# This scoring matrix targets alignments with the following properties.
# Percent identity: 92.1563
# Percent A+T: 78.935
# Ratio of transitions to transversions: 0.332553
# Ratio of transition rate to transversion rate (alpha/beta): 1
# Expected number of transitions per site: 0.0208262
# Expected number of transversions per site: 0.0626253
# Expected number of substitutions per site: 0.0834515
# Scale parameter (lambda): 0.427882
   a  c  g  t
a  2 -5 -5 -5
c -5  5 -5 -5
g -5 -5  5 -5
t -5 -5 -5  2
