra finch taeGut2</TH> | <TH>Zebra finch taeGut2</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Spotted gar lepOcu1</TH> | <TH>Spotted gar lepOcu1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>X. tropicalis xenTro7</TH> | <TH>X. tropicalis xenTro7</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Coelacanth latCha1</TH> | <TH>Coelacanth latCha1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Atlantic cod gadMor1</TH> | <TH>Atlantic cod gadMor1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Stickleback gasAcu1</TH> | <TH>Stickleback gasAcu1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Nile tilapia oreNil2</TH> | <TH>Nile tilapia oreNil2</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Tetraodon tetNig2</TH> | <TH>Tetraodon tetNig2</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Princess of Burundi neoBri1</TH> | <TH>Princess of Burundi neoBri1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Yellowbelly pufferfish takFla1</TH> | <TH>Yellowbelly pufferfish takFla1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Burton's mouthbreeder hapBur1</TH> | <TH>Burton's mouthbreeder hapBur1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Fugu fr3</TH> | <TH>Fugu fr3</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Mexican tetra (cavefish) astMex1</TH> | <TH>Mexican tetra (cavefish) astMex1</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
</TR><TR> | </TR> | ||
<TR> | |||
<TH>Lamprey petMar2</TH> | <TH>Lamprey petMar2</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> | ||
Revision as of 18:22, 13 February 2015
See Also
- Human 100-way Hg38 100-way Genome size statistics
- Human 100-way Hg38 100-way 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(0) | K(3000) | L(3000) | Q | Y(9400) | program run | E(30) | H(0) | O(400) | T(1) | chain table date |
% of hg38 matched (chainLink table) |
% of query matched (chainLinkHg38) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chimp panTro4 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz-distrib-1.03.52/bin/lastz | 150 | 2000 | 600 | 2 | 2014-05-27 | 93.112% | 95.664% |
| Gorilla gorGor3 | no | 254 | 3000 | 3000 | hg38.gorGor3.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-15 | 88.005% | 91.695% |
| Orangutan ponAbe2 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz-distrib-1.03.52/bin/lastz | 150 | 2000 | 600 | 2 | 2014-09-02 | 89.187% | 89.656% |
| Gibbon nomLeu3 | no | 254 | 3000 | 3000 | hg38.nomLeu3.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-12 | 86.379% | 90.470% |
| Crab-eating macaque macFas5 | no | 254 | 3000 | 3000 | hg38.macFas5.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-14 | 85.675% | 87.749% |
| Rhesus rheMac3 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz-distrib-1.03.52/bin/lastz | 150 | 2000 | 600 | 2 | 2014-01-28 | 79.729% | 86.715% |
| Baboon papAnu2 | no | 254 | 3000 | 3000 | hg38.papAnu2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-13 | 84.179% | 84.502% |
| Squirrel monkey saiBol1 | no | 254 | 3000 | 3000 | hg38.saiBol1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-13 | 70.565% | 81.466% |
| Green monkey chlSab2 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz-distrib-1.03.52/bin/lastz | 150 | 2000 | 600 | 2 | 2014-07-11 | 84.393% | 88.264% |
| Marmoset calJac3 | no | 254 | 3000 | 3000 | hg38.calJac3.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-13 | 71.709% | 76.757% |
| Aardvark oryAfe1 | no | 50 | 3000 | 3000 | hg38.oryAfe1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-11 | 36.526% | 30.701% |
| Bushbaby otoGar3 | no | 254 | 3000 | 3000 | hg38.otoGar3.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-13 | 49.485% | 60.561% |
| White rhinoceros cerSim1 | no | 50 | 3000 | 3000 | hg38.cerSim1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-11 | 53.075% | 64.822% |
| Cape golden mole chrAsi1 | no | 50 | 3000 | 3000 | hg38.chrAsi1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-11 | 29.208% | 25.571% |
