# 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 lastal
# to use these gap costs:
#lastal -a 400 -b 30
# Let's also use a minimum alignment score of 4000:
#lastal -e 4000
# The accompanying E-value tables suggest that 4000 is not
# unreasonable for comparing gigabase-scale sequences.  In any case,
# you can override these parameters by setting options when running
# lastal.  Finally, here is the matrix:

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