strange behaviour of GCG's fasta

[William R. Pearson]

I believe that the different alignments have different initn scores
because FASTA counts a N:A match as an identity and a N:G as a
non-identity.

The solution is to always do searches with oligonucleotide primers with
ktup=2 or ktup=1; that would fix the problem I think.

Bill Pearson