Fr3 conservation lastz parameters

See Also

• Fugu 6-way Fr3 Genome size statistics
• Fugu 6-way Fr3 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 fr3 matched (chainLink table)	% of query matched (chainLinkFr3)
Tetraodon tetNig2	no	50	3000	3000	HoxD55.q	9400	lastz	30	2000	400	1	2011-12-01	70.912%	80.674%
Nile tilapia oreNil1	no	50	3000	3000	HoxD55.q	9400	lastz	30	2000	400	1	2011-12-02	57.240%	30.736%
Stickleback gasAcu1	no	50	3000	3000	HoxD55.q	9400	lastz	30	2000	400	1	2011-12-02	55.527%	48.038%
Medaka oryLat2	no	50	3000	3000	HoxD55.q	9400	lastz	30	2000	400	1	2011-12-02	43.863%	25.905%
Zebrafish danRer7	no	50	3000	3000	HoxD55.q	9400	lastz	30	2000	400	1	2011-12-02	22.823%	7.365%