Hg38 20-way conservation lastz parameters

See Also

• Human 20-way Hg38 20-way Genome size statistics
• Human 20-way Hg38 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 hg38 matched (chainLink table)	% of query matched (chainLinkHg38)
Chimp panTro4	no	254	4500	3000	human_chimp.v2.q	15000	lastz-distrib-1.03.52/bin/lastz	150	2000	600	2	2014-05-27	93.112%	95.664%
Bonobo panPan1	no	254	3000	3000	hg38.panPan1.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-11	92.929%	97.795%
Gorilla gorGor3	no	254	3000	3000	hg38.gorGor3.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-15	88.005%	91.695%
Orangutan ponAbe2	no	254	4500	3000	human_chimp.v2.q	15000	lastz-distrib-1.03.52/bin/lastz	150	2000	600	2	2014-09-02	89.187%	89.656%
Gibbon nomLeu3	no	254	3000	3000	hg38.nomLeu3.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-12	86.379%	90.470%
Proboscis monkey nasLar1	no	254	3000	3000	hg38.nasLar1.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-15	74.541%	89.972%
Golden snub-nosed monkey rhiRox1	no	254	3000	3000	hg38.rhiRox1.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2015-02-23	85.109%	86.629%
Crab-eating macaque macFas5	no	254	3000	3000	hg38.macFas5.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-14	85.675%	87.749%
Rhesus rheMac3	no	254	4500	3000	human_chimp.v2.q	15000	lastz-distrib-1.03.66/bin/lastz	150	2000	600	2	2015-04-09	80.828%	88.220%
Baboon papAnu2	no	254	3000	3000	hg38.papAnu2.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-13	84.179%	84.502%
Squirrel monkey saiBol1	no	254	3000	3000	hg38.saiBol1.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-13	70.565%	81.466%
Green monkey chlSab2	no	254	4500	3000	human_chimp.v2.q	15000	lastz-distrib-1.03.52/bin/lastz	150	2000	600	2	2014-07-11	84.393%	88.264%
Marmoset calJac3	no	254	3000	3000	hg38.calJac3.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-13	71.709%	76.757%
Tarsier tarSyr2	no	50	3000	3000	hg38.tarSyr2.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2014-12-12	56.022%	52.305%
Mouse lemur micMur1	no	254	3000	3000	hg38.micMur1.tuning.Q.txt	3400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	2	2015-03-22	42.653%	67.655%
Bushbaby otoGar3	no	254	3000	3000	default	9400	lastz-distrib-1.03.66/bin/lastz	30	2000	400	2	2015-02-23	53.196%	64.899%
Dog canFam3	no	0	3000	3000	default	9400	lastz-distrib-1.03.66/bin/lastz	30	2000	400	1	2015-04-10	50.395%	60.861%
Tree shrew tupBel1	no	254	3000	3000	default	9400	lastz-distrib-1.03.54/bin/lastz	30	2000	400	1	2015-03-27	35.019%	49.422%
Mouse mm10	no	0	3000	3000	default	9400	lastz-distrib-1.03.66/bin/lastz	30	2000	400	1	2015-04-09	31.653%	35.372%