!!NA_SCORING_MATRIX_RECT 1.0

Default scoring matrix used by REPEAT for the comparision of nucleic 
acid sequences.  This matrix scores a match for any overlap between two
IUB nucleic acid ambiguity symbols EXCEPT X/N.

                     February 20, 1996 14:34   ..

      A    B    C    D    G     H    K    M    R    S     T    U    V    W    Y  
A     1    0    0    1    0     1    0    1    1    0     0    0    1    1    0  
B     0    1    1    1    1     1    1    1    1    1     1    1    1    1    1  
C     0    1    1    0    0     1    0    1    0    1     0    0    1    0    1  
D     1    1    0    1    1     1    1    1    1    1     1    1    1    1    1  
G     0    1    0    1    1     0    1    0    1    1     0    0    1    0    0  

H     1    1    1    1    0     1    1    1    1    1     1    1    1    1    1  
K     0    1    0    1    1     1    1    0    1    1     1    1    1    1    1  
M     1    1    1    1    0     1    0    1    1    1     0    0    1    1    1  
R     1    1    0    1    1     1    1    1    1    1     0    0    1    1    0  
S     0    1    1    1    1     1    1    1    1    1     0    0    1    0    1  

T     0    1    0    1    0     1    1    0    0    0     1    1    0    1    1  
U     0    1    0    1    0     1    1    0    0    0     1    1    0    1    1  
V     1    1    1    1    1     1    1    1    1    1     0    0    1    1    1  
W     1    1    0    1    0     1    1    1    1    0     1    1    1    1    1  
Y     0    1    1    1    0     1    1    1    0    1     1    1    1    1    1