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

my @data = qw(AAA ATG TTT GTC);
my %hash;

for my $entry (@data) {
    my @codes = split //, $entry;

    ++$hash{$codes[$_]}[$_] for 0 .. $#codes;
}

print Dumper (\%hash);

foreach my $entry (values %hash) {
    $entry = [map {defined $_ ? $_ : 0} @$entry];
}

print Dumper (\%hash);