CalJac3 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 calJac3
matched
(chainLink table)
% of query
matched
(chainLinkCalJac3)
Orangutan ponAbe2 no25445003000human_chimp.v2.q 15000lastz15006002 2010-02-1271.893% 67.448%
Human hg19 no25445003000human_chimp.v2.q 15000lastz15006002 2010-02-1173.768% 70.654%
Chimp panTro2 no25445003000human_chimp.v2.q 15000lastz15006002 2010-02-1172.304% 69.302%
Gorilla gorGor2 no25430003000default 9400lastz3004001 2010-02-2376.343% 75.481%
Rhesus rheMac2 no25445003000human_chimp.v2.q 15000lastz15006002 2010-02-1269.625% 70.711%
Baboon papHam1 no25445003000human_chimp.v2.q 15000lastz15006002 2010-02-1870.053% 69.607%
Tarsier tarSyr1 no25430003000default 9400lastz3004001 2010-02-2446.729% N/A
Mouse lemur micMur1 no25430003000default 9400lastz3004001 2010-02-2145.726% 67.145%
Bushbaby otoGar1 no25430003000default 9400lastz3004001 2010-02-2142.743% 58.837%
Dog canFam2 no5030003000default 9400lastz3004001 2010-02-1450.766% 57.162%
Mouse mm9 no5030003000default 9400lastz3004001 2010-02-1431.310% 32.815%
Opossum monDom5 no5030003000default 9400lastz3004001 2010-02-147.906% 6.174%