Does a single file have a single sequence? You said these polyA tails are at (or near?) the end.

If the files have just one sequence and are small enough to fit in memory, slurp into a scalar, strip any irrelevant characters, and the regular expression qr/[AN]{10,}/ would find the tails.

If the files are too large, or have more than one sequence, you'll have to work a little harder to fit in memory. Reading a couple lines at a time, searching the tailing line(s) for a matching tail.

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