Mm10 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:
 The mouse_rat_2.q
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

 
 ACGT
A100-139-54-170
C-13995-83-54
G-54-8395-139
T-170-54-139100

O=600 E=55

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 mm10
matched
(chainLink table)
% of query
matched
(chainLinkMm10)
Rat rn5 yes030003000mouse_rat_2.q 5000lastz-distrib-1.03.02/bin/lastz5520006002 2012-03-2667.353% 70.278%
Squirrel speTri2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1634.217% 39.244%
Kangaroo rat dipOrd1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1619.460% 27.512%
Naked mole rat hetGla2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-1432.753% 37.989%
Guinea pig cavPor3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1728.447% 29.115%
Rabbit oryCun2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1725.248% 25.677%
Pika ochPri2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2414.542% 19.908%
Tree shrew tupBel1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1719.766% 25.144%
Human hg19 yes030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0838.226% 35.249%
Gorilla gorGor3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0833.987% 34.349%
Chimp panTro4 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1034.674% 31.924%
Gibbon nomLeu2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-1434.031% 32.274%
Orangutan ponAbe2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0934.496% 30.610%
Tarsier tarSyr1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1224.560% 24.986%
Chinese rhesus rheMac3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0933.931% 33.464%
Baboon papHam1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1033.577% 32.023%
Bushbaby otoGar3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1329.795% 32.926%
Marmoset calJac3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0932.450% 31.301%
Mouse lemur micMur1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1326.636% 37.574%
Squirrel monkey saiBol1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0932.339% 33.848%
Horse equCab2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1634.415% 37.138%
Alpaca vicPac1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1722.636% 31.769%
Dolphin turTru2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-1430.267% 33.492%
Pig susScr3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-1425.685% 29.445%
Cow bosTau7 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2226.255% 25.383%
Sheep oviAri1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2215.341% 31.925%
Megabat pteVam1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2027.345% 38.627%
Microbat myoLuc2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2224.363% 33.650%
Cat felCat5 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-1429.725% 32.244%
Dog canFam3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2029.144% 31.624%
Panda ailMel1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2030.979% 35.562%
Hedgehog eriEur1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-249.856% 12.264%
Shrew sorAra1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-249.382% 13.569%
Sloth choHof1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2218.019% 23.687%
Armadillo dasNov3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-1425.201% 21.066%
Rock hyrax proCap1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2315.147% 16.214%
Tenrec echTel1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2410.947% 14.117%
Manatee triMan1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-3026.546% 24.649%
Elephant loxAfr3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2025.823% 21.616%
Wallaby macEug2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-244.353% 4.448%
Tasmanian devil sarHar1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-308.479% 7.888%
Opossum monDom5 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-309.584% 7.205%
Platypus ornAna1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-305.348% 7.334%
Chicken galGal4 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-033.676% 8.100%
Zebra finch taeGut1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-033.599% 7.304%
Turkey melGal1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-033.511% 8.211%
Budgerigar melUnd1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-303.589% 7.350%
Lizard anoCar2 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-033.331% 4.988%
Painted turtle chrPic1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-304.731% 5.488%
X. tropicalis xenTro3 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-033.125% 6.651%
Coelacanth latCha1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-032.715% 3.380%
Atlantic cod gadMor1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-031.726% 6.810%
Stickleback gasAcu1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-032.016% 10.927%
Fugu fr3 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-031.789% 12.134%
Nile tilapia oreNil2 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-111.957% 6.091%
Tetraodon tetNig2 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-021.735% 13.642%
Zebrafish danRer7 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-032.602% 5.107%
Medaka oryLat2 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-031.936% 6.561%
Lamprey petMar1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-041.101% 3.159%
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