Hi! Is this a school/university assignment? If so, I would suggest you to start trying things and playing with the code and data a bit by yourself, without really thinking of "the best algorithm". If they are already asking you to "not write so much code", I doubt that their goal is to develop the best method to carry this task. Also, there are many and very good alignment tools out there already. I would start by taking a given sequence of length N, and extracting a subsequence from it, manually modify one letter of this subsequence and try to write code to map this subsequence into the larger sequence allowing mismatches. See this for some inspiration.