Mm10 conservation lastz parameters

See Also

• Mouse 60-way Mm10 Genome size statistics
• Mouse 60-way Mm10 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 mm10 matched (chainLink table)	% of query matched (chainLinkMm10)
Rat rn4	no	0	4500	2200	human_chimp.v2.q	15000	lastz-distrib-1.03.02/bin/lastz	150	2000	600	2	2012-03-08	54.645%	56.348%
Squirrel speTri2	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-16	34.217%	39.244%
Mouse lemur micMur1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-13	26.636%	37.574%
Kangaroo rat dipOrd1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-16	19.460%	27.512%
Squirrel monkey saiBol1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-09	32.339%	33.848%
Naked mole-rat hetGla1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-16	32.163%	36.427%
Human hg19	yes	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-08	38.226%	35.249%
Gorilla gorGor3	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-08	33.987%	34.349%
Chimp panTro4	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-10	34.674%	31.924%
Gibbon nomLeu1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-08	34.132%	32.372%
Orangutan ponAbe2	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-09	34.496%	30.610%
Tarsier tarSyr1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-12	24.560%	24.986%
Chinese rhesus rheMac3	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-09	33.931%	33.464%
Baboon papHam1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-10	33.577%	32.023%
Bushbaby otoGar3	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-13	29.795%	32.926%
Marmoset calJac3	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-09	32.450%	31.301%
Horse equCab2	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-16	34.415%	37.138%
Guinea pig cavPor3	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-17	28.447%	29.115%
Alpaca vicPac1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-17	22.636%	31.769%
Dolphin turTru1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-17	28.761%	32.385%
Tree shrew tupBel1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-17	19.766%	25.144%
Pig susScr2	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-17	23.248%	29.422%
Rabbit oryCun2	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-17	25.248%	25.677%
Sloth choHof1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-22	in progress	N/A
Megabat pteVam1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-20	27.345%	38.627%
Elephant loxAfr3	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-20	25.823%	21.616%
Cat felCat4	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-20	24.033%	30.953%
Panda ailMel1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-20	30.979%	35.562%
Dog canFam3	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-20	29.144%	31.624%
Armadillo dasNov2	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	in progress	in progress	N/A
Microbat myoLuc2	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-22	24.363%	33.650%
Cow bosTau7	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-22	26.255%	25.383%
Sheep oviAri1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	2012-03-22	15.341%	31.925%
Rock hyrax proCap1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	in progress	in progress	N/A
Pika ochPri2	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	in progress	in progress	N/A
Hedgehog eriEur1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	in progress	in progress	N/A
Tenrec echTel1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	in progress	in progress	N/A
Shrew sorAra1	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	in progress	in progress	N/A
Wallaby macEug2	no	0	3000	2200	default	9400	lastz-distrib-1.03.02/bin/lastz	30	2000	400	1	in progress	in progress	N/A
Opossum monDom5	TBD
Tasmanian devil sarHar1	TBD
N/A ailMis1	TBD
N/A croPor1	TBD
Platypus ornAna1	TBD
Chicken galGal4	TBD
Zebra finch taeGut1	TBD
Turkey melGal1	TBD
N/A chrPic1	TBD
Lizard anoCar2	TBD
X. tropicalis xenTro3	TBD
Coelacanth latCha1	TBD
Atlantic cod gadMor1	TBD
Nile tilapia oreNil1	TBD
Stickleback gasAcu1	TBD
Fugu fr3	TBD
Tetraodon tetNig2	TBD
Zebrafish danRer7	TBD
Medaka oryLat2	TBD
Lamprey petMar1	TBD