See here: https://news.ycombinator.com/item?id=9096064 https://news.ycombinator.com/item?id=9096064 Turns out they aren't actually after an alignment per se, b

See here: https://news.ycombinator.com/item?id=9096064 https://news.ycombinator.com/item?id=9096064 Turns out they aren't actually after an alignment per se, but rather trying to match a DNA binding motif. (You're right though about this not being an alignment, rather just a substring search with degeneracy).