GeoFor1 conservation lastz parameters

See Also

• Medium ground finch 7-way GeoFor1 Genome size statistics
• Medium ground finch 7-way GeoFor1 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 geoFor1 matched (chainLink table)	% of query matched (chainLinkGeoFor1)
Zebra finch taeGut1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-07-31	92.532%	92.089%
Chicken galGal4	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-07-30	70.718%	72.077%
Turkey melGal1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-07-29	67.079%	72.625%
Budgerigar melUnd1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-07-29	80.650%	76.598%
Human hg19	no	0	2200	10000	HoxD55.q	3400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-07-29	8.504%	3.503%
Mouse mm10	no	0	2200	6000	HoxD55.q	3400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-07-29	7.709%	3.543%