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my $str = "BEBEBEHUHUHUJJFAFALL";
my $length = 2;
...
    $cnt{$substring}++;                              # increasing the 
+counter for the substring
    $index += $length;                               # increasing the 
+offset by $length
}

   'BE' => 3
   'FA' => 2
   'HU' => 3
   'JJ' => 1
   'LL' => 1