| Big brown bat eptFus1 | no | 50 | 3000 | 3000 | hg38.eptFus1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-11 | 36.386% | 58.072% |
| Chinese tree shrew tupChi1 | no | 50 | 3000 | 3000 | hg38.tupChi1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-10 | 37.022% | 41.180% |
| Horse equCab2 | no | 50 | 3000 | 3000 | hg38.equCab2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-11 | 52.083% | 62.447% |
| Bactrian camel camFer1 | no | 50 | 3000 | 3000 | hg38.camFer1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-11 | 46.206% | 67.274% |
| Alpaca vicPac2 | no | 50 | 3000 | 3000 | hg38.vicPac2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-11 | 45.887% | 64.565% |
| Dolphin turTru2 | no | 50 | 3000 | 3000 | hg38.turTru2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-11 | 46.072% | 56.998% |
| Dog canFam3 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.52/bin/lastz | 30 | 2000 | 400 | 1 | 2014-01-27 | 49.978% | 60.083% |
| Killer whale orcOrc1 | no | 50 | 3000 | 3000 | hg38.orcOrc1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-11 | 47.281% | 60.190% |
| Squirrel speTri2 | no | 50 | 3000 | 3000 | hg38.speTri2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2015-02-10 | 44.729% | 57.271% |
| Black flying-fox pteAle1 | no | 50 | 3000 | 3000 | hg38.pteAle1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-12 | 45.612% | 67.399% |
| Pig susScr3 | no | 50 | 3000 | 3000 | hg38.susScr3.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-12 | 41.326% | 53.005% |
| Elephant loxAfr3 | no | 50 | 3000 | 3000 | hg38.loxAfr3.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-12 | 41.904% | 39.143% |
| Naked mole-rat hetGla2 | no | 50 | 3000 | 3000 | hg38.hetGla2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2015-02-11 | 42.315% | 54.061% |
| Megabat pteVam1 | no | 50 | 3000 | 3000 | hg38.pteVam1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2015-02-11 | 41.012% | 65.155% |
| Cat felCat8 | no | 50 | 3000 | 3000 | hg38.felCat8.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-12 | 47.700% | 54.165% |
| Panda ailMel1 | no | 50 | 3000 | 3000 | hg38.ailMel1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-12 | 48.226% | 61.650% |
| Ferret musFur1 | no | 50 | 3000 | 3000 | hg38.musFur1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-12 | 45.782% | 57.657% |
| Guinea pig cavPor3 | no | 50 | 3000 | 3000 | hg38.cavPor3.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2015-02-11 | 37.901% | 42.902% |
| Armadillo dasNov3 | no | 50 | 3000 | 3000 | hg38.dasNov3.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2015-02-11 | 42.233% | 38.915% |
| Rabbit oryCun2 | no | 50 | 3000 | 3000 | hg38.oryCun2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-12 | 38.631% | 43.643% |
| Tibetan antelope panHod1 | no | 50 | 3000 | 3000 | hg38.panHod1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-12 | 41.357% | 47.712% |
| Weddell seal lepWed1 | no | 50 | 3000 | 3000 | hg38.lepWed1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-12 | 47.437% | 61.113% |
| Pacific walrus odoRosDiv1 | no | 50 | 3000 | 3000 | hg38.odoRosDiv1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-12 | 47.985% | 59.858% |
| David's myotis (bat) myoDav1 | no | 50 | 3000 | 3000 | hg38.myoDav1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2015-02-12 | 34.892% | 54.580% |
| Cow bosTau8 | no | 254 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2014-10-16 | 45.975% | 50.440% |
| Domestic goat capHir1 | no | 50 | 3000 | 3000 | hg38.capHir1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | in progress | in progress | N/A |
| Sheep oviAri3 | no | 254 | 3000 | 3000 | hg38.oviAri3.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-01-21 | 41.193% | 47.075% |
| Microbat myoLuc2 | no | 50 | 3000 | 3000 | hg38.myoLuc2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2015-02-12 | 35.148% | 54.674% |
| Cape elephant shrew eleEdw1 | no | 50 | 3000 | 3000 | hg38.eleEdw1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-12 | 22.161% | N/A |
