>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..'