!!NA_SCORING_MATRIX_RECT 1.0

Default (from upam.gbl) scoring matrix used by FASTA for the comparison
of nucleic acid sequences. FASTA uses the method of Pearson and Lipman
to find sequences in a data library that are similar to a query
sequence.

This matrix was updated for FASTA version 2.0, and thus differs from
the older versions of the matrix.

                     February 20, 1996 14:33   ..

{
GAP_CREATE 16
GAP_EXTEND 4
}

      A    B    C    D    G     H    K    M    N    R     S    T    U    V    W     X    Y 
A     5   -2   -4    1   -4     1   -1    2   -1    2    -1   -4   -4    1    2    -1   -1 
B    -2    1    1   -1    1    -1    1   -1   -1   -1     1    1    1   -1   -1    -1    1 
C    -4    1    5   -2   -4     1   -1    2   -1   -1     2   -4   -4    1   -1    -1    2 
D     1   -1   -2    1    1    -1    1   -1   -1    1    -1    1    1   -1    1    -1   -1 
G    -4    1   -4    1    5    -2    2   -1   -1    2     2   -4   -4    1   -1    -1   -1 

H     1   -1    1   -1   -2     1   -1    1   -1   -1    -1    1    1   -1    1    -1    1 
K    -1    1   -1    1    2    -1    2   -1   -1    1     1    2    2   -1    1    -1    1 
M     2   -1    2   -1   -1     1   -1    2   -1   -1     1   -1   -1    1    1    -1   -1 
N    -1   -1   -1   -1   -1    -1   -1   -1   -1   -1    -1   -1   -1   -1   -1    -1   -1 
R     2   -1   -1    1    2    -1    1   -1   -1    2     1   -1   -1    1    1    -1   -2 

S    -1    1    2   -1    2    -1    1    1   -1    1     2   -1   -1    1   -1    -1    1 
T    -4    1   -4    1   -4     1    2   -1   -1   -1    -1    5    5   -2    2    -1    2 
U    -4    1   -4    1   -4     1    2   -1   -1   -1    -1    5    5   -1    2    -1    2 
V     1   -1    1   -1    1    -1   -1    1   -1    1     1   -2   -1    1   -1    -1   -1 
W     2   -1   -1    1   -1     1    1    1   -1    1    -1    2    2   -1    2    -1    1 

X    -1   -1   -1   -1   -1    -1   -1   -1   -1   -1    -1   -1   -1   -1   -1    -1   -1 
Y    -1    1    2   -1   -1     1    1   -1   -1   -2     1    2    2   -1    1    -1    2