PanTro3 conservation lastz parameters

See Also

• Chimp 12-way PanTro3 Genome size statistics
• Chimp 12-way PanTro3 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 panTro3 matched (chainLink table)	% of query matched (chainLinkPanTro3)
Human hg19	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	0	600	2	2011-02-23	95.597%	N/A
Orangutan ponAbe2	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	0	600	2	2011-03-06	89.586%	87.748%
Rhesus rheMac2	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	0	600	2	2011-03-06	81.342%	85.681%
Marmoset calJac3	no	254	4500	3000	human_chimp.v2.q	15000	lastz	150	0	600	2	2011-03-06	69.662%	72.471%
Horse equCab2	no	0	3000	3000	default	9400	lastz	30	0	400	1	2011-03-06	56.504%	65.863%
Dog canFam2	no	0	3000	3000	default	9400	lastz	30	0	400	1	2011-03-06	51.588%	60.315%
Mouse mm9	no	0	3000	3000	default	9400	lastz	30	0	400	1	2011-03-07	32.044%	35.182%
Rat rn4	no	0	3000	3000	default	9400	lastz	30	0	400	1	2011-03-17	30.350%	34.038%
Opossum monDom5	no	50	2200	6000	HoxD55.q	3400	lastz	30	0	400	1	2011-03-11	13.743%	11.337%
Chicken galGal3	no	50	2200	6000	HoxD55.q	3400	lastz	30	0	400	1	2011-03-02	4.557%	11.116%
Zebrafish danRer7	no	50	2200	6000	HoxD55.q	3400	lastz	30	0	400	1	2011-03-01	2.558%	5.821%