!!NA_SCORING_MATRIX_RECT 1.0

Default scoring matrix used by BESTFIT for the comparison of nucleic
acid sequences.  BESTFIT uses the method of Smith/Waterman to make alignments.
X's and N's are treated as matches to any IUB ambiguity symbol. All
mismatches for IUB symbols are -9, making BESTFIT clip off the best
fitting segment at the point where the sequences stop being very similar. 

                     February 20, 1996 14:35   ..

{
GAP_CREATE 50
GAP_EXTEND 3
}

      A    B    C    D    G     H    K    M    N    R     S    T    U    V    W     X    Y 
A    10   -9   -9   10   -9    10   -9   10   10   10    -9   -9   -9   10   10    10   -9 
B    -9   10   10   10   10    10   10   10   10   10    10   10   10   10   10    10   10 
C    -9   10   10   -9   -9    10   -9   10   10   -9    10   -9   -9   10   -9    10   10 
D    10   10   -9   10   10    10   10   10   10   10    10   10   10   10   10    10   10 
G    -9   10   -9   10   10    -9   10   -9   10   10    10   -9   -9   10   -9    10   -9 

H    10   10   10   10   -9    10   10   10   10   10    10   10   10   10   10    10   10 
K    -9   10   -9   10   10    10   10   -9   10   10    10   10   10   10   10    10   10 
M    10   10   10   10   -9    10   -9   10   10   10    10   -9   -9   10   10    10   10 
N    10   10   10   10   10    10   10   10   10   10    10   10   10   10   10    10   10 
R    10   10   -9   10   10    10   10   10   10   10    10   -9   -9   10   10    10   -9 

S    -9   10   10   10   10    10   10   10   10   10    10   -9   -9   10   -9    10   10 
T    -9   10   -9   10   -9    10   10   -9   10   -9    -9   10   10   -9   10    10   10 
U    -9   10   -9   10   -9    10   10   -9   10   -9    -9   10   10   -9   10    10   10 
V    10   10   10   10   10    10   10   10   10   10    10   -9   -9   10   10    10   10 
W    10   10   -9   10   -9    10   10   10   10   10    -9   10   10   10   10    10   10 

X    10   10   10   10   10    10   10   10   10   10    10   10   10   10   10    10   10 
Y    -9   10   10   10   -9    10   10   10   10   -9    10   10   10   10   10    10   10