Here's one way to match overlapping patterns: 

#!/usr/bin/perl

# http://perlmonks.org/?node_id=1124725

use Data::Dump qw(pp);
use strict;
$| = 1;
my %answer;

for my $line ( 'AAALVDENEC', 'AATLVDEGDG' )
  {
  $answer{$line}{$_}++ for $line =~
    /(?=(AA|AL|DA|DE|DV|VD|DW|QD|SD|HD|ED|DY|VE|EN|EI|KE|NV|VP|FV|SS|W
+K|KK))/g;
  }

pp \%answer;

[download]

which produces: 

{
  AAALVDENEC => { AA => 2, AL => 1, DE => 1, EN => 1, VD => 1 },
  AATLVDEGDG => { AA => 1, DE => 1, VD => 1 },
}

[download]

That has the 5 and 3 you are looking for.

In reply to Re^3: how do i count the 22 selected di-peptides from a multifasta file separately for each sequence by Anonymous Monk
in thread how do i count the 22 selected di-peptides from a multifasta file separately for each sequence by SOMEN

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