!!AA_SCORING_MATRIX_RECT 1.0

This matrix is the default scoring matrix used by FASTA and TFASTA for
the comparison of amino acid sequences.  TFASTA ignores the gap creation
and extension penalties specified in this matrix and using a GAPweight
of 16 and a LENgthweight of 4 if this matrix is used.

                     February 20, 1996 14:33   ..

{
GAP_CREATE 10
GAP_EXTEND 2
!GAP_CREATE 16 for TFASTA
!GAP_EXTEND 4 for TFASTA
}

      A    B    C    D    E     F    G    H    I    K     L    M    N    P    Q     R    S    T    V    W     X    Y    Z 
A     5   -2   -1   -2   -1    -3    0   -2   -1   -1    -2   -1   -1   -1   -1    -2    1    0    0   -3    -1   -2   -1 
B    -2    5   -3    5    1    -4   -1    0   -4    0    -4   -3    4   -2    0    -1    0    0   -4   -5    -1   -3    2 
C    -1   -3   13   -4   -3    -2   -3   -3   -2   -3    -2   -2   -2   -4   -3    -4   -1   -1   -1   -5    -2   -3   -3 
D    -2    5   -4    8    2    -5   -1   -1   -4   -1    -4   -4    2   -1    0    -2    0   -1   -4   -5    -1   -3    1 
E    -1    1   -3    2    6    -3   -3    0   -4    1    -3   -2    0   -1    2     0   -1   -1   -3   -3    -1   -2    5 

F    -3   -4   -2   -5   -3     8   -4   -1    0   -4     1    0   -4   -4   -4    -3   -3   -2   -1    1    -2    4   -4 
G     0   -1   -3   -1   -3    -4    8   -2   -4   -2    -4   -3    0   -2   -2    -3    0   -2   -4   -3    -2   -3   -2 
H    -2    0   -3   -1    0    -1   -2   10   -4    0    -3   -1    1   -2    1     0   -1   -2   -4   -3    -1    2    0 
I    -1   -4   -2   -4   -4     0   -4   -4    5   -3     2    2   -3   -3   -3    -4   -3   -1    4   -3    -1   -1   -3 
K    -1    0   -3   -1    1    -4   -2    0   -3    6    -3   -2    0   -1    2     3    0   -1   -3   -3    -1   -2    1 

L    -2   -4   -2   -4   -3     1   -4   -3    2   -3     5    3   -4   -4   -2    -3   -3   -1    1   -2    -1   -1   -3 
M    -1   -3   -2   -4   -2     0   -3   -1    2   -2     3    7   -2   -3    0    -2   -2   -1    1   -1    -1    0   -1 
N    -1    4   -2    2    0    -4    0    1   -3    0    -4   -2    7   -2    0    -1    1    0   -3   -4    -1   -2    0 
P    -1   -2   -4   -1   -1    -4   -2   -2   -3   -1    -4   -3   -2   10   -1    -3   -1   -1   -3   -4    -2   -3   -1 
Q    -1    0   -3    0    2    -4   -2    1   -3    2    -2    0    0   -1    7     1    0   -1   -3   -1    -1   -1    4 

R    -2   -1   -4   -2    0    -3   -3    0   -4    3    -3   -2   -1   -3    1     7   -1   -1   -3   -3    -1   -1    0 
S     1    0   -1    0   -1    -3    0   -1   -3    0    -3   -2    1   -1    0    -1    5    2   -2   -4    -1   -2    0 
T     0    0   -1   -1   -1    -2   -2   -2   -1   -1    -1   -1    0   -1   -1    -1    2    5    0   -3     0   -2   -1 
V     0   -4   -1   -4   -3    -1   -4   -4    4   -3     1    1   -3   -3   -3    -3   -2    0    5   -3    -1   -1   -3 
W    -3   -5   -5   -5   -3     1   -3   -3   -3   -3    -2   -1   -4   -4   -1    -3   -4   -3   -3   15    -3    2   -2 

X    -1   -1   -2   -1   -1    -2   -2   -1   -1   -1    -1   -1   -1   -2   -1    -1   -1    0   -1   -3    -1   -1   -1 
Y    -2   -3   -3   -3   -2     4   -3    2   -1   -2    -1    0   -2   -3   -1    -1   -2   -2   -1    2    -1    8   -2 
Z    -1    2   -3    1    5    -4   -2    0   -3    1    -3   -1    0   -1    4     0    0   -1   -3   -2    -1   -2    5