__DATA__
ABCD
EFGH

##</code><code>##

$VAR1 = {
           '0' => [
                   'AB',
                    EF
                 ],

          '1' => [
                   'BC',
                   'FG'
                 ],

          '2' => [
                   'CD',
                   'GH',
                 ]
        };

##</code><code>##

#!/usr/bin/perl -w
use strict;
use Data::Dumper;

my $enum_size =0;
my %hash;

my $sub_length = 2;
my $lmer;

while( <DATA>  ) {
 chomp;
 my @array;

 $enum_size = length ($_)  - $sub_length +1;

 for (my $j =0 ;$j <$enum_size ;$j++)
 {
   $lmer = substr ($_, $j, $sub_length);
   push @array, $lmer;
   $hash{$j}=[@array];
 }

}

 print Dumper \%hash;
 #Then do sth with the %hash