!!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 100
GAP_EXTEND 2
}

      A     C      G      T      U  
A   -.9    0.01   -.9     0.5    0.5 
C  0.01    -0.9    1      -.9   -.9  
G    -.9     1    -.9    0.25   0.25
T    0.5    -.9   0.25     -.9  -0.9
U    0.5   -.9     .25    -.9   -.9