#!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
use List::Util qw(shuffle);

my $sequence = "CTGCAC";
# chomp($sequence = <STDIN>);

my @trips = unpack("(A3)*", $sequence);
print Dumper \@trips;

my @shuffled = shuffle @trips ;
print Dumper \@shuffled;

__END__

 perl test.pl
$VAR1 = [
          'CTG',
          'CAC'
        ];
$VAR1 = [
          'CAC',
          'CTG'
        ];