CalJac3 conservation lastz parameters

See Also

• Marmoset 13-way CalJac3 Genome size statistics
• Marmoset 13-way CalJac3 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 calJac3 matched (chainLink table)	% of query matched (chainLinkCalJac3)
Orangutan ponAbe2	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	0	600	2	2010-02-12	71.893%	67.448%
Human hg19	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	0	600	2	2010-02-11	73.768%	70.654%
Chimp panTro2	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	0	600	2	2010-02-11	72.304%	69.302%
Gorilla gorGor2	no	254	3000	3000	default	9400	lastz	30	0	400	1	2010-02-23	76.343%	75.481%
Rhesus rheMac2	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	0	600	2	2010-02-12	69.625%	70.711%
Baboon papHam1	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	0	600	2	2010-02-18	70.053%	69.607%
Tarsier tarSyr1	no	254	3000	3000	default	9400	lastz	30	0	400	1	2010-02-24	46.729%	N/A
Mouse lemur micMur1	no	254	3000	3000	default	9400	lastz	30	0	400	1	2010-02-21	45.726%	67.145%
Bushbaby otoGar1	no	254	3000	3000	default	9400	lastz	30	0	400	1	2010-02-21	42.743%	58.837%
Dog canFam2	no	50	3000	3000	default	9400	lastz	30	0	400	1	2010-02-14	50.766%	57.162%
Mouse mm9	no	50	3000	3000	default	9400	lastz	30	0	400	1	2010-02-14	31.310%	32.815%
Opossum monDom5	no	50	3000	3000	default	9400	lastz	30	0	400	1	2010-02-14	7.906%	6.174%