Hg38 100-way conservation lastz parameters

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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%
Rhesus rheMac3 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.66/bin/lastz15020006002 2015-04-0980.828% 88.220%
Crab-eating macaque macFas5 no25430003000hg38.macFas5.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1485.675% 87.749%
Baboon papAnu2 no25430003000hg38.papAnu2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1384.179% 84.502%
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%
Squirrel monkey saiBol1 no25430003000hg38.saiBol1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1370.565% 81.466%
Bushbaby otoGar3 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004002 2015-02-2353.196% 64.899%
Chinese tree shrew tupChi1 no030003000default 9400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1945.256% 50.350%
Squirrel speTri2 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2948.283% 61.854%
Lesser Egyptian jerboa jacJac1 no030003000default 9400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1934.153% 40.300%
Prairie vole micOch1 no030003000default 9400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1431.489% 43.539%
Chinese hamster criGri1 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-02-2033.169% 42.426%
Golden hamster mesAur1 no030003000default 9400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1930.803% 43.095%
Mouse mm10 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-0931.653% 35.372%
Rat rn6 no030003000default 9400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1431.077% 34.899%
Naked mole-rat hetGla2 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2946.248% 58.855%
Guinea pig cavPor3 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2842.371% 48.000%
Chinchilla chiLan1 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2845.665% 58.002%
Brush-tailed rat octDeg1 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2440.238% 47.651%
Rabbit oryCun2 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2842.911% 48.360%
Pika ochPri3 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2833.618% 49.837%
Pig susScr3 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2944.676% 57.273%
Alpaca vicPac2 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2948.909% 68.755%
Bactrian camel camFer1 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2449.095% 71.268%
Dolphin turTru2 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2949.728% 61.393%
Killer whale orcOrc1 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2950.709% 64.364%
Tibetan antelope panHod1 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2845.619% 52.526%
Cow bosTau8 no25430003000default 9400lastz3020004001 2014-10-1645.975% 50.440%
Sheep oviAri3 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004002 2015-04-2745.352% 51.787%
Domestic goat capHir1 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2845.257% 52.668%
Horse equCab2 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-02-2355.459% 66.600%
White rhinoceros cerSim1 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-02-2356.633% 69.232%
Cat felCat8 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2951.684% 58.750%
Dog canFam3 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-1050.395% 60.861%
Ferret  musFur1 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2949.631% 62.396%
Panda ailMel1 no5030003000hg38.ailMel1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1248.226% 61.650%
Pacific walrus odoRosDiv1 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2952.193% 64.897%
Weddell seal lepWed1 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2951.073% 65.642%
Black flying-fox pteAle1 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2948.281% 71.168%
Megabat pteVam1 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2943.924% 69.545%
Big brown bat eptFus1 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2439.123% 62.229%
David's myotis (bat) myoDav1 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2838.713% 60.286%
Microbat myoLuc2 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2838.591% 59.729%
Hedgehog eriEur2 no030003000default 9400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1925.488% 31.297%
Shrew sorAra2 no030003000default 9400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-2026.905% 35.760%
Star-nosed mole conCri1 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2935.911% 61.017%
Elephant loxAfr3 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2945.214% 42.303%
Cape elephant shrew eleEdw1 no030003000default 9400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1926.839% 24.181%
Manatee triMan1 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2945.346% 46.939%
Cape golden mole chrAsi1 no030003000default 9400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-2033.314% 29.068%
Tenrec echTel2 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2929.310% 32.753%
Aardvark oryAfe1 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2340.563% 34.102%
Armadillo dasNov3 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2945.349% 41.895%
Opossum monDom5 no5022006000HoxD55.q 3400lastz-distrib-1.03.52/bin/lastz3020004001 2014-05-2914.370% 11.996%
Tasmanian devil sarHar1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1412.754% 12.925%
Wallaby macEug2 no030003000default 9400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-196.378% 7.213%
Platypus ornAna1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-137.769% 11.784%
Rock pigeon colLiv1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-134.712% 10.220%
Saker falcon falChe1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-134.828% 9.878%
Peregrine falcon falPer1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-134.926% 10.027%
Collared flycatcher ficAlb2 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-184.822% 10.748%
White-throated sparrow zonAlb1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-184.494% 10.570%
Medium ground finch geoFor1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-194.445% 10.366%
Zebra finch taeGut2 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-195.893% 12.356%
Tibetan ground jay pseHum1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-195.146% 11.937%
Budgerigar melUnd1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-194.474% 9.862%
Parrot amaVit1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-134.186% 9.480%
Scarlet Macaw araMac1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-173.787% 9.039%
Mallard duck anaPla1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-134.268% 9.679%
Chicken galGal4 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-134.696% 10.888%
Turkey melGal1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-134.328% 10.927%
American alligator allMis1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-147.561% 8.665%
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 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-145.716% 7.207%
Spiny softshell turtle apaSpi1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-144.611% 6.320%
Lizard anoCar2 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-063.593% 5.222%
X. tropicalis xenTro7 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-193.811% 7.967%
Coelacanth latCha1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-202.873% 3.449%
Tetraodon tetNig2 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-181.743% 14.323%
Fugu fr3 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-181.784% 12.394%
Yellowbelly pufferfish takFla1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-181.548% 11.317%
Nile tilapia oreNil2 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-181.868% 6.241%
Princess of Burundi neoBri1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-181.767% 6.840%
Burton's mouthbreeder hapBur1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-181.783% 6.861%
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%
Stickleback gasAcu1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-182.080% 11.956%
Atlantic cod gadMor1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-181.660% 6.911%
Zebrafish danRer10 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-083.357% 7.110%
Mexican tetra (cavefish) astMex1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-182.225% 6.365%
Spotted gar lepOcu1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-192.511% 6.634%
Lamprey petMar2 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-061.265% 3.960%