use strict;
use warnings;
my $seq = 'ATCGGCGCCTAT' ;
my %count;
our( $A1, $A2, $A3, $T1, $T2, $T3, $C1, $C2, $C3, $G1, $G2, $G3 )
    = (0) x 12;
foreach my $i (0 .. length($seq)-1 ) {
    my $pos = $i % 3 + 1;
    my $base = substr $seq, $i, 1;
    {no strict 'refs'; ${$base.$pos}++;}
}

print $A1, $A2, $A3, $T1, $T2, $T3, $C1, $C2, $C3, $G1, $G2, $G3;