XenTro9 11-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 xenTro9
matched
(chainLink table)
% of query
matched
(chainLinkXenTro9)
African clawed frog xenLae2 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2017-04-0654.877% 45.983%
Tibetan frog nanPar1 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2017-03-308.180% 6.700%
Painted turtle chrPic2 no022006000HoxD55.q 3400lastz-distrib-1.03.66/bin/lastz3020004001 2017-04-076.459% 4.977%
Opossum monDom5 no022008000HoxD55.q 3400lastz-distrib-1.03.66/bin/lastz3020004001 2017-04-075.414% 2.218%
Chicken galGal5 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2017-04-073.387% 3.601%
Lizard anoCar2 no022006000HoxD55.q 3400lastz-distrib-1.03.66/bin/lastz3020004001 2017-04-075.977% 4.794%
Dog canFam3 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2017-04-063.311% 1.890%
Human hg38 no5022006000HoxD55.q 3400lastz-distrib-1.03.66/bin/lastz3020004001 2017-03-307.950% 3.861%
Mouse mm10 no022006000HoxD55.q 3400lastz-distrib-1.03.66/bin/lastz3020004001 2017-03-306.581% 3.282%
Fugu fr3 no022006000HoxD55.q 3400lastz-distrib-1.03.66/bin/lastz3020004001 2017-04-073.777% 12.822%