| Manatee triMan1 | no | 50 | 3000 | 3000 | hg38.triMan1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-12 | 41.443% | N/A |
| Lesser Egyptian jerboa jacJac1 | no | 50 | 3000 | 3000 | hg38.jacJac1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-12 | 27.899% | N/A |
| Chinchilla chiLan1 | no | 50 | 3000 | 3000 | hg38.chiLan1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-12 | 40.808% | 52.036% |
| Star-nosed mole conCri1 | no | 50 | 3000 | 3000 | hg38.conCri1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-12 | 33.037% | N/A |
| Brush-tailed rat octDeg1 | no | 50 | 3000 | 3000 | hg38.octDeg1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-12 | 35.827% | 42.618% |
| Pika ochPri3 | no | 50 | 3000 | 3000 | hg38.ochPri3.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-12 | 30.261% | N/A |
| Hedgehog eriEur2 | no | 50 | 3000 | 3000 | hg38.eriEur2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2015-02-12 | 21.643% | 26.641% |
| Tenrec echTel2 | no | 50 | 3000 | 3000 | hg38.echTel2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2015-02-12 | 27.550% | 30.796% |
| Mouse mm10 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.52/bin/lastz | 30 | 2000 | 400 | 1 | 2014-01-25 | 31.629% | 35.323% |
| Rat rn6 | TBD | |||||||||||||
| Chinese hamster criGri1 | TBD | |||||||||||||
| Golden hamster mesAur1 | TBD | |||||||||||||
| Prairie vole micOch1 | TBD | |||||||||||||
| Shrew sorAra2 | TBD | |||||||||||||
| Wallaby macEug2 | TBD | |||||||||||||
| Opossum monDom5 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.52/bin/lastz | 30 | 2000 | 400 | 1 | 2014-05-29 | 14.370% | 11.996% |
| Tasmanian devil sarHar1 | TBD | |||||||||||||
| Spiny softshell turtle apaSpi1 | TBD | |||||||||||||
| Green seaturtle cheMyd1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-06 | 6.296% | 7.960% |
| Painted turtle chrPic2 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-06 | 6.708% | 8.554% |
| Chinese softshell turtle pelSin1 | TBD | |||||||||||||
| Platypus ornAna1 | TBD | |||||||||||||
| American alligator allMis1 | TBD | |||||||||||||
| Rock pigeon colLiv1 | TBD | |||||||||||||
| Chicken galGal4 | TBD | |||||||||||||
| Lizard anoCar2 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-06 | 3.593% | 5.222% |
| Mallard duck anaPla1 | TBD | |||||||||||||
| Turkey melGal1 | TBD | |||||||||||||
| Saker falcon falChe1 | TBD | |||||||||||||
| Peregrine falcon falPer1 | TBD | |||||||||||||
| Parrot amaVit1 | TBD | |||||||||||||
| Scarlet Macaw araMac1 | TBD | |||||||||||||
| Tibetan ground jay pseHum1 | TBD | |||||||||||||
| Budgerigar melUnd1 | TBD | |||||||||||||
| Collared flycatcher ficAlb2 | TBD | |||||||||||||
| White-throated sparrow zonAlb1 | TBD | |||||||||||||
| Medium ground finch geoFor1 | TBD | |||||||||||||
| Zebra finch taeGut2 | TBD | |||||||||||||
| Spotted gar lepOcu1 | TBD | |||||||||||||
| X. tropicalis xenTro7 | TBD | |||||||||||||
| Coelacanth latCha1 | TBD | |||||||||||||
| Atlantic cod gadMor1 | TBD | |||||||||||||
| Stickleback gasAcu1 | TBD | |||||||||||||
| Nile tilapia oreNil2 | TBD | |||||||||||||
| Tetraodon tetNig2 | TBD | |||||||||||||
| Princess of Burundi neoBri1 | TBD | |||||||||||||
| Yellowbelly pufferfish takFla1 | TBD | |||||||||||||
| Burton's mouthbreeder hapBur1 | TBD | |||||||||||||
| Fugu fr3 | TBD | |||||||||||||
| Mexican tetra (cavefish) astMex1 | TBD | |||||||||||||
| Lamprey petMar2 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-06 | 1.265% | 3.960% |
| Zebrafish danRer10 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-08 | 3.357% | 7.110% |
| Zebra Mbuna mayZeb1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-07 | 1.805% | 6.780% |
| Pundamilia nyererei punNye1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-06 | 1.787% | 6.864% |
| Medaka oryLat2 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-06 | 2.002% | 6.853% |
| Southern platyfish xipMac1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-02-06 | 1.898% | 7.435% |
