I really wanted to solve this problem as it was rather interesting, but I couldn't figure out what you were looking for in @seg_mis, so you might want to read the node that broquaint suggested. In the meantime, here's what I whipped up. It's a bit closer, but not quite what you need. If you can show sample output for both arrays, that would help.

#!/usr/bin/perl -w
use strict;
use Data::Dumper;

my @segments = map { [split //] } qw( ATCG AAGG );
print Dumper get_mismatches(@segments);

sub get_mismatches   {
    my ($segment, $comp_segment) = make_base_pairs(@_);
    my @seg_mismatches;
    my @seg_mis;

    foreach my $i ( 0 .. $#$segment ) {
        my $p1 = $segment->[$i];
        my $p2 = $comp_segment->[$i];
        if (
              bad_pair($p1->[0],$p2->[0]) or                       
              bad_pair($p1->[1],$p2->[1])
        ) {
            push @seg_mismatches => sprintf "%s%s/%s%s", @$p1, @$p2;
        }
    }
    return (\@seg_mismatches, \@seg_mis);
}

sub make_base_pairs {
    my @segment = @_;
    # assumes length of 4.  Don't know if this is correct
    my @results;
    foreach my $dna (@segment) {
        push @results => [ [@{$dna}[0..1]], [@{$dna}[2..3]] ];
    }
    return @results;
}

sub bad_pair {
    my ($a,$b) = @_;
    my %good_pairs = (
        'A'=> 'T',
        'C' => 'G',
        'G' => 'C',
        'T' => 'A'
    );
    return 1 if exists $good_pairs{$a} and $good_pairs{$a} eq $b;
}
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Cheers,
Ovid

New address of my CGI Course.
Silence is Evil (feel free to copy and distribute widely - note copyright text)