Since you're dealing with frequency, I'd use a hash to store the occurrences of A, C, G, and T in each position of the word. I'd loop over the DNA sequences for each character, looking at character 1 first in all strands, then character 2, etc. 
sub consensus {
  my $len = length($_[0]);  # all strands are of one length, right?
  my @cons;

  # loop over the positions in the strands
  for my $i (0 .. $len - 1) {
    my %freq;
    my $max = 0;

    # loop over character $i in each of the strands
    for (map substr($_, $i, 1), @_) {
      $freq{$_}++;

      # save the max value
      $max = $freq{$_} if $freq{$_} > $max;
    }

    # store only those who occur the most times
    push @cons, [grep $freq{$_} == $max, keys %freq];
  }

  return \@cons;
}

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Then it's your task to turn the array of array references into the string you want.
Jeff japhy Pinyan, P.L., P.M., P.O.D, X.S.: Perl, regex, and perl hacker
How can we ever be the sold short or the cheated, we who for every service have long ago been overpaid? ~~ Meister Eckhart

In reply to Re: Finding Consensus String by japhy
in thread Finding Consensus String by monkfan

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