!!NA_SCORING_MATRIX_RECT 1.0

Default scoring matrix used by GELMERGE for the comparison of nucleic
acid sequences (used in the alignment of contig fragments).  Values for
comparisons involving IUB nucleotide ambiguity symbols are ignored since
those ambiguity symbols are converted into a weighted composition of
unambiguous bases (G, A, T, C) by GELMERGE.

                     February 20, 1996 14:33   ..

{
GAP_CREATE 8
GAP_EXTEND 2
}

      A    C    G    T    .     ~ 
A    10    0    0    0   -2    -2 
C     0   10    0    0   -2    -2 
G     0    0   10    0   -2    -2 
T     0    0    0   10   -2    -2 
.    -2   -2   -2   -2    0     0 

~    -2   -2   -2   -2    0     0