Table 1.

LASTZ alignment parameters

Parameter	Primates				Other
Gap open penalty (O)	400				400
Gap extend penalty (E)	30				30
HSP threshold (K)	5000				3000
Threshold for gapped extension (L)	5000				3000
Threshold for alignments between gapped alignment blocks (H)	3000				2200
Masking count (M)	10				–
Seed and transition value (T)	1				1
Scoring matrix (Q)	A	C	G	T	A	C	G	T
	90	−330	−236	−356	91	−114	−31	−123
	−330	100	−318	−236	−114	100	−125	−31
	−236	−318	100	−330	−31	−125	100	−114
	−356	−236	−330	90	−123	−31	−114	91