Rn5 13-way conservation lastz parameters

See Also

• Rat 13-way Rn5 13-way Genome size statistics
• Rat 13-way Rn5 13-way conservation alignment
• all other UCSC Multiple Alignments

The default scoring matrix is:		The HoxD55 scoring matrix is:		The mouse_rat_2 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 100 -139 -54 -170 C -139 95 -83 -54 G -54 -83 95 -139 T -170 -54 -139 100 O=400 E=30

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 rn5 matched (chainLink table)	% of query matched (chainLinkRn5)
Mouse mm10	yes	0	3000	3000	mouse_rat_2.q	5000	lastz-distrib-1.03.02/bin/lastz	55	2000	600	2	2012-03-27	70.278%	67.353%
Guinea pig cavPor3	no	0	3000	3000	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-12-01	29.127%	28.164%
Human hg38	no	0	3000	3000	default	9400	lastz-distrib-1.03.52/bin/lastz	30	2000	400	1	2014-03-26	36.312%	30.788%
Chimp panTro4	no	0	3000	3000	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-12-01	35.616%	31.061%
Rhesus rheMac3	no	254	3000	3000	default	9400	lastz	30	2000	400	1	2012-07-11	34.835%	32.516%
Dog canFam3	no	0	3000	3000	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-12-03	29.852%	30.695%
Panda ailMel1	no	0	3000	3000	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-12-01	31.818%	34.580%
Cow bosTau7	no	0	3000	3000	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-12-01	26.820%	24.528%
Opossum monDom5	no	254	2200	6000	HoxD55.q	3400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-12-04	9.694%	6.902%
Chicken galGal4	no	0	2200	6000	HoxD55.q	3400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-11-30	3.788%	7.860%
Turkey melGal1	no	0	2200	6000	HoxD55.q	3400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-11-14	3.630%	7.975%
Zebrafish danRer7	no	0	2200	6000	HoxD55.q	3400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-11-14	2.588%	4.824%