Mm39 35-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 mm39
matched
(chainLink table)
% of query
matched
(chainLinkMm39)
Rat rn6 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-10-2070.901% 71.075%
Chinese hamster GCF_003668045.3 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-12-0858.000% 65.829%
Beaver casCan1 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2436.600% 40.919%
Squirrel speTri2 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2534.147% 39.374%
Chinese pangolin manPen1 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2427.322% 35.593%
Guinea pig cavPor3 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2528.378% 29.113%
Malayan flying lemur galVar1 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2435.714% 36.152%
Marmoset calJac4 no25430003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-09-0433.090% 30.958%
Gorilla gorGor6 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2435.064% 34.067%
Human hg38 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-08-1835.372% 31.072%
Bonobo panPan3 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2435.282% 33.905%
Chimp panTro6 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2435.291% 31.035%
Tarsier tarSyr2 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2332.278% 26.476%
Rhesus rheMac10 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-10-2034.838% 31.329%
Bushbaby otoGar3 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2429.729% 32.896%
Horse equCab3 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2434.831% 37.377%
Dolphin turTru2 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2430.188% 33.447%
Dog canFam4 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2429.376% 31.252%
Tree shrew tupBel1 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2519.691% 25.089%
Pig susScr3 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2425.611% 29.405%
Elephant loxAfr3 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2425.756% 21.582%
Rabbit oryCun2 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2425.182% 25.654%
Sheep oviAri4 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2426.200% 26.350%
Hawaiian monk seal neoSch1 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2431.257% 34.352%
Cow bosTau9 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2326.588% 25.668%
Pika ochPri3 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2518.559% 24.585%
Hedgehog eriEur2 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2413.450% 14.799%
Tenrec echTel2 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2514.456% 14.589%
Shrew sorAra2 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-2513.370% 15.772%
Opossum monDom5 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-255.382% 4.044%
X. tropicalis xenTro9 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-251.936% 3.896%
Chicken galGal6 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-252.537% 5.377%
Lamprey petMar3 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-240.905% 2.170%
Zebrafish danRer11 no030003000default 9400lastz-distrib-1.04.03/bin/lastz3020004001 2020-11-251.416% 2.801%