Hg19 100way conservation lastz parameters: Difference between revisions
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<UL> | <UL> | ||
<LI>100way statistics [http://hgwdev-hiram.cse.ucsc.edu/cgi-bin/genomeStats/100way.pl interactive table]</LI> | |||
<LI>Human 100-way [[Hg19 100way Genome size statistics]]</LI> | <LI>Human 100-way [[Hg19 100way Genome size statistics]]</LI> | ||
<LI>Human 100-way [[Hg19 100way conservation alignment]]</LI> | <LI>Human 100-way [[Hg19 100way conservation alignment]]</LI> | ||
Revision as of 18:55, 17 July 2013
See Also
- 100way statistics interactive table
- Human 100-way Hg19 100way Genome size statistics
- Human 100-way Hg19 100way 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
uncat: C
| 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 hg19 matched (chainLink table) |
% of query matched (chainLinkHg19) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chimp panTro4 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz-distrib-1.03.02/bin/lastz | 150 | 2000 | 600 | 2 | 2013-01-25 | 95.279% | 95.563% |
| Gorilla gorGor3 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 2000 | 600 | 2 | 2011-10-17 | 89.876% | 91.109% |
| Orangutan ponAbe2 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 2000 | 600 | 2 | 2009-08-15 | 91.350% | 89.617% |
| Gibbon nomLeu3 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 2000 | 600 | 2 | 2013-03-22 | 87.764% | 89.943% |
| Chlorocebus sabaeus chlSab1 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 2000 | 600 | 2 | 2013-06-30 | 86.446% | 88.132% |
| Macaca fascicularis macFas5 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 2000 | 600 | 2 | 2013-06-30 | 86.666% | 86.757% |
| Rhesus rheMac3 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 2000 | 600 | 2 | 2013-07-04 | 82.859% | 88.131% |
| Baboon papHam1 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 2000 | 600 | 2 | 2009-09-02 | 82.810% | 85.825% |
| Squirrel monkey saiBol1 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 2000 | 600 | 2 | 2013-06-30 | 69.598% | 78.834% |
| Marmoset calJac3 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 2000 | 600 | 2 | 2010-02-11 | 70.654% | 73.768% |
| Bushbaby otoGar3 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-02 | 54.830% | 65.026% |
| Tupaia chinensis tupChi1 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-06 | 46.558% | 50.286% |
| White rhinoceros cerSim1 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-10-19 | 58.103% | 69.204% |
| Horse equCab2 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2009-09-02 | 57.050% | 66.774% |
| Camelus ferus camFer1 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-13 | 50.419% | 71.204% |
| Alpaca vicPac2 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2013-06-18 | 50.193% | 68.707% |
| Orcinus orca orcOrc1 | TBD | |||||||||||||
| Dolphin turTru2 | TBD | |||||||||||||
| Ferret musFur1 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-12 | 50.993% | 62.328% |
| Orycteropus afer oryAfe1 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-09 | 41.668% | 34.051% |
| Squirrel speTri2 | TBD | |||||||||||||
| Pteropus alecto pteAle1 | TBD | |||||||||||||
| Pig susScr3 | TBD | |||||||||||||
| Manatee triMan1 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-11 | 46.580% | 46.912% |
| Octodon degus octDeg1 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-07 | 41.385% | 47.619% |
| Megabat pteVam1 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2009-09-02 | 45.414% | 69.685% |
| Elephant loxAfr3 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2009-09-02 | 46.636% | 42.430% |
| Cat felCat5 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-13 | 52.426% | 61.479% |
| Panda ailMel1 | no | 50 | 2200 | 6000 | default | 3400 | lastz | 30 | 2000 | 400 | 2 | 2010-02-04 | 50.022% | 62.884% |
| Dog canFam3 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-07-04 | 51.848% | 60.817% |
| Chrysochloris asiatica chrAsi1 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-09 | 34.209% | 29.033% |
| Armadillo dasNov3 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-09 | 46.571% | 41.884% |
| Rabbit oryCun2 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2009-09-02 | 44.317% | 48.405% |
| Myotis Davidii myoDav1 | TBD | |||||||||||||
| Pantholops hodgsonii panHod1 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-17 | 46.863% | N/A |
| Leptonychotes weddellii lepWed1 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-12 | 52.424% | 65.567% |
| Odobenus rosmarus divergens odoRosDiv1 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-13 | 53.559% | 64.797% |
| Microbat myoLuc2 | TBD | |||||||||||||
| Eptesicus fuscus eptFus1 | TBD | |||||||||||||
| Cow bosTau7 | no | 254 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2012-01-23 | 46.971% | 49.508% |
| Capra hircus capHir1 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-17 | 46.498% | N/A |
| Sheep oviAri3 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2013-06-26 | 46.833% | 51.939% |
