Hg38 5-way conservation lastz parameters

See Also

• Human 5-way Hg38 5-way Genome size statistics
• Human 5-way Hg38 5-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 hg38 matched (chainLink table)	% of query matched (chainLinkHg38)
Malayan flying lemur galVar1	no	254	3000	3000	default	9400	lastz-distrib-1.03.66/bin/lastz	30	2000	400	1	2016-04-26	57.036%	64.881%
Chinese tree shrew tupChi1	no	0	3000	3000	default	9400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	1	2015-02-19	45.256%	50.350%
Guinea pig cavPor3	no	254	3000	3000	default	9400	lastz-distrib-1.03.66/bin/lastz	30	2000	400	1	2015-04-28	42.371%	48.000%
Mouse mm10	no	0	3000	3000	default	9400	lastz-distrib-1.03.66/bin/lastz	30	2000	400	1	2015-04-09	31.653%	35.372%