GorGor3 conservation lastz parameters

See Also

• Gorilla 11-way GorGor3 Genome size statistics
• Gorilla 11-way GorGor3 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 gorGor3 matched (chainLink table)	% of query matched (chainLinkGorGor3)
Chimp panTro3	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	2000	600	2	2011-10-26	89.043%	88.043%
Human hg19	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	2000	600	2	2011-10-21	91.109%	89.876%
Gibbon nomLeu1	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	2000	600	2	2011-10-26	83.476%	84.119%
Orangutan ponAbe2	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	2000	600	2	2011-10-23	86.354%	83.548%
Baboon papHam1	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	2000	600	2	2011-10-31	79.434%	80.874%
Rhesus rheMac2	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	2000	600	2	2011-10-23	79.244%	82.188%
Marmoset calJac3	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	2000	600	2	2011-10-27	68.507%	70.073%
Tarsier tarSyr1	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	2000	600	2	2011-11-05	19.482%	20.481%
Mouse lemur micMur1	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	2000	600	2	2011-11-03	22.908%	34.556%
Bushbaby otoGar1	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	2000	600	2	2011-10-27	12.017%	17.083%