I am not certain about your objectives, but maybe something like the following would do what you want. It doesn't use a window but it does add numbers, as I understand your description.

use strict;
use warnings;

my $string = "ATATGCGCAT";

my %levels = (
    A   => 3,
    T   => 2,
    G   => 2,
    C   => 1,
);

my @letters = split(//,$string);
my $max = $#letters;

my @numbers = map { 1 } @letters;

while(1) {
    # Print the current combination of letters and numbers
    print "~";
    for my $n (0..$max) {
        print $letters[$n] . $numbers[$n];
    }
    print "~\n";

    # Calculate the next set of numbers
    my $n = 0;
    $numbers[$n]++;
    while($numbers[$n] > $levels{$letters[$n]}) {
        $numbers[$n] = 1;
        $n++;
        last if($n > $max);
        $numbers[$n]++;
    }
    last if($n > $max);
}
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