Mm10 conservation lastz parameters: Difference between revisions
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</TR> | </TR> | ||
<TR> | <TR> | ||
<TH>Rat | <TH>Rat rn5</TH> | ||
<TD> | <TD>yes</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>mouse_rat_2.q</TD> | ||
<TD> | <TD>5000</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>55</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | ||
<TD>2012-03- | <TD>2012-03-26</TD><TD ALIGN=RIGHT>67.353%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>70.278%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Squirrel speTri2</TH> | <TH>Squirrel speTri2</TH> | ||
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<TD ALIGN=RIGHT>27.512%</TD></TR> | <TD ALIGN=RIGHT>27.512%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Naked mole | <TH>Naked mole rat hetGla2</TH> | ||
<TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | ||
<TD>9400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>9400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2012- | <TD>2012-04-14</TD><TD ALIGN=RIGHT>32.753%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>37.989%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Guinea pig cavPor3</TH> | <TH>Guinea pig cavPor3</TH> | ||
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<TD ALIGN=RIGHT>31.924%</TD></TR> | <TD ALIGN=RIGHT>31.924%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Gibbon | <TH>Gibbon nomLeu2</TH> | ||
<TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | ||
<TD>9400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>9400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2012- | <TD>2012-04-14</TD><TD ALIGN=RIGHT>34.031%</TD> | ||
<TD ALIGN=RIGHT>32. | <TD ALIGN=RIGHT>32.274%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Orangutan ponAbe2</TH> | <TH>Orangutan ponAbe2</TH> | ||
| Line 185: | Line 185: | ||
<TD ALIGN=RIGHT>31.769%</TD></TR> | <TD ALIGN=RIGHT>31.769%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Dolphin | <TH>Dolphin turTru2</TH> | ||
<TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | ||
<TD>9400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>9400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2012- | <TD>2012-04-14</TD><TD ALIGN=RIGHT>30.267%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>33.492%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Pig | <TH>Pig susScr3</TH> | ||
<TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | ||
<TD>9400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>9400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2012- | <TD>2012-04-14</TD><TD ALIGN=RIGHT>25.685%</TD> | ||
<TD ALIGN=RIGHT>29. | <TD ALIGN=RIGHT>29.445%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Cow bosTau7</TH> | <TH>Cow bosTau7</TH> | ||
| Line 221: | Line 221: | ||
<TD ALIGN=RIGHT>33.650%</TD></TR> | <TD ALIGN=RIGHT>33.650%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Cat | <TH>Cat felCat5</TH> | ||
<TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | ||
<TD>9400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>9400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2012- | <TD>2012-04-14</TD><TD ALIGN=RIGHT>29.725%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>32.244%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Dog canFam3</TH> | <TH>Dog canFam3</TH> | ||
| Line 257: | Line 257: | ||
<TD ALIGN=RIGHT>23.687%</TD></TR> | <TD ALIGN=RIGHT>23.687%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Armadillo | <TH>Armadillo dasNov3</TH> | ||
<TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | ||
<TD>9400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>9400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2012- | <TD>2012-04-14</TD><TD ALIGN=RIGHT>25.201%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>21.066%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Rock hyrax proCap1</TH> | <TH>Rock hyrax proCap1</TH> | ||
| Line 377: | Line 377: | ||
<TD ALIGN=RIGHT>12.134%</TD></TR> | <TD ALIGN=RIGHT>12.134%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Nile tilapia | <TH>Nile tilapia oreNil2</TH> | ||
<TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD> | <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD> | ||
<TD>3400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2012-04- | <TD>2012-04-11</TD><TD ALIGN=RIGHT>1.957%</TD> | ||
<TD ALIGN=RIGHT>6.091%</TD></TR> | <TD ALIGN=RIGHT>6.091%</TD></TR> | ||
<TR> | <TR> | ||
Revision as of 20:34, 16 April 2012
See Also
- Mouse 60-way Mm10 Genome size statistics
- Mouse 60-way Mm10 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 mm10 matched (chainLink table) |
% of query matched (chainLinkMm10) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Rat rn5 | yes | 0 | 3000 | 3000 | mouse_rat_2.q | 5000 | lastz-distrib-1.03.02/bin/lastz | 55 | 2000 | 600 | 2 | 2012-03-26 | 67.353% | 70.278% |
| Squirrel speTri2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-16 | 34.217% | 39.244% |
| Kangaroo rat dipOrd1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-16 | 19.460% | 27.512% |
| Naked mole rat hetGla2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-14 | 32.753% | 37.989% |
| Guinea pig cavPor3 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-17 | 28.447% | 29.115% |
