I am still not sure what your input is, but I hope you might find one of the following two solutions helpful:

use Data::Dumper;

my $string = 'MHDLKNDHASDRWT';
my %count_string;
$count_string{$_}++ for $string =~ /(?=(..))/g; # Uses look-ahead to o
+nly progress by one character.

my @array = split //, $string;
my %count_array;
$count_array{ join q(), @array[$_, $_ + 1] }++ for 0 .. $#array - 1;

print Dumper \%count_string, \%count_array;
[download]

Note: /AA/ matches the capital letter A followed by the capital letter A. It does not stand for "anything" in regular expressions.

Updated: Added the hashes.