TarSyr2 20-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 tarSyr2
matched
(chainLink table)
% of query
matched
(chainLinkTarSyr2)
Squirrel monkey saiBol1 no5030003000saiBol1.tarSyr2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1548.208% 59.766%
Marmoset calJac3 no5030003000calJac3.tarSyr2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1348.629% 55.800%
Gorilla gorGor3 no5030003000gorGor3.tarSyr2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1350.262% 56.297%
Gibbon nomLeu3 no5030003000nomLeu3.tarSyr2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1350.545% 56.775%
Orangutan ponAbe2 no5030003000ponAbe2.tarSyr2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1351.302% 55.431%
Human hg38 no5030003000hg38.tarSyr2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1352.305% 56.022%
Bonobo panPan1 no5030003000panPan1.tarSyr2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1652.289% 59.834%
Chimp panTro4 no5030003000panTro4.tarSyr2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1551.284% 56.630%
Proboscis monkey nasLar1 no5030003000nasLar1.tarSyr2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1647.164% 61.165%
Golden snub-nosed monkey rhiRox1 no5030003000rhiRox1.tarSyr2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2015-02-2451.539% 56.545%
Crab-eating macaque macFas5 no5030003000macFas5.tarSyr2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1651.814% 57.176%
Rhesus rheMac3 no5030003000rheMac3.tarSyr2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1650.710% 59.428%
Baboon papAnu2 no5030003000papAnu2.tarSyr2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1551.652% 56.346%
Green monkey chlSab2 no5030003000chlSab2.tarSyr2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1651.691% 58.191%
Mouse lemur micMur1 no5030003000micMur1.tarSyr2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1338.087% 64.649%
Bushbaby otoGar3 no5030003000otoGar3.tarSyr2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1544.814% 59.044%
Dog canFam3 no030003000default 9400lastz-distrib-1.03.54/bin/lastz3020004001 2015-04-0544.555% 57.932%
Tree shrew tupBel1 no5030003000default 9400lastz-distrib-1.03.54/bin/lastz3020004001 2015-04-0231.268% 47.221%
Mouse mm10 no030003000default 9400lastz-distrib-1.03.54/bin/lastz3020004001 2015-04-0226.433% 32.301%