Hg38 7-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%
Rhesus rheMac3 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.52/bin/lastz15020006002 2014-01-2879.729% 86.715%
Dog canFam3 no030003000default 9400lastz-distrib-1.03.52/bin/lastz3020004001 2014-01-2749.978% 60.083%
Mouse mm10 no030003000default 9400lastz-distrib-1.03.52/bin/lastz3020004001 2014-01-2531.629% 35.323%
Rat rn5 no030003000default 9400lastz-distrib-1.03.52/bin/lastz3020004001 2014-03-0130.788% 36.312%
Opossum monDom5 no5022006000HoxD55.q 3400lastz-distrib-1.03.52/bin/lastz3020004001 2014-05-2914.370% 11.996%