Rn6 20-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 rn6
matched
(chainLink table)
% of query
matched
(chainLinkRn6)
Mouse mm10 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2016-04-0871.015% 70.886%
Prairie vole micOch1 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2017-01-1857.205% 70.134%
Guinea pig cavPor3 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2017-01-1327.834% 28.362%
Human hg38 no030003000default 9400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-1734.899% 31.077%
Chimp panTro5 no022006000HoxD55.q 3400lastz-distrib-1.03.66/bin/lastz3020004001 2017-01-1340.816% 35.356%
Tarsier tarSyr2 no022006000HoxD55.q 3400lastz-distrib-1.03.66/bin/lastz3020004001 2017-01-1838.509% 32.607%
Rhesus rheMac8 no022006000HoxD55.q 3400lastz-distrib-1.03.66/bin/lastz3020004001 2017-01-1440.165% 33.468%
Dog canFam3 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2017-01-1328.540% 30.864%
Rabbit oryCun2 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2017-01-1724.654% 24.981%
Cat felCat8 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2017-01-1729.520% 29.673%
Panda ailMel1 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2017-01-1630.404% 34.777%
Cow bosTau8 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2017-01-1625.902% 25.355%
Opossum monDom5 no25422006000HoxD55.q 3400lastz-distrib-1.03.66/bin/lastz3020004001 2017-01-139.652% 7.191%
Platypus ornAna2 no25422006000HoxD55.q 3400lastz-distrib-1.03.66/bin/lastz3020004001 2017-01-186.389% 8.652%
X. tropicalis xenTro7 no022006000HoxD55.q 3400lastz-distrib-1.03.66/bin/lastz3020004001 2017-01-124.104% 7.913%
Chicken galGal5 no022006000HoxD55.q 3400lastz-distrib-1.03.66/bin/lastz3020004001 2016-05-033.983% 7.853%
Turkey melGal5 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2017-01-172.440% 4.910%
Elephant shark calMil1 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2017-01-181.664% 4.309%
Zebrafish danRer10 no022006000HoxD55.q 3400lastz-distrib-1.03.66/bin/lastz3020004001 2015-09-183.232% 5.815%