#!/usr/bin/perl -w
use strict;

my @dna = qw(GTTC TTTT GGGG CCCC GAAC);
my %seen;

for my $index_1 ( 0 .. $#dna ) {

    next if $seen{$index_1};
    $seen{$index_1} = 1;
    my $dna1 = reverse $dna[ $index_1 ];

    for my $index_2 ( 0 .. $#dna ) {

        next if $seen{$index_2};
        my $dna2 = $dna[ $index_2 ];

        if ( match($dna1 , $dna2) ) {
            $seen{$index_2} = 1;
            print join " : " , $dna1, $index_1, $dna2, $index_2;
            print $/;
        }
    }
}

sub match {
    my @dna = map { [ split // ] } @_;
    my %val = ( A => -1, T => 1, G => -2, C => 2 );

    for ( 0 .. $#{$dna[0]} ) {
        return 0 if $val{ $dna[0]->[$_] } + $val{ $dna[1]->[$_] };
    }
    return 1;
}
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Cheers - L~R