Ce9 conservation lastz parameters

See Also:

• Ce9 Genome size statistics
• Ce9 conservation alignment
• Hg19 Genome size statistics
• Hg19 conservation alignment
• Hg19 Andy's alignment notes
• Hg18 44way blastz parameters
• Hg18 Genome size statistics
• Hg18 44way alignment

The default 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

lastz parameters

Automatically generated table, do not edit

query	abridged repeats(no)	M(40M)	K(3000)	L(3000)	Q	Y(9400)	program run	E(30)	H(0)	O(400)	T(1)	chain table date	% of ce9 matched (chainLink table)	% of query matched (chainLinkCe9)
C. briggsae cb3	no	50	3000	3000	default	9400	lastz	30	2000	400	1	2010-09-20	42.300%	39.763%
C. remanei caeRem3	no	50	3000	3000	default	9400	lastz	30	2000	400	1	2010-09-20	41.722%	33.467%
C. brenneri caePb2	no	50	3000	3000	default	9400	lastz	30	2000	400	1	2010-09-20	40.677%	32.313%
C. japonica caeJap3	no	50	3000	3000	default	9400	lastz	30	2000	400	1	2010-09-22	27.580%	19.464%
H. contortus haeCon1	no	50	3000	3000	default	9400	lastz	30	2000	400	1	2010-09-23	7.463%	3.178%
P. pacificus priPac2	no	50	3000	3000	default	9400	lastz	30	2000	400	1	2010-09-29	5.862%	4.692%
M. hapla melHap1	no	50	3000	3000	default	9400	lastz	30	2000	400	1	2010-09-22	3.922%	6.849%
M. incognita melInc1	no	50	3000	3000	default	9400	lastz	30	2000	400	1	2010-09-22	3.301%	5.166%
B. malayi bruMal1	no	50	3000	3000	default	9400	lastz	30	2000	400	1	2010-09-22	4.790%	5.457%