!!NA_SCORING_MATRIX_RECT 1.0

Alternative scoring matrix that could be used by PROFILEMAKE to create a
profile from a group of aligned nucleic acid sequences.  This matrix may
be appropriate if you use the /GLObal switch with PROFILEGAP or
PROFILESEGMENTS.

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  0

                     March 26, 1996 10:38   ..

{
GAP_CREATE 31
GAP_EXTEND 3
}

      A    B    C    D    G     H    K    M    R    S     T    U    V    W    Y  
A    10    0    0    2    0     2    0    6    6    0     0    0    2    6    0  
B     0    2    2    2    2     2    2    2    2    2     2    2    2    2    2  
C     0    2   10    0    0     2    0    6    0    6     0    0    2    0    6  
D     2    2    0    2    2     2    2    2    2    2     2    2    2    2    2  
G     0    2    0    2   10     0    6    0    6    6     0    0    2    0    0  

H     2    2    2    2    0     2    2    2    2    2     2    2    2    2    2  
K     0    2    0    2    6     2    6    0    6    6     6    6    2    6    6  
M     6    2    6    2    0     2    0    6    6    6     0    0    2    6    6  
R     6    2    0    2    6     2    6    6    6    6     0    0    2    6    0  
S     0    2    6    2    6     2    6    6    6    6     0    0    2    0    6  

T     0    2    0    2    0     2    6    0    0    0    10   10    0    6    6  
U     0    2    0    2    0     2    6    0    0    0    10   10    0    6    6  
V     2    2    2    2    2     2    2    2    2    2     0    0    2    2    2  
W     6    2    0    2    0     2    6    6    6    0     6    6    2    6    6  
Y     0    2    6    2    0     2    6    6    0    6     6    6    2    6    6