use strict; use warnings; my $string = "AAAATTTAGTTCTTAAGGCTGACATCACGTCAGCGTTACCCCCCAAGATTGGGGACTTT"; my $len = 0; my $best = ''; $best = $1, $len = length $1 while $string =~ /((.)\2{$len,})/g; print "best: $best ($len)\n"