my $string1 = 'ACTG';
my $string2 = 'TGAT';

my %corresponding = ('A' => 'T',
                     'T' => 'A',
                     'C' => 'G',
                     'G' => 'C');

my $count = 0;
for (split '', $string1) {
   my $char = substr($string2, $count++, 1);
   if ($char ne $corresponding{$_}) {
      print "Position $count incorrect:  1: $_, 2: $char\n";
   }
}