PonAbe2 conservation lastz parameters

See Also

• Orangutan 8-way PonAbe2 Genome size statistics
• Orangutan 8-way PonAbe2 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 ponAbe2 matched (chainLink table)	% of query matched (chainLinkPonAbe2)
Human hg18	no	50	3000	3000	default	9400	lastz	30	0	400	1	2009-09-02	91.302%	92.892%
Chimp panTro2	no	50	3000	3000	default	9400	lastz	30	0	400	1	2009-08-15	89.431%	91.033%
Rhesus rheMac2	no	50	3000	3000	default	9400	lastz	30	0	400	1	2009-08-15	82.623%	88.157%
Marmoset calJac1	no	50	3000	3000	default	9400	lastz	30	0	400	1	2009-08-15	74.694%	76.925%
Mouse mm9	no	50	3000	3000	default	9400	lastz	30	0	400	1	2009-08-15	30.659%	34.902%
Opossum monDom4	no	50	2200	6000	HoxD55.q	3400	lastz	30	0	400	1	2009-08-15	13.137%	11.306%
Platypus ornAna1	no	50	2200	6000	HoxD55.q	3400	lastz	30	0	400	1	2009-08-15	6.936%	10.931%