Are my assumptions correct ?? Or the sequences are already aligned and you just wish to count the differences ?

In both cases, when alignment is done to count the diff you just iterate through both arrays count triplets, hash them and the for every triplet make a subhash that will record the type and the count of a specific change.

Example:

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);

[download]

$VAR1 = {
          '1' => {
                   'G2T' => 3,
                   'T2G' => 1,
                   'A2G' => 1
                 },
          '3' => {
                   'G2T' => 1,
                   'C2A' => 1,
                   'T2G' => 2,
                   'A2T' => 1
                 },
          '2' => {
                   'G2T' => 1,
                   'T2G' => 1,
                   'A2-' => 1,
                   'A2C' => 1,
                   'T2-' => 1
                 }
        };

[download]

This time, what you're looking for is scarcely more than an extension or adaptation of the advice (and solutions) you've been given previously.

You'll do better to start now to try to solve your own homework(?) or $work(?). Twenty-one posts with little evidence that you've made a serious attempt to think through your own questions is not a good reflection on your desire to learn... which is what PM is largely about.