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> | ||
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% |
