Hg38 100-way conservation lastz parameters

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Revision as of 18:22, 13 February 2015 by Hiram (talk | contribs) (updated)
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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

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 hg38
matched
(chainLink table)		 % of query
matched
(chainLinkHg38)
Chimp panTro4 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.52/bin/lastz15020006002 2014-05-2793.112% 95.664%
Gorilla gorGor3 no25430003000hg38.gorGor3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1588.005% 91.695%
Orangutan ponAbe2 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.52/bin/lastz15020006002 2014-09-0289.187% 89.656%
Gibbon nomLeu3 no25430003000hg38.nomLeu3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1286.379% 90.470%
Crab-eating macaque macFas5 no25430003000hg38.macFas5.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1485.675% 87.749%
Rhesus rheMac3 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.52/bin/lastz15020006002 2014-01-2879.729% 86.715%
Baboon papAnu2 no25430003000hg38.papAnu2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1384.179% 84.502%
Squirrel monkey saiBol1 no25430003000hg38.saiBol1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1370.565% 81.466%
Green monkey chlSab2 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.52/bin/lastz15020006002 2014-07-1184.393% 88.264%
Marmoset calJac3 no25430003000hg38.calJac3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1371.709% 76.757%
Aardvark oryAfe1 no5030003000hg38.oryAfe1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1136.526% 30.701%
Bushbaby otoGar3 no25430003000hg38.otoGar3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1349.485% 60.561%
White rhinoceros cerSim1 no5030003000hg38.cerSim1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1153.075% 64.822%
Cape golden mole chrAsi1 no5030003000hg38.chrAsi1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1129.208% 25.571%
Big brown bat eptFus1 no5030003000hg38.eptFus1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1136.386% 58.072%
Chinese tree shrew tupChi1 no5030003000hg38.tupChi1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1037.022% 41.180%
Horse equCab2 no5030003000hg38.equCab2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1152.083% 62.447%
Bactrian camel camFer1 no5030003000hg38.camFer1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1146.206% 67.274%
Alpaca vicPac2 no5030003000hg38.vicPac2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1145.887% 64.565%
Dolphin turTru2 no5030003000hg38.turTru2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1146.072% 56.998%
Dog canFam3 no030003000default 9400lastz-distrib-1.03.52/bin/lastz3020004001 2014-01-2749.978% 60.083%
Killer whale orcOrc1 no5030003000hg38.orcOrc1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1147.281% 60.190%
Squirrel speTri2 no5030003000hg38.speTri2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2015-02-1044.729% 57.271%
Black flying-fox pteAle1 no5030003000hg38.pteAle1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1245.612% 67.399%
Pig susScr3 no5030003000hg38.susScr3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1241.326% 53.005%
Elephant loxAfr3 no5030003000hg38.loxAfr3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1241.904% 39.143%
Naked mole-rat hetGla2 no5030003000hg38.hetGla2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2015-02-1142.315% 54.061%
Megabat pteVam1 no5030003000hg38.pteVam1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2015-02-1141.012% 65.155%
Cat felCat8 no5030003000hg38.felCat8.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1247.700% 54.165%
Panda ailMel1 no5030003000hg38.ailMel1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1248.226% 61.650%
Ferret  musFur1 no5030003000hg38.musFur1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1245.782% 57.657%
Guinea pig cavPor3 no5030003000hg38.cavPor3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2015-02-1137.901% 42.902%
Armadillo dasNov3 no5030003000hg38.dasNov3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2015-02-1142.233% 38.915%
Rabbit oryCun2 no5030003000hg38.oryCun2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1238.631% 43.643%
Tibetan antelope panHod1 no5030003000hg38.panHod1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1241.357% 47.712%
Weddell seal lepWed1 no5030003000hg38.lepWed1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1247.437% 61.113%
Pacific walrus odoRosDiv1 no5030003000hg38.odoRosDiv1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1247.985% 59.858%
David's myotis (bat) myoDav1 no5030003000hg38.myoDav1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2015-02-1234.892% 54.580%
Cow bosTau8 no25430003000default 9400lastz3020004001 2014-10-1645.975% 50.440%
Domestic goat capHir1 no5030003000hg38.capHir1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 in progressin progress N/A
Sheep oviAri3 no25430003000hg38.oviAri3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-01-2141.193% 47.075%
Microbat myoLuc2 no5030003000hg38.myoLuc2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2015-02-1235.148% 54.674%
Cape elephant shrew eleEdw1 no5030003000hg38.eleEdw1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1222.161% N/A
Manatee triMan1 no5030003000hg38.triMan1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1241.443% N/A
Lesser Egyptian jerboa jacJac1 no5030003000hg38.jacJac1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1227.899% N/A
Chinchilla chiLan1 no5030003000hg38.chiLan1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1240.808% 52.036%
Star-nosed mole conCri1 no5030003000hg38.conCri1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1233.037% N/A
Brush-tailed rat octDeg1 no5030003000hg38.octDeg1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1235.827% 42.618%
Pika ochPri3 no5030003000hg38.ochPri3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1230.261% N/A
Hedgehog eriEur2 no5030003000hg38.eriEur2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2015-02-1221.643% 26.641%
Tenrec echTel2 no5030003000hg38.echTel2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2015-02-1227.550% 30.796%
Mouse mm10 no030003000default 9400lastz-distrib-1.03.52/bin/lastz3020004001 2014-01-2531.629% 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 no5022006000HoxD55.q 3400lastz-distrib-1.03.52/bin/lastz3020004001 2014-05-2914.370% 11.996%
Tasmanian devil sarHar1 TBD
Spiny softshell turtle apaSpi1 TBD
Green seaturtle cheMyd1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-066.296% 7.960%
Painted turtle chrPic2 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-066.708% 8.554%
Chinese softshell turtle pelSin1 TBD
Platypus ornAna1 TBD
American alligator allMis1 TBD
Rock pigeon colLiv1 TBD
Chicken galGal4 TBD
Lizard anoCar2 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-063.593% 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 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-061.265% 3.960%
Zebrafish danRer10 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-083.357% 7.110%
Zebra Mbuna mayZeb1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-071.805% 6.780%
Pundamilia nyererei punNye1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-061.787% 6.864%
Medaka oryLat2 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-062.002% 6.853%
Southern platyfish xipMac1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-061.898% 7.435%
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