Hg19 100way conservation lastz parameters

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Revision as of 18:55, 17 July 2013 by Hiram (talk | contribs) (add link to 100way.pl interactive table)
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See Also


The default
scoring matrix is:		  The HoxD55
scoring matrix is:		 The human-chimp.v2
scoring matrix is:
 ACGT
A91-114-31-123
C-114100-125-31
G-31-125100-114
T-123-31-11491

O=400 E=30

 
 ACGT
A91-90-25-100
C-90100-100-25
G-25-100100-90
T-100-25-9091

O=400 E=30

 
 ACGT
A90-330-236-356
C-330100-318-236
G-236-318100-330
T-356-236-33090

O=600 E=150

do not edit, automatically generated table

uncat: C

query abridged
repeats(no)		 M(0)K(3000) L(3000)QY(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 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.02/bin/lastz15020006002 2013-01-2595.279% 95.563%
Gorilla gorGor3 no25445003000human_chimp.v2.q 15000lastz15020006002 2011-10-1789.876% 91.109%
Orangutan ponAbe2 no25445003000human_chimp.v2.q 15000lastz15020006002 2009-08-1591.350% 89.617%
Gibbon nomLeu3 no25445003000human_chimp.v2.q 15000lastz15020006002 2013-03-2287.764% 89.943%
Chlorocebus sabaeus chlSab1 no25445003000human_chimp.v2.q 15000lastz15020006002 2013-06-3086.446% 88.132%
Macaca fascicularis macFas5 no25445003000human_chimp.v2.q 15000lastz15020006002 2013-06-3086.666% 86.757%
Rhesus rheMac3 no25445003000human_chimp.v2.q 15000lastz15020006002 2013-07-0482.859% 88.131%
Baboon papHam1 no25445003000human_chimp.v2.q 15000lastz15020006002 2009-09-0282.810% 85.825%
Squirrel monkey saiBol1 no25445003000human_chimp.v2.q 15000lastz15020006002 2013-06-3069.598% 78.834%
Marmoset calJac3 no25445003000human_chimp.v2.q 15000lastz15020006002 2010-02-1170.654% 73.768%
Bushbaby otoGar3 no030003000default 9400lastz3020004001 2013-07-0254.830% 65.026%
Tupaia chinensis tupChi1 no030003000default 9400lastz3020004001 2013-07-0646.558% 50.286%
White rhinoceros cerSim1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-10-1958.103% 69.204%
Horse equCab2 no030003000default 9400lastz3020004001 2009-09-0257.050% 66.774%
Camelus ferus camFer1 no030003000default 9400lastz3020004001 2013-07-1350.419% 71.204%
Alpaca vicPac2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2013-06-1850.193% 68.707%
Orcinus orca orcOrc1 TBD
Dolphin turTru2 TBD
Ferret  musFur1 no030003000default 9400lastz3020004001 2013-07-1250.993% 62.328%
Orycteropus afer oryAfe1 no030003000default 9400lastz3020004001 2013-07-0941.668% 34.051%
Squirrel speTri2 TBD
Pteropus alecto pteAle1 TBD
Pig susScr3 TBD
Manatee triMan1 no030003000default 9400lastz3020004001 2013-07-1146.580% 46.912%
Octodon degus octDeg1 no030003000default 9400lastz3020004001 2013-07-0741.385% 47.619%
Megabat pteVam1 no030003000default 9400lastz3020004001 2009-09-0245.414% 69.685%
Elephant loxAfr3 no5030003000default 9400lastz3020004001 2009-09-0246.636% 42.430%
Cat felCat5 no030003000default 9400lastz3020004001 2013-07-1352.426% 61.479%
Panda ailMel1 no5022006000default 3400lastz3020004002 2010-02-0450.022% 62.884%
Dog canFam3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-07-0451.848% 60.817%
Chrysochloris asiatica chrAsi1 no030003000default 9400lastz3020004001 2013-07-0934.209% 29.033%
Armadillo dasNov3 no030003000default 9400lastz3020004001 2013-07-0946.571% 41.884%
Rabbit oryCun2 no5030003000default 9400lastz3020004001 2009-09-0244.317% 48.405%
Myotis Davidii myoDav1 TBD
Pantholops hodgsonii panHod1 no030003000default 9400lastz3020004001 2013-07-1746.863% N/A
Leptonychotes weddellii lepWed1 no030003000default 9400lastz3020004001 2013-07-1252.424% 65.567%
Odobenus rosmarus divergens odoRosDiv1 no030003000default 9400lastz3020004001 2013-07-1353.559% 64.797%
Microbat myoLuc2 TBD
Eptesicus fuscus eptFus1 TBD
Cow bosTau7 no25430003000default 9400lastz3020004001 2012-01-2346.971% 49.508%
