# This matrix assigns a score of 2 to matches, -1 to transitions, and
# -2 to transversions.  When used with a gap existence cost of 16 and
# a gap extension cost of 1, it gives very sensitive and accurate
# alignments of distantly-related protein-coding sequences (MC Frith
# et al. 2010, BMC Bioinformatics).  The next line tells LAST to use
# these gap costs:
#last -a 16 -b 1
# Let's also use a minimum alignment score of 90:
#last -e 90
# lastex suggests that 90 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
A  2 -2 -1 -2
C -2  2 -2 -1
G -1 -2  2 -2
T -2 -1 -2  2