XenTro9 11-way conservation lastz parameters

See Also

• X. tropicalis 11-way XenTro9 11-way Genome size statistics
• X. tropicalis 11-way XenTro9 11-way conservation alignment
• all other UCSC Multiple Alignments

The default scoring matrix is:		The HoxD55 scoring matrix is:		The human-chimp.v2 scoring matrix is:
A C G T A 91 -114 -31 -123 C -114 100 -125 -31 G -31 -125 100 -114 T -123 -31 -114 91 O=400 E=30		A C G T A 91 -90 -25 -100 C -90 100 -100 -25 G -25 -100 100 -90 T -100 -25 -90 91 O=400 E=30		A C G T A 90 -330 -236 -356 C -330 100 -318 -236 G -236 -318 100 -330 T -356 -236 -330 90 O=600 E=150

do not edit, automatically generated table

query	abridged repeats(no)	M(0)	K(3000)	L(3000)	Q	Y(9400)	program run	E(30)	H(0)	O(400)	T(1)	chain table date	% of xenTro9 matched (chainLink table)	% of query matched (chainLinkXenTro9)
African clawed frog xenLae2	no	0	3000	3000	default	9400	lastz-distrib-1.03.66/bin/lastz	30	2000	400	1	2017-04-06	54.877%	45.983%
Tibetan frog nanPar1	no	0	3000	3000	default	9400	lastz-distrib-1.03.66/bin/lastz	30	2000	400	1	2017-03-30	8.180%	6.700%
Painted turtle chrPic2	no	0	2200	6000	HoxD55.q	3400	lastz-distrib-1.03.66/bin/lastz	30	2000	400	1	2017-04-07	6.459%	4.977%
Opossum monDom5	no	0	2200	8000	HoxD55.q	3400	lastz-distrib-1.03.66/bin/lastz	30	2000	400	1	2017-04-07	5.414%	2.218%
Chicken galGal5	no	0	3000	3000	default	9400	lastz-distrib-1.03.66/bin/lastz	30	2000	400	1	2017-04-07	3.387%	3.601%
Lizard anoCar2	no	0	2200	6000	HoxD55.q	3400	lastz-distrib-1.03.66/bin/lastz	30	2000	400	1	2017-04-07	5.977%	4.794%
Dog canFam3	no	0	3000	3000	default	9400	lastz-distrib-1.03.66/bin/lastz	30	2000	400	1	2017-04-06	3.311%	1.890%
Human hg38	no	50	2200	6000	HoxD55.q	3400	lastz-distrib-1.03.66/bin/lastz	30	2000	400	1	2017-03-30	7.950%	3.861%
Mouse mm10	no	0	2200	6000	HoxD55.q	3400	lastz-distrib-1.03.66/bin/lastz	30	2000	400	1	2017-03-30	6.581%	3.282%
Fugu fr3	no	0	2200	6000	HoxD55.q	3400	lastz-distrib-1.03.66/bin/lastz	30	2000	400	1	2017-04-07	3.777%	12.822%