| Naked mole-rat hetGla2 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-17 | 47.600% | N/A |
| Elephantulus edwardii eleEdw1 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-09 | 27.675% | 24.222% |
| Jaculus jaculus jacJac1 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-16 | 35.106% | 40.217% |
| Chinchilla chiLan1 | TBD | |||||||||||||
| Guinea pig cavPor3 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2009-09-02 | 43.680% | 48.043% |
| Condylura cristata conCri1 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-10 | 37.034% | 60.981% |
| Pika ochPri3 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2013-06-18 | 34.676% | 49.855% |
| Hedgehog eriEur2 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-09 | 26.149% | 31.250% |
| Tenrec echTel2 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2013-06-17 | 30.135% | 32.736% |
| Mouse mm10 | yes | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-07 | 35.249% | 38.226% |
| Rat rn5 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2012-06-27 | 31.662% | 36.299% |
| Cricetulus griseus criGri1 | TBD | |||||||||||||
| Mesocricetus auratus mesAur1 | TBD | |||||||||||||
| Microtus ochrogaster micOch1 | TBD | |||||||||||||
| Shrew sorAra2 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2013-06-18 | 27.681% | 35.514% |
| Wallaby macEug2 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-11 | 6.534% | 7.229% |
| Opossum monDom5 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2009-09-02 | 14.358% | 11.615% |
| Chelonia mydas cheMyd1 | TBD | |||||||||||||
| Tasmanian devil sarHar1 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-10 | 7.414% | 6.937% |
| Painted turtle chrPic1 | TBD | |||||||||||||
| Apalone spinifera apaSpi1 | TBD | |||||||||||||
| Pelodiscus sinensis pelSin1 | TBD | |||||||||||||
| Platypus ornAna1 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2009-09-02 | 7.627% | 11.259% |
| Columba livia colLiv1 | no | 0 | 2200 | 10000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2013-06-29 | 3.683% | 8.468% |
| Falco cherrug falChe1 | no | 0 | 2200 | 10000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2013-06-27 | 3.812% | 8.232% |
| Falco peregrinus falPer1 | no | 0 | 2200 | 10000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2013-06-27 | 3.879% | 8.365% |
| American alligator allMis1 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2013-06-28 | 7.084% | 8.120% |
| Anas platyrhynchos anaPla1 | no | 0 | 2200 | 10000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2013-06-27 | 3.509% | 8.215% |
| Chicken galGal4 | no | 0 | 2200 | 10000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2013-06-29 | 3.684% | 8.990% |
| Turkey melGal1 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2011-03-28 | 2.645% | 6.637% |
| Parrot amaVit1 | no | 0 | 2200 | 10000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2013-06-28 | 3.298% | 7.807% |
| Ara macao araMac1 | no | 0 | 2200 | 10000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2013-06-29 | 2.912% | 7.320% |
| Budgerigar melUnd1 | no | 0 | 2200 | 10000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2013-06-27 | 3.577% | 8.237% |
| Ficedula albicollis ficAlb2 | no | 0 | 2200 | 10000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2013-06-29 | 3.715% | 8.625% |
| Lizard anoCar2 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2011-04-19 | 3.552% | 5.190% |
| Zebra finch taeGut2 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2013-06-17 | 5.321% | 11.613% |
| Pseudopodoces humilis pseHum1 | no | 0 | 2200 | 10000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2013-06-29 | 3.982% | 9.685% |
| Medium ground finch geoFor1 | no | 0 | 2200 | 10000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-07-29 | 3.503% | 8.504% |
| Zonotrichia albicollis zonAlb1 | no | 0 | 2200 | 10000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2013-06-26 | 3.476% | 8.622% |
| Lepisosteus oculatus lepOcu1 | TBD | |||||||||||||
| X. tropicalis xenTro7 | TBD | |||||||||||||
| Coelacanth latCha1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2013-07-16 | 2.749% | 3.419% |
| Atlantic cod gadMor1 | TBD | |||||||||||||
| Neolamprologus brichardi neoBri1 | TBD | |||||||||||||
| Nile tilapia oreNil2 | TBD | |||||||||||||
| Stickleback gasAcu1 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2009-09-02 | 1.916% | 11.175% |
| Tetraodon tetNig2 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2009-09-02 | 1.712% | 14.194% |
| Haplochromis burtoni hapBur1 | TBD | |||||||||||||
| Takifugu flavidus takFla1 | TBD | |||||||||||||
| Maylandia zebra mayZeb1 | TBD | |||||||||||||
| Pundamilia nyererei punNye1 | TBD | |||||||||||||
| Fugu fr3 | TBD | |||||||||||||
| Astyanax mexicanus astMex1 | TBD | |||||||||||||
| Zebrafish danRer7 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2010-12-18 | 2.790% | 6.151% |
| Medaka oryLat2 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2009-09-02 | 1.849% | 6.705% |
| Xiphophorus maculatus xipMac1 | TBD | |||||||||||||
| Lamprey petMar2 | no | 50 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-10-17 | 1.046% | 3.324% |
