I've been working with a pseudo-consensus amino acid sequence (pseudo in the sense that it is not necessarily a true/accurate representation of the population due to sampling bias) via the Geneious program. In order to create the consensus sequence, a conservation threshold must be designated. If the proportion of matching residues at a given position exceed the set threshold, the residue is preserved in the consensus. Otherwise, it is listed as unknown. It would better suite my purposes if I could instead list multiple residues that exceed a reduced, more lenient threshold at a given position as a regular expression. Example:

Sequence 1 = ABCABC

Sequence 2 = BBCDAA

Sequence 3 = BBACAC

Sequence 4 = ACAABC

Output with required threshold at >=75% and no regular expressions = XBXXXC

Output with required threshold at >=50% and regular expressions allowed = [AB]B[CA]A[AB]C

My thought is this would be more accommodating for alignment scoring similar to how scoring matrices score residues based on similarity/dissimilarity. I'm trying to optimize alignments of sequences originating from single stranded RNA viruses with high rates of mutation and recombination. I'm also more interested in unique sequences/residues (harder to match/align) than the prevalence of reoccurring residues. This brings me to my question: Are there any alignment programs that accept regular expressions as input?

Edit: I feel it's necessary to emphasize that the odds of coincidental homologous/similar regions within "my" genome are low due to size (15kb in total length)