CavPor3 6-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 cavPor3
matched
(chainLink table)
% of query
matched
(chainLinkCavPor3)
Malayan flying lemur galVar1 no030003000default 9400lastz-distrib-1.03.54/bin/lastz3020004001 2016-04-1548.820% 48.448%
Human hg38 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2948.000% 42.371%
Chinese tree shrew tupChi1 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2017-11-1741.511% 41.225%
Tree shrew tupBel1 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2016-04-1527.994% 34.990%
Mouse mm10 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1929.115% 28.447%