use strict;
use warnings;
use Readonly;
use Data::Dumper qw( Dumper );
Readonly::Scalar my $seq => "ATCGGCGCCTAT" ;
my %count;
@count{ qw(A1 A2 A3 T1 T2 T3 C1 C2 C3 G1 G2 G3 ) } = (0) x (3*4); 
foreach my $i (0 .. length($seq)-1 ) {
    my $pos = $i % 3 + 1;
    my $base = substr $seq, $i, 1;
    $count{$base.$pos}++;
}

$Data::Dumper::Sortkeys = 1;
print Dumper \%count;