CavPor3 6-way conservation lastz parameters

See Also

• Guinea pig 6-way CavPor3 6-way Genome size statistics
• Guinea pig 6-way CavPor3 6-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 cavPor3 matched (chainLink table)	% of query matched (chainLinkCavPor3)
Malayan flying lemur galVar1	no	0	3000	3000	default	9400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	1	2016-04-15	48.820%	48.448%
Human hg38	no	254	3000	3000	default	9400	lastz-distrib-1.03.66/bin/lastz	30	2000	400	1	2015-04-29	48.000%	42.371%
Chinese tree shrew tupChi1	no	0	3000	3000	default	9400	lastz-distrib-1.03.66/bin/lastz	30	2000	400	1	2017-11-17	41.511%	41.225%
Tree shrew tupBel1	no	0	3000	3000	default	9400	lastz-distrib-1.03.66/bin/lastz	30	2000	400	1	2016-04-15	27.994%	34.990%
Mouse mm10	no	0	3000	3000	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-19	29.115%	28.447%