The indentation in your code makes it a bit difficult to see what is in your foreach loops and what isn't. In addition to the problems with @pairs that jasonk and meetraz pointed out, there are some other things that don't make sense with the code pasted.

• You declare and assign to $base and $pair but never use them.
• In your last foreach you have $nn_pair as the loop variable, but use $_ inside the loop.
• At the top you say @pairs = get_nn_pairs (@segment1); but you are printing @sorted_array at the end of the sub, not returning the array.

You may want to try something like the code below:

sub get_nn_pairs {
    my @segment1 = @_;
    my @pairs;

    #  find and print all nn pairs form the sequence.

    foreach my $i (1 .. $#segment1) {
        push @pairs, "$segment1[$i-1]$segment1[$i]";
    }

    my %freq;
    foreach my $nn_pair (@pairs) {
        $freq{$nn_pair}++;
    }
    my @sorted_array = sort { $freq{$b} <=> $freq{$a} } keys %freq;
    return @sorted_array;
}


my @ordered_pairs = get_nn_pairs(@input);
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