!!AA_SCORING_MATRIX_RECT 1.0

Dayhoff table (Schwartz, R. M. and Dayhoff, M. O. [1979] in Atlas of
Protein Sequence and Structure, Dayhoff, M. O. Ed, pp. 353-358, National
Biomedical Research Foundation, Washington D.C.) rescaled by dividing
each value by the sum of its row and column, and normalizing to a mean
of 0 and standard deviation of 1.0.  The value for FY (Phe-Tyr) = RW =
1.425.  Perfect matches are set to 1.5 and no matches on any row are
better than perfect matches. 

Each value multiplied by 10 to convert to integer scoring matrix.

Table used by Gribskov and Burgess NAR 14(16) 6745-6763

                     February 20, 1996 14:55   ..

{
GAP_CREATE 30
GAP_EXTEND 1
}

      A    B    C    D    E     F    G    H    I    K     L    M    N    P    Q     R    S    T    V    W     Y    Z 
A    15    2    3    3    3    -5    7   -1    0    0    -1    0    2    5    2    -3    4    4    2   -8    -3    2 
B     2   11   -4   11    7    -7    6    4   -2    4    -5   -3   11    1    5     1    3    2   -2   -7    -3    6 
C     3   -4   15   -5   -6    -1    2   -1    2   -6    -8   -6   -3    1   -6    -3    7    2    2  -12    10   -6 
D     3   11   -5   15   10   -10    7    4   -2    3    -5   -4    7    1    7     0    2    2   -2  -11    -5    9 
E     3    7   -6   10   15    -7    5    4   -2    3    -3   -2    5    1    7     0    2    2   -2  -11    -5   11 

F    -5   -7   -1  -10   -7    15   -6   -1    7   -7    12    5   -5   -7   -8    -5   -3   -3    2   13    14   -7 
G     7    6    2    7    5    -6   15   -2   -3   -1    -5   -3    4    3    2    -3    6    4    2  -10    -7    3 
H    -1    4   -1    4    4    -1   -2   15   -3    1    -2   -3    5    2    7     5   -2   -1   -3   -1     3    5 
I     0   -2    2   -2   -2     7   -3   -3   15   -2     8    6   -3   -2   -3    -3   -1    2   11   -5     1   -2 
K     0    4   -6    3    3    -7   -1    1   -2   15    -3    2    4    1    4     8    2    2   -2    1    -6    4 

L    -1   -5   -8   -5   -3    12   -5   -2    8   -3    15   13   -4   -3   -1    -4   -4   -1    8    5     3   -2 
M     0   -3   -6   -4   -2     5   -3   -3    6    2    13   15   -3   -2    0     2   -3    0    6   -3    -1   -1 
N     2   11   -3    7    5    -5    4    5   -3    4    -4   -3   15    0    4     1    3    2   -3   -3    -1    4 
P     5    1    1    1    1    -7    3    2   -2    1    -3   -2    0   15    3     3    4    3    1   -8    -8    2 
Q     2    5   -6    7    7    -8    2    7   -3    4    -1    0    4    3   15     4   -1   -1   -2   -5    -6   11 

R    -3    1   -3    0    0    -5   -3    5   -3    8    -4    2    1    3    4    15    1   -1   -3   14    -6    2 
S     4    3    7    2    2    -3    6   -2   -1    2    -4   -3    3    4   -1     1   15    3   -1    3    -4    0 
T     4    2    2    2    2    -3    4   -1    2    2    -1    0    2    3   -1    -1    3   15    2   -6    -3    1 
V     2   -2    2   -2   -2     2    2   -3   11   -2     8    6   -3    1   -2    -3   -1    2   15   -8    -1   -2 
W    -8   -7  -12  -11  -11    13  -10   -1   -5    1     5   -3   -3   -8   -5    14    3   -6   -8   15    11   -8 

Y    -3   -3   10   -5   -5    14   -7    3    1   -6     3   -1   -1   -8   -6    -6   -4   -3   -1   11    15   -6 
Z     2    6   -6    9   11    -7    3    5   -2    4    -2   -1    4    2   11     2    0    1   -2   -8    -6   11