my $i;
my $j;
my $dna;
my $temp_dna;

for ($i=0; $i < @array1; $i++) {
   $dna = $array1[$i];
   $temp_dna = $dna;
   $dna = reverse $dna;
   $dna =~ tr/actg/tgac/;

   for ($j=0; $j < @array1; $j++) {
      if ($dna eq $array1[$j]) {
         print "FOUND $temp_dna\t$array[$j]\n";
      }
   }
}
[download]

Well, if it's just finding matches inside the same array, it's just a variation on finding uniques in an array. Here's one way of solving it:

#!/usr/bin/perl

use strict;
use warnings;

my @array = qw /TATG GTTC GAAC AATA/;
        
# DNA's tend to be loooooooooooooooong, so we create a lookup
# table to calculate the reversed inverse.
my %table;
my @chars = qw /A C G T/;
foreach my $c1 (@chars) {
    foreach my $c2 (@chars) {
        foreach my $c3 (@chars) {
            foreach my $c4 (@chars) {
                my $val = reverse my $key = "$c1$c2$c3$c4";
                   $val =~ y/ACGT/TGCA/;
                $table {$key} = $val;
            }
        }
    }
}

my %tmp; @tmp {@array} = ();
my @matches = grep {exists $tmp {$table {$_}}} @array;

print "@matches\n";

__END__
[download]

Abigail