DanRer10 12-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 danRer10
matched
(chainLink table)
% of query
matched
(chainLinkDanRer10)
Stickleback gasAcu1 no25430003000HoxD55.q 9400lastz-distrib-1.03.66/bin/lastz3020004001 2017-02-109.814% 27.557%
Spotted gar lepOcu1 no25430003000HoxD55.q 9400lastz-distrib-1.04.00/bin/lastz3020004001 2020-02-258.409% 11.294%
Tetraodon tetNig2 no25430003000HoxD55.q 9400lastz-distrib-1.03.66/bin/lastz3020004001 2017-02-096.063% 23.344%
Fugu fr3 no25430003000HoxD55.q 9400lastz-distrib-1.03.66/bin/lastz3020004001 2017-02-097.080% 22.699%
Medaka oryLat2 no25430003000HoxD55.q 9400lastz-distrib-1.03.66/bin/lastz3020004001 2017-02-099.640% 17.684%
X. tropicalis xenTro9 no022006000HoxD55.q 3400lastz-distrib-1.04.00/bin/lastz3020004001 2020-02-256.731% 7.029%
Chicken galGal6 no25422004000HoxD55.q 3400lastz-distrib-1.04.00/bin/lastz3020004001 2020-02-255.871% 6.171%
Elephant shark calMil1 no25430003000HoxD55.q 9400lastz-distrib-1.04.00/bin/lastz3020004001 2020-02-255.599% 7.088%
Human hg38 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-097.110% 3.357%
Mouse mm10 no022006000HoxD55.q 3400lastz-distrib-1.03.66/bin/lastz3020004001 2015-09-185.228% 2.769%
Coelacanth latCha1 no25430003000HoxD55.q 9400lastz-distrib-1.04.00/bin/lastz3020004001 2020-02-256.319% 4.504%