use strict;
use warnings;
my %bucket = (
      key1 =>   {   '1' => 3},
       key2 =>  {  '1' => 3,
                   '2' => 2},
      key3 =>   {   '1' => 11,
                    '2' => 36}
  );

my %spair = ();
my $cnt =0;

  foreach my $kmer ( keys %bucket  )
  {
     foreach my $si (keys %{$bucket{$kmer}})
     {     foreach my $sn (keys %{$bucket{$kmer}}) 
	   { 
	     next if exists $spair{$sn."-".$si};
	     if ( $si == $sn )
	     {
        	$cnt = $bucket{$kmer}{$si};
	     }
	     else
	     {
                $cnt = $bucket{$kmer}{$si}*$bucket{$kmer}{$sn};
	     }
		$spair{$si."-".$sn} +=$cnt; 
            }
     }     # ----- end foreach ----- 
  }  # ----- end foreach -----

use Data::Dumper;
print Dumper \%spair;


##</code><code>##

$VAR1 = {
          '1-1' => 17, # 3+3+11
          '2-2' => 38, # 2+36
          '1-2' => 402 # (3*2)+(11*36), this is correct already
        };

##</code><code>##

$VAR1 = {
          '1-1' => 3,  #wrong
          '2-2' => 2,  #wrong
          '1-2' => 402 #correct
        };