XenTro3 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 xenTro3
matched
(chainLink table)
% of query
matched
(chainLinkXenTro3)
Lizard anoCar2 no5022008000HoxD55.q 3400lastz3020004001 2011-09-206.775% 5.110%
Chicken galGal3 no022008000HoxD55.q 3400lastz3020004001 2011-09-204.730% 5.273%
Turkey melGal1 no030002200default 9400lastz3020004001 2011-09-233.120% 3.846%
Opossum monDom5 no022008000HoxD55.q 3400lastz3020004001 2011-09-235.492% 2.144%
Rat rn4 no022008000HoxD55.q 3400lastz3020004001 2011-09-235.216% 2.574%
Mouse mm9 no022006000HoxD55.q 3400lastz3020004001 2011-09-216.609% 3.126%
Human hg19 no022006000HoxD55.q 3400lastz3020004001 2011-09-216.694% 3.035%
Zebrafish danRer7 no022006000HoxD55.q 3400lastz3020004001 2011-09-217.107% 6.510%