# 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