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use strict; use warnings;

open READER, '<', 'rna.txt';
...
open RESULTS, '>', 'results.txt';
   print RESULTS "$protein\n";
close RESULTS;

...NEWTAWFLNSPAAGPNQCQIVY...   # Answer I should get

...NEWTAWFLNSPK  PNQCQIVY...   # My answer