XenTro3 conservation lastz parameters

See Also

• X. tropicalis 8-way XenTro3 Genome size statistics
• X. tropicalis 8-way XenTro3 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 xenTro3 matched (chainLink table)	% of query matched (chainLinkXenTro3)
Lizard anoCar2	no	50	2200	8000	HoxD55.q	3400	lastz	30	2000	400	1	2011-09-20	6.775%	5.110%
Chicken galGal3	no	0	2200	8000	HoxD55.q	3400	lastz	30	2000	400	1	2011-09-20	4.730%	5.273%
Turkey melGal1	no	0	2200	8000	HoxD55.q	3400	lastz	30	2000	400	1	2011-09-28	4.203%	5.244%
Opossum monDom5	no	0	2200	8000	HoxD55.q	3400	lastz	30	2000	400	1	2011-09-23	5.492%	2.144%
Rat rn4	no	0	2200	8000	HoxD55.q	3400	lastz	30	2000	400	1	2011-09-23	5.216%	2.574%
Mouse mm9	no	0	2200	6000	HoxD55.q	3400	lastz	30	2000	400	1	2011-09-21	6.609%	3.126%
Human hg19	no	0	2200	6000	HoxD55.q	3400	lastz	30	2000	400	1	2011-09-21	6.694%	3.035%
Zebrafish danRer7	no	0	2200	6000	HoxD55.q	3400	lastz	30	2000	400	1	2011-09-21	7.107%	6.510%