# This is the default matrix used by SPDBV; it comes from SIM (Huang & Miller)
#  "A Time-Efficient, Linear-Space Local Similarity Algorithm"
#   Advances in Applied Mathematics, vol. 12 (1991), pp. 337-357.
#
#
# PAM 200 substitution matrix (scale = 0.346574)
#
# Number of letters in alphabet = 23
# Lowest score = -6, Highest score = 12
#
   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X
   2 -2  0  0 -2 -1  0  1 -1 -1 -2 -1 -1 -3  1  1  1 -5 -3  0  1  1  0 A
  -2  5  0 -1 -3  1 -1 -3  1 -2 -2  2  0 -3  0  0 -1  1 -4 -2  0  1  0 R
   0  0  2  2 -3  0  1  0  1 -1 -2  1 -2 -2  0  1  0 -4 -1 -2  3  2  0 N
   0 -1  2  3 -4  1  3  0  0 -2 -3  0 -2 -4 -1  0  0 -6 -3 -2  4  3  0 D
  -2 -3 -3 -4  8 -4 -4 -3 -3 -2 -5 -4 -4 -4 -2  0 -2 -6  0 -2 -3 -3  0 C
  -1  1  0  1 -4  4  2 -1  2 -2 -1  0 -1 -4  0 -1 -1 -4 -3 -2  2  4  0 Q
   0 -1  1  3 -4  2  3  0  0 -2 -3  0 -2 -4  0  0  0 -6 -3 -2  3  4  0 E
   1 -3  0  0 -3 -1  0  4 -2 -2 -3 -2 -3 -3 -1  1  0 -5 -4 -1  1  0  0 G
  -1  1  1  0 -3  2  0 -2  5 -2 -2  0 -2 -1  0 -1 -1 -3  0 -2  2  2  0 H
  -1 -2 -1 -2 -2 -2 -2 -2 -2  4  2 -1  2  1 -2 -1  0 -5 -1  3 -1 -1  0 I
  -2 -2 -2 -3 -5 -1 -3 -3 -2  2  4 -2  3  1 -2 -2 -1 -4 -1  1 -2 -1  0 L
  -1  2  1  0 -4  0  0 -2  0 -1 -2  4  1 -4 -1  0  0 -3 -4 -2  1  1  0 K
  -1  0 -2 -2 -4 -1 -2 -3 -2  2  3  1  5  0 -2 -1  0 -4 -2  1 -1  0  0 M
  -3 -3 -2 -4 -4 -4 -4 -3 -1  1  1 -4  0  7 -4 -2 -2  0  5 -1 -2 -3  0 F
   1  0  0 -1 -2  0  0 -1  0 -2 -2 -1 -2 -4  5  1  0 -5 -4 -1  0  1  0 P
   1  0  1  0  0 -1  0  1 -1 -1 -2  0 -1 -2  1  2  1 -2 -2 -1  1  1  0 S
   1 -1  0  0 -2 -1  0  0 -1  0 -1  0  0 -2  0  1  3 -4 -2  0  1  0  0 T
  -5  1 -4 -6 -6 -4 -6 -5 -3 -5 -4 -3 -4  0 -5 -2 -4 12  0 -6 -3 -4  0 W
  -3 -4 -1 -3  0 -3 -3 -4  0 -1 -1 -4 -2  5 -4 -2 -2  0  7 -2 -1 -2  0 Y
   0 -2 -2 -2 -2 -2 -2 -1 -2  3  1 -2  1 -1 -1 -1  0 -6 -2  4 -1 -1  0 V
   1  0  3  4 -3  2  3  1  2 -1 -2  1 -1 -2  0  1  1 -3 -1 -1  4  4  0 B
   1  1  2  3 -3  4  4  0  2 -1 -1  1  0 -3  1  1  0 -4 -2 -1  4  5  0 Z
   0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0 X
