from what i understand :

$x = "MAAGAAAAFAAAATTTTTTTTFTTTTTTTTTTTTAAAAEAAAARAAAAAA";
$y = "TTTTTTTTFTTTTTTTTTTTT";

if ($x =~ /$y/o) {print "the second amino acid is in the first";}
if ($y =~ /$x/o) {print "the first amino acid is in the second";}
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