Capra hircus capHir1 no030003000default 9400lastz3020004001 2013-07-1746.498% N/A
Sheep oviAri3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2013-06-2646.833% 51.939%
Naked mole-rat hetGla2 no030003000default 9400lastz3020004001 2013-07-1747.600% N/A
Elephantulus edwardii eleEdw1 no030003000default 9400lastz3020004001 2013-07-0927.675% 24.222%
Jaculus jaculus jacJac1 no030003000default 9400lastz3020004001 2013-07-1635.106% 40.217%
Chinchilla chiLan1 TBD
Guinea pig cavPor3 no030003000default 9400lastz3020004001 2009-09-0243.680% 48.043%
Condylura cristata conCri1 no030003000default 9400lastz3020004001 2013-07-1037.034% 60.981%
Pika ochPri3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2013-06-1834.676% 49.855%
Hedgehog eriEur2 no030003000default 9400lastz3020004001 2013-07-0926.149% 31.250%
Tenrec echTel2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2013-06-1730.135% 32.736%
Mouse mm10 yes030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0735.249% 38.226%
Rat rn5 no030003000default 9400lastz3020004001 2012-06-2731.662% 36.299%
Cricetulus griseus criGri1 TBD
Mesocricetus auratus mesAur1 TBD
Microtus ochrogaster micOch1 TBD
Shrew sorAra2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2013-06-1827.681% 35.514%
Wallaby macEug2 no030003000default 9400lastz3020004001 2013-07-116.534% 7.229%
Opossum monDom5 no5022006000HoxD55.q 3400lastz3020004001 2009-09-0214.358% 11.615%
Chelonia mydas cheMyd1 TBD
Tasmanian devil sarHar1 no030003000default 9400lastz3020004001 2013-07-107.414% 6.937%
Painted turtle chrPic1 TBD
Apalone spinifera apaSpi1 TBD
Pelodiscus sinensis pelSin1 TBD
Platypus ornAna1 no022006000HoxD55.q 3400lastz3020004001 2009-09-027.627% 11.259%
Columba livia colLiv1 no0220010000HoxD55.q 3400lastz3020004001 2013-06-293.683% 8.468%
Falco cherrug falChe1 no0220010000HoxD55.q 3400lastz3020004001 2013-06-273.812% 8.232%
Falco peregrinus falPer1 no0220010000HoxD55.q 3400lastz3020004001 2013-06-273.879% 8.365%
American alligator allMis1 no022006000HoxD55.q 3400lastz3020004001 2013-06-287.084% 8.120%
Anas platyrhynchos anaPla1 no0220010000HoxD55.q 3400lastz3020004001 2013-06-273.509% 8.215%
Chicken galGal4 no0220010000HoxD55.q 3400lastz3020004001 2013-06-293.684% 8.990%
Turkey melGal1 no030003000default 9400lastz3020004001 2011-03-282.645% 6.637%
Parrot amaVit1 no0220010000HoxD55.q 3400lastz3020004001 2013-06-283.298% 7.807%
Ara macao araMac1 no0220010000HoxD55.q 3400lastz3020004001 2013-06-292.912% 7.320%
Budgerigar melUnd1 no0220010000HoxD55.q 3400lastz3020004001 2013-06-273.577% 8.237%
Ficedula albicollis ficAlb2 no0220010000HoxD55.q 3400lastz3020004001 2013-06-293.715% 8.625%
Lizard anoCar2 no022006000HoxD55.q 3400lastz3020004001 2011-04-193.552% 5.190%
Zebra finch taeGut2 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2013-06-175.321% 11.613%
Pseudopodoces humilis pseHum1 no0220010000HoxD55.q 3400lastz3020004001 2013-06-293.982% 9.685%
Medium ground finch geoFor1 no0220010000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-07-293.503% 8.504%
Zonotrichia albicollis zonAlb1 no0220010000HoxD55.q 3400lastz3020004001 2013-06-263.476% 8.622%
Lepisosteus oculatus lepOcu1 TBD
X. tropicalis xenTro7 TBD
Coelacanth latCha1 no5022006000HoxD55.q 3400lastz3020004001 2013-07-162.749% 3.419%
Atlantic cod gadMor1 TBD
Neolamprologus brichardi neoBri1 TBD
Nile tilapia oreNil2 TBD
Stickleback gasAcu1 no5022006000HoxD55.q 3400lastz3020004001 2009-09-021.916% 11.175%
Tetraodon tetNig2 no5022006000HoxD55.q 3400lastz3020004001 2009-09-021.712% 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 no022006000HoxD55.q 3400lastz3020004001 2010-12-182.790% 6.151%
Medaka oryLat2 no5022006000HoxD55.q 3400lastz3020004001 2009-09-021.849% 6.705%
Xiphophorus maculatus xipMac1 TBD
Lamprey petMar2 no5022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-10-171.046% 3.324%
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