GorGor3 conservation lastz parameters

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Revision as of 21:18, 15 August 2012 by Hiram (talk | contribs) (fixup default L value)
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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 gorGor3
matched
(chainLink table)
% of query
matched
(chainLinkGorGor3)
Chimp panTro3 no25445003000human_chimp.v2.q 15000lastz15020006002 2011-10-2689.043% 88.043%
Human hg19 no25445003000human_chimp.v2.q 15000lastz15020006002 2011-10-2191.109% 89.876%
Gibbon nomLeu1 no25445003000human_chimp.v2.q 15000lastz15020006002 2011-10-2683.476% 84.119%
Orangutan ponAbe2 no25445003000human_chimp.v2.q 15000lastz15020006002 2011-10-2386.354% 83.548%
Baboon papHam1 no25445003000human_chimp.v2.q 15000lastz15020006002 2011-10-3179.434% 80.874%
Rhesus rheMac2 no25445003000human_chimp.v2.q 15000lastz15020006002 2011-10-2379.244% 82.188%
Marmoset calJac3 no25445003000human_chimp.v2.q 15000lastz15020006002 2011-10-2768.507% 70.073%
Tarsier tarSyr1 no25445003000human_chimp.v2.q 15000lastz15020006002 2011-11-0519.482% 20.481%
Mouse lemur micMur1 no25445003000human_chimp.v2.q 15000lastz15020006002 2011-11-0322.908% 34.556%
Bushbaby otoGar1 no25445003000human_chimp.v2.q 15000lastz15020006002 2011-10-2712.017% 17.083%