Rn5 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 rn5
matched
(chainLink table)
% of query
matched
(chainLinkRn5)
Mouse mm10 yes030003000mouse_rat_2.q 5000lastz-distrib-1.03.02/bin/lastz5520006002 2012-03-2770.278% 67.353%
Guinea pig cavPor3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-12-0129.127% 28.164%
Human hg19 no030003000default 9400lastz3020004001 2012-06-2836.299% 31.662%
Chimp panTro4 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-12-0135.616% 31.061%
Rhesus rheMac3 no25430003000default 9400lastz3020004001 2012-07-1134.835% 32.516%
Dog canFam3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-12-0329.852% 30.695%
Panda ailMel1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-12-0131.818% 34.580%
Cow bosTau7 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-12-0126.820% 24.528%
Opossum monDom5 no25422006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-12-049.694% 6.902%
Chicken galGal4 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-11-303.788% 7.860%
Turkey melGal1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-11-143.630% 7.975%
Zebrafish danRer7 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-11-142.588% 4.824%