PonAbe2 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 ponAbe2
matched
(chainLink table)
% of query
matched
(chainLinkPonAbe2)
Human hg18 no5030003000default 9400lastz3004001 2009-09-0291.302% 92.892%
Chimp panTro2 no5030003000default 9400lastz3004001 2009-08-1589.431% 91.033%
Rhesus rheMac2 no5030003000default 9400lastz3004001 2009-08-1582.623% 88.157%
Marmoset calJac1 no5030003000default 9400lastz3004001 2009-08-1574.694% 76.925%
Mouse mm9 no5030003000default 9400lastz3004001 2009-08-1530.659% 34.902%
Opossum monDom4 no5022006000HoxD55.q 3400lastz3004001 2009-08-1513.137% 11.306%
Platypus ornAna1 no5022006000HoxD55.q 3400lastz3004001 2009-08-156.936% 10.931%