Hello WouterVG,

Welcome to the Monastery. You can search the forum it contains a lot of information as your question was asked before e.g. How do I shuffle an array?

Something like that should do what you want, assuming you want to shuffle array element (3 characters).

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

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

my @data;
push @data, $1 while ($sequence =~ /(.{1,3})/msxog);

print Dumper \@data;

my @random = shuffle @data;

print Dumper \@random;

__END__

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

Update: In case you want to use unpack see bellow:

#!/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'
        ];
[download]

Hope this helps, BR.