i think i understand what you're after. a feature of the TK language is tagging in text/area fields. the tags are a way of marking positions (starting and ending) in text, which does not change the character count of the text. so what i have in mind is that you compare the reference sequence to each comparative sequence in turn, adding tags as you go. then at the end you do some post-processing to insert/delete/amend/other the text field depending on the tags inserted. or if you want the tags to immediately do something, you can bind them to actions (callbacks.) Anyway, I can't say enough about this really neat feature in TK. Most perls have TK or you can install it and the bindings.
hope that's what you were looking for.