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#!/usr/bin/perl

...
  print "String: $string     Positions: ", join( ', ', @found ), "\n";
}

String: GNNTCGANNTT     Positions: 2, 8
String: GAATCGNNNTT     Positions: 2
String: GANNCGNNNNN     Positions: 0, 7

$,=42;for(34,0,-3,9,-11,11,-17,7,-5){$*.=pack'c'=>$,+=$_}for(reverse s
+plit//=>$*
){$%++?$ %%2?push@C,$_,$":push@c,$_,$":(push@C,$_,$")&&push@c,$"}$C[$#
+C]=$/;($#C
>$#c)?($ c=\@C)&&($ C=\@c):($ c=\@c)&&($C=\@C);$%=$|;for(@$c){print$_^
+$$C[$%++]}