Tool for nucleotide alignment with all nucleotide codes (e.g. R, Y, W, S, etc.)?
If you're looking for an exact match, you don't really need a complex aligner. Perl regular expressions are pretty powerful at string transformations or conditional matching of substrings. For example, to find all matches of AASYWSRA in a nucleotide sequence $seq, you can do:

@matches = $seq =~ m/AA[CG][CT][AT][CG][AG]A/g;


The [] brackets are known as Perl character classes, which allow different characters in a position.