Not addressing your problem but you might be able to save some typing and avoid mistakes by building your @array programmatically. The following code uses a recursive subroutine to construct an anonymous array ($raTerms), which is then dereferenced (@$raTerms) and printed. Running it with a maximum of three letters for brevity here.

use strict;
use warnings;

use 5.014;

my $raItems = [ qw{ A T G C } ];
my $raTerms = [];

makeCombos( $raTerms, 3, $raItems );
say for @$raTerms;

sub makeCombos
{
    my( $raTerms, $iters, $raItems, @terms ) = @_;

    my @localTerms;
    if ( @terms )
    {
        push @localTerms,
           map {
               my $item = $_;
               map {
                   $_ . $item
                   } @terms
               } @$raItems;
    }
    else
    {
        push @localTerms, @$raItems;
    }

    $iters --;
    push @$raTerms, @localTerms;

    return
       $iters
       ? makeCombos( $raTerms, $iters, $raItems, @localTerms )
       : ();
}
[download]

The output.

A
T
G
C
AA
TA
GA
CA
AT
TT
GT
CT
AG
TG
GG
CG
AC
TC
GC
CC
AAA
TAA
GAA
CAA
ATA
TTA
GTA
CTA
AGA
TGA
GGA
CGA
ACA
TCA
GCA
CCA
AAT
TAT
GAT
CAT
ATT
TTT
GTT
CTT
AGT
TGT
GGT
CGT
ACT
TCT
GCT
CCT
AAG
TAG
GAG
CAG
ATG
TTG
GTG
CTG
AGG
TGG
GGG
CGG
ACG
TCG
GCG
CCG
AAC
TAC
GAC
CAC
ATC
TTC
GTC
CTC
AGC
TGC
GGC
CGC
ACC
TCC
GCC
CCC
[download]

I hope this is helpful.