Suboptimal Local Alignment

The Lalign program for finding multiple alternative matches via suboptimal alignment is available here.

http://rosalind.info/problems/subo/

Given: Two DNA strings s and t in FASTA format that share some short inexact repeat r of 32-40 bp. By "inexact" we mean that r may appear with slight modifications (each repeat differ by ≤3 changes/indels).

Return: The total number of occurrences of r as a substring of s, followed by the total number of occurrences of r as a substring of t.