Hg38 17-way conservation lastz parameters

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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 hg38
matched
(chainLink table)
% of query
matched
(chainLinkHg38)
Chimp panTro4 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.52/bin/lastz15020006002 2014-05-2793.112% 95.664%
Bonobo panPan1 no25430003000hg38.panPan1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1192.929% 97.795%
Gorilla gorGor3 no25430003000hg38.gorGor3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1588.005% 91.695%
Orangutan ponAbe2 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.52/bin/lastz15020006002 2014-09-0289.187% 89.656%
Gibbon nomLeu3 no25430003000hg38.nomLeu3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1286.379% 90.470%
Proboscis monkey nasLar1 no25430003000hg38.nasLar1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1574.541% 89.972%
Golden snub-nosed monkey rhiRox1 no25430003000hg38.rhiRox1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1274.547% 71.639%
Green monkey chlSab2 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.52/bin/lastz15020006002 2014-07-1184.393% 88.264%
Crab-eating macaque macFas5 no25430003000hg38.macFas5.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1485.675% 87.749%
Rhesus rheMac3 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.52/bin/lastz15020006002 2014-01-2879.729% 86.715%
Baboon papAnu2 no25430003000hg38.papAnu2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1384.179% 84.502%
Squirrel monkey saiBol1 no25430003000hg38.saiBol1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1370.565% 81.466%
Marmoset calJac3 no25430003000hg38.calJac3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1371.709% 76.757%
Tarsier tarSyr2 no5030003000hg38.tarSyr2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1256.022% 52.305%
Mouse lemur micMur1 no25430003000hg38.micMur1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1942.653% 67.655%
Bushbaby otoGar3 no25430003000hg38.otoGar3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1349.485% 60.561%