use strict;
use Data::Dumper;

my $r = 'AAATGTGATGTGAACGT';
my $t = 'AATGTGTCGT-TG-ATG';

my @a = split('',$r);
my @v = split('',$t);

my %hash =();

my $tt = @a>@v ? @a : @v;


for(my $i = 0 ; $i<$tt;$i++){
  my $z = 1+$i %3; # Update - suggested by Perlbotics, better !
  unless ($a[$i] eq $v[$i]){
    $hash{$z}->{"$a[$i]2$v[$i]"}++;
  }
} 

print Dumper(\%hash);