I guess by "not conserved" you mean you're looking for columns that aren't the same in each line. If that's true, this might get you started: 
use strict;
use warnings;

my $first = <DATA>;
chomp $first;
my $template = '';
while (<DATA>) {
    chomp;
    $template |= $first ^ $_;
}
for (split //, $template) {
    print ord == 0 ? '.' : 'X';
}
print "\n";

__DATA__
ATCG--ATCG-ATCG
ATGC--ATCG-ATCG
ATGC-A-TCG-ATCG
ATGC--ATCG-ATCG
ATCG--ATCG-AACG

[download]

The output produces a dot for each column where all rows have the same character, and an X for those where there are at least two different characters: 

..XX.XX.....X..

[download]

If that's not what you want, please make your description more verbose, and include the expected output for your example input.

Perl 6 - second systems done right

In reply to Re: manipulating alignment data by moritz
in thread manipulating alignment data by AWallBuilder

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