Hg38 30-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 hg38
matched
(chainLink table)
% of query
matched
(chainLinkHg38)
Chimp panTro5 no25445004500human_chimp.v2.q 15000lastz-distrib-1.03.66/bin/lastz15020006002 2016-08-0495.355% 93.714%
Bonobo panPan2 no25445004500human_chimp.v2.q 15000lastz-distrib-1.03.66/bin/lastz15020006002 2016-05-2492.685% 97.742%
Gorilla gorGor5 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.66/bin/lastz15020006002 2016-06-2594.691% 89.804%
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%
Black snub-nosed monkey rhiBie1 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.66/bin/lastz15020006002 2017-03-2383.065% 81.306%
Golden snub-nosed monkey rhiRox1 no25430003000hg38.rhiRox1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2015-02-2385.109% 86.629%
Angolan colobus colAng1 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.66/bin/lastz15020006002 2017-02-2781.641% 87.875%
Crab-eating macaque macFas5 no25430003000hg38.macFas5.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1485.675% 87.749%
Rhesus rheMac8 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.66/bin/lastz15020006002 2016-02-0884.506% 79.540%
Baboon papAnu3 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2017-06-2286.336% 86.461%
Pig-tailed macaque macNem1 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.66/bin/lastz15020006002 2017-02-2783.524% 85.402%
Sooty mangabey cerAty1 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.66/bin/lastz15020006002 2017-09-2783.847% 86.974%
Squirrel monkey saiBol1 no25430003000hg38.saiBol1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1370.565% 81.466%
Green monkey chlSab2 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.52/bin/lastz15020006002 2014-07-1184.393% 88.264%
Drill manLeu1 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.66/bin/lastz15020006002 2017-09-2582.498% 88.550%
Ma's night monkey aotNan1 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.66/bin/lastz15020006002 2017-09-2570.629% 77.791%
Marmoset calJac3 no25430003000hg38.calJac3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1371.709% 76.757%
White-faced sapajou cebCap1 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.66/bin/lastz15020006002 2017-09-2870.683% 78.656%
Sclater's lemur eulFla1 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.66/bin/lastz15020006002 2017-10-0333.326% 46.309%
Black lemur eulMac1 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.66/bin/lastz15020006002 2017-10-0433.708% 46.640%
Tarsier tarSyr2 no5030003000hg38.tarSyr2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1256.022% 52.305%
Coquerel's sifaka proCoq1 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.66/bin/lastz15020006002 2017-09-2832.467% 45.739%
Mouse lemur micMur3 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.66/bin/lastz15020006002 2017-03-0429.728% 36.904%
Bushbaby otoGar3 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004002 2015-02-2353.196% 64.899%
Dog canFam3 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-1050.395% 60.861%
Armadillo dasNov3 no25430003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-2945.349% 41.895%
Mouse mm10 no030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-04-0931.653% 35.372%