my @dna;  # contains the sequence
my @comp; # contains the complement


while (@dna)   {

    foreach my $base (@dna)   {

             ++$counter;

      }

   foreach my $base2 (@comp)   {

             ++$counter2;

      }

   if (($base[$counter] == 'A')  && ($base2[$counter2] !~ 'T')  {
  
              print "mismatch : $base[$counter] \t $base2[$counter2]\n";

     }

#  etc

}