>perl -wMstrict -le
"use List::Util qw(reduce);
 use vars qw($a $b);
 ;;
 my @seqs = qw(
   ATCG--ATCG-ATCG
   ATGC--ATCG-ATCG
   ATGC-A-TCG-ATCG
   ATGC--ATCG-ATCG
   ATCG--ATCG-AACG
   );
 ;;
 my $cons = reduce { $a ^ $b } @seqs;
 defined($cons) or die 'no sequences given';
 ;;
 my $mask = @seqs % 2 ? $seqs[0] : (qq{\0} x length $seqs[0]);
 $cons ^= $mask;
 $cons =~ tr{\0-\xff}{.X};
 print qq{'$cons'};
"
'..XX.XX.....X..'
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The code assumes all sequences have the same length. (I'm not sure just what happens if they don't.) The  use vars qw($a $b); statement suppresses some pesky "Name ... used only once: possible typo at..." messages.

BTW: Both moritz and I get 2, 3, 5, 6 and 12 (not 8) as non-conserved positions. Is this correct?

Important Update: Bug! Sorry, this solution is sensitive to data sequence. To see the problem exemplified, try the sequence set

my @seqs = qw(
  CTCG--ATCG-ATCG
  CTGC--ATCG-ATCG
  ATGC-A-TCG-ATCG
  ATGC--ATCG-ATCG
  );
[download]