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

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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.

davis
It wasn't easy to juggle a pregnant wife and a troubled child, but somehow I managed to fit in eight hours of TV a day.

In reply to Re: splitting a sequence using unpack by davis
in thread splitting a sequence using unpack by Rashmun

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