#!/usr/bin/perl
use strict;
use warnings;

my $big_dna = 'TGAACCCGGGATTTGAGATTCCGGGGTTAAAAACGATTGAACCCGGGATTTGAGATTCCGGGGTTAAAAA';
my $cutter = 'GATT';

my @cutted_parts;
my $cutter_length=length($cutter);
my $pos=0;
while( (my $p=index($big_dna,$cutter,$pos)) > -1 )
{
  push(@cutted_parts, substr($big_dna,$pos,$p-$pos) );
  $pos=$p+$cutter_length;
}
push(@cutted_parts,substr($big_dna,$pos)) if($pos<length($big_dna));

print "$_\n" for(@cutted_parts);