# This matrix was derived from aligned segments of human and mouse DNA
# (F Chiaromonte, VB Yap, W Miller, PSB 2002:115-126).  It is the
# default score matrix for BLASTZ v7, along with a gap existence cost
# of 400 and a gap extension cost of 30.  The next line tells LAST to
# use these gap costs:
#last -a 400 -b 30
# Let's also use a minimum alignment score of 4500:
#last -e 4500
# lastex suggests that 4500 is not unreasonable for comparing
# mammalian genomes.  In any case, you can override these parameters
# by setting options when running LAST.  Finally, here is the matrix:

     A    C    G    T    N
A   91 -114  -31 -123 -100
C -114  100 -125  -31 -100
G  -31 -125  100 -114 -100
T -123  -31 -114   91 -100
N -100 -100 -100 -100 -100
