TarSyr2 20-way conservation lastz parameters

See Also

• Tarsier 20-way TarSyr2 20-way Genome size statistics
• Tarsier 20-way TarSyr2 20-way 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 tarSyr2 matched (chainLink table)	% of query matched (chainLinkTarSyr2)
Squirrel monkey saiBol1	no	50	3000	3000	saiBol1.tarSyr2.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-15	48.208%	59.766%
Marmoset calJac3	no	50	3000	3000	calJac3.tarSyr2.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-13	48.629%	55.800%
Gorilla gorGor3	no	50	3000	3000	gorGor3.tarSyr2.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-13	50.262%	56.297%
Gibbon nomLeu3	no	50	3000	3000	nomLeu3.tarSyr2.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-13	50.545%	56.775%
Orangutan ponAbe2	no	50	3000	3000	ponAbe2.tarSyr2.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-13	51.302%	55.431%
Human hg38	no	50	3000	3000	hg38.tarSyr2.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-13	52.305%	56.022%
Bonobo panPan1	no	50	3000	3000	panPan1.tarSyr2.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-16	52.289%	59.834%
Chimp panTro4	no	50	3000	3000	panTro4.tarSyr2.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-15	51.284%	56.630%
Proboscis monkey nasLar1	no	50	3000	3000	nasLar1.tarSyr2.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-16	47.164%	61.165%
Golden snub-nosed monkey rhiRox1	no	50	3000	3000	rhiRox1.tarSyr2.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2015-02-24	51.539%	56.545%
Crab-eating macaque macFas5	no	50	3000	3000	macFas5.tarSyr2.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-16	51.814%	57.176%
Rhesus rheMac3	no	50	3000	3000	rheMac3.tarSyr2.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-16	50.710%	59.428%
Baboon papAnu2	no	50	3000	3000	papAnu2.tarSyr2.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-15	51.652%	56.346%
Green monkey chlSab2	no	50	3000	3000	chlSab2.tarSyr2.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-16	51.691%	58.191%
Mouse lemur micMur1	no	50	3000	3000	micMur1.tarSyr2.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-13	38.087%	64.649%
Bushbaby otoGar3	no	50	3000	3000	otoGar3.tarSyr2.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-15	44.814%	59.044%
Dog canFam3	no	0	3000	3000	default	9400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	1	2015-04-05	44.555%	57.932%
Tree shrew tupBel1	no	50	3000	3000	default	9400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	1	2015-04-02	31.268%	47.221%
Mouse mm10	no	0	3000	3000	default	9400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	1	2015-04-02	26.433%	32.301%