It's a little unclear what your question is, but if you're trying to split every 3 characters, what about:

#!/usr/bin/perl

use warnings;
use strict;
use Data::Dumper;

while(<DATA>) {
        chomp;
        my @triplets = $_ =~ /(.{1,3})/gs;
        print Dumper \@triplets;
}
__DATA__
atgcatccctttaat
tctgtctga
[download]

This splits using a regular expression, matching between 1 and 3 characters per "chunk", and it'll endeavour to match as many characters per chunk as possible.