!!NA_SCORING_MATRIX_RECT 1.0

Default scoring matrix used by SEGMENTS for the comparison of
nucleic acid sequences.  SEGMENTS uses the method of Smith/Waterman to
make alignments.

This matrix weights all matches                            as  10
This matrix weights all matches to 2 way ambiugity symbols as   6
This matrix weights all matches to 3 way ambiugity symbols as   2
This matrix weights all matches to 4 way ambiugity symbols as   0
This matrix weights all gaps                               as   0
This matrix weights all mismatches                         as  -6

                     February 20, 1996 14:34   ..

{
GAP_CREATE 50
GAP_EXTEND 3
}

      A    B    C    D    G     H    K    M    R    S     T    U    V    W    Y  
A    10   -6   -6    2   -6     2   -6    6    6   -6    -6   -6    2    6   -6  
B    -6    2    2    2    2     2    2    2    2    2     2    2    2    2    2  
C    -6    2   10   -6   -6     2   -6    6   -6    6    -6   -6    2   -6    6  
D     2    2   -6    2    2     2    2    2    2    2     2    2    2    2    2  
G    -6    2   -6    2   10    -6    6   -6    6    6    -6   -6    2   -6   -6  

H     2    2    2    2   -6     2    2    2    2    2     2    2    2    2    2  
K    -6    2   -6    2    6     2    6   -6    6    6     6    6    2    6    6  
M     6    2    6    2   -6     2   -6    6    6    6    -6   -6    2    6    6  
R     6    2   -6    2    6     2    6    6    6    6    -6   -6    2    6   -6  
S    -6    2    6    2    6     2    6    6    6    6    -6   -6    2   -6    6  

T    -6    2   -6    2   -6     2    6   -6   -6   -6    10   10   -6    6    6  
U    -6    2   -6    2   -6     2    6   -6   -6   -6    10   10   -6    6    6  
V     2    2    2    2    2     2    2    2    2    2    -6   -6    2    2    2  
W     6    2   -6    2   -6     2    6    6    6   -6     6    6    2    6    6  
Y    -6    2    6    2   -6     2    6    6   -6    6     6    6    2    6    6