I do quite a bit of bioinformatics programming in Perl and would consider myself fairly experienced on these kind of problems. Still, even I do not understand what you want to accomplish.

Are your paired sequences already aligned with other software? Are they amino acid or nucleotide sequences?

Are you aiming to compare amino acid usage/signatures among sequences using sliding windows of various lengths? Do you plan to have the slider partially overlap previous windows as it slides along the sequences or not?

Could you please elaborate a bit on your problem and workflow and preferably provide some code for us to have a go at?