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To be fair, to my knowledge, LASTZ, BLAST, or BLAT don't treat IUPAC ambiguous bases (K, Y, R, etc.) in the way the OP was looking for. That's not to blame the tools, since they have a very good reason not to (they build an index on the target first, and treating ambiguous bases properly would increase the size of the index).

That said, I wonder if grep wouldn't be much faster, since this program is only looking for exact matches, which are easily transformed into a regex by replacing the ambiguous nucleotides with something like (A|T|C).