| Rabbit oryCun2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-17 | 25.248% | 25.677% |
| Pika ochPri2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-24 | 14.542% | 19.908% |
| Tree shrew tupBel1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-17 | 19.766% | 25.144% |
| Human hg19 | yes | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-08 | 38.226% | 35.249% |
| Gorilla gorGor3 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-08 | 33.987% | 34.349% |
| Chimp panTro4 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-10 | 34.674% | 31.924% |
| Gibbon nomLeu2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-14 | 34.031% | 32.274% |
| Orangutan ponAbe2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-09 | 34.496% | 30.610% |
| Tarsier tarSyr1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-12 | 24.560% | 24.986% |
| Chinese rhesus rheMac3 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-09 | 33.931% | 33.464% |
| Baboon papHam1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-10 | 33.577% | 32.023% |
| Bushbaby otoGar3 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-13 | 29.795% | 32.926% |
| Marmoset calJac3 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-09 | 32.450% | 31.301% |
| Mouse lemur micMur1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-13 | 26.636% | 37.574% |
| Squirrel monkey saiBol1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-09 | 32.339% | 33.848% |
| Horse equCab2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-16 | 34.415% | 37.138% |
| Alpaca vicPac1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-17 | 22.636% | 31.769% |
| Dolphin turTru2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-14 | 30.267% | 33.492% |
| Pig susScr3 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-14 | 25.685% | 29.445% |
| Cow bosTau7 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-22 | 26.255% | 25.383% |
| Sheep oviAri1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-22 | 15.341% | 31.925% |
| Megabat pteVam1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-20 | 27.345% | 38.627% |
| Microbat myoLuc2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-22 | 24.363% | 33.650% |
| Cat felCat5 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-14 | 29.725% | 32.244% |
| Dog canFam3 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-20 | 29.144% | 31.624% |
| Panda ailMel1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-20 | 30.979% | 35.562% |
| Hedgehog eriEur1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-24 | 9.856% | 12.264% |
| Shrew sorAra1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-24 | 9.382% | 13.569% |
| Sloth choHof1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-22 | 18.019% | 23.687% |
| Armadillo dasNov3 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-14 | 25.201% | 21.066% |
| Rock hyrax proCap1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-23 | 15.147% | 16.214% |
| Tenrec echTel1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-24 | 10.947% | 14.117% |
| Manatee triMan1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-30 | 26.546% | 24.649% |
| Elephant loxAfr3 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-20 | 25.823% | 21.616% |
| Wallaby macEug2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-24 | 4.353% | 4.448% |
| Tasmanian devil sarHar1 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-30 | 8.479% | 7.888% |
| Opossum monDom5 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-30 | 9.584% | 7.205% |
| Platypus ornAna1 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-30 | 5.348% | 7.334% |
| Chicken galGal4 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-03 | 3.676% | 8.100% |
| Zebra finch taeGut1 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-03 | 3.599% | 7.304% |
| Turkey melGal1 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-03 | 3.511% | 8.211% |
| Budgerigar melUnd1 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-30 | 3.589% | 7.350% |
| Lizard anoCar2 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-03 | 3.331% | 4.988% |
| Painted turtle chrPic1 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-30 | 4.731% | 5.488% |
| X. tropicalis xenTro3 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-03 | 3.125% | 6.651% |
| Coelacanth latCha1 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-03 | 2.715% | 3.380% |
| Atlantic cod gadMor1 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-03 | 1.726% | 6.810% |
| Stickleback gasAcu1 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-03 | 2.016% | 10.927% |
| Fugu fr3 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-03 | 1.789% | 12.134% |
| Nile tilapia oreNil2 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-11 | 1.957% | 6.091% |
| Tetraodon tetNig2 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-02 | 1.735% | 13.642% |
| Zebrafish danRer7 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-03 | 2.602% | 5.107% |
| Medaka oryLat2 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-03 | 1.936% | 6.561% |
| Lamprey petMar1 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-04-04 | 1.101% | 3.159% |
