How do you know which part refers to which sequence ($s1 vs $s2 for example)?

Sorry, but you are going to have to clarify that question. Which "part" of what?

(You should also have used <code></code> tags;

and it is helpful when you reference another post to link to it Re: Hamming Distance Between 2 Strings - Fast(est) Way? using [id://500244])

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In reply to Re^10: Comparing 2 different-sized strings by BrowserUk
in thread Comparing 2 different-sized strings by AdrianJ217

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