human-chimp.v2.mat

# This is a DNA substitution score matrix from UCSC.  It is
# reasonable, though not necessarily ideal, for human-chimp
# alignments.

# This sets the default gap costs for the LAST aligner:
#last -a500 -b30
# These differ from the gap costs used by UCSC, for an explanation see:
# MC Frith & R Kawaguchi, Genome Biol. 2015 16:106.

      A    C    G    T    N
A     90 -330 -236 -356 -100
C   -330  100 -318 -236 -100
G   -236 -318  100 -330 -100
T   -356 -236 -330   90 -100
N   -100 -100 -100 -100 -100