Hg38 7-way conservation lastz parameters

See Also

• Human 7-way Hg38 7-way Genome size statistics
• Human 7-way Hg38 7-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)
Chimp panTro4	no	254	4500	3000	human_chimp.v2.q	15000	lastz-distrib-1.03.52/bin/lastz	150	2000	600	2	2014-05-27	93.112%	95.664%
Rhesus rheMac3	no	254	4500	3000	human_chimp.v2.q	15000	lastz-distrib-1.03.52/bin/lastz	150	2000	600	2	2014-01-28	79.729%	86.715%
Dog canFam3	no	0	3000	3000	default	9400	lastz-distrib-1.03.52/bin/lastz	30	2000	400	1	2014-01-27	49.978%	60.083%
Mouse mm10	no	0	3000	3000	default	9400	lastz-distrib-1.03.52/bin/lastz	30	2000	400	1	2014-01-25	31.629%	35.323%
Rat rn5	no	0	3000	3000	default	9400	lastz-distrib-1.03.52/bin/lastz	30	2000	400	1	2014-03-01	30.788%	36.312%
Opossum monDom5	no	50	2200	6000	HoxD55.q	3400	lastz-distrib-1.03.52/bin/lastz	30	2000	400	1	2014-05-29	14.370%	11.996%