You didn't say in what way the code is behaving differently from your expectation but it's a fairly simple problem to solve correctly; even without recursion.

#!/usr/bin/perl -w
use strict;
use warnings;
use Data::Dumper;

my $length = 2;

my @motif = ( '' );

for my $i ( 1 .. $length ) {
    @motif = map {
        my $motif = $_;
        map $motif . $_, qw( a t c g );
    } @motif;
}

print Dumper \@motif;
[download]

Ie we start out with a list with a single empty string and then on each round, we create four new strings for every string we already have.

(The shard-eyed will notice that this code does the same work as the recursive variant, only explicitly — well, and in different order.)

Makeshifts last the longest.