open (DATA, $results) || die "couldn't open the file!"; my %unique = (); while( ){ chomp; $unique{ join( "\t", sort split /\t/ ) } ++; } my @pairs = (); my @not_pairs = (); for my $item (sort keys %unique ){ if( $unique{$item} > 1 ){ push @pairs, $item; }else{ push @not_pairs, $item; } } print join( "\n", @pairs ), "\n";