for (split //, $template) {
    print ord == 0 ? '.' : 'X';
}
print "\n";

[download]

Another way to do that: 

$template =~ tr/\0/X/c;
$template =~ tr/\0/./;
print "$template\n";

[download]

But this looks like it produces the output the OP wants: 

print "position $-[0] is not conserved\n" while $template =~ /[^\0]/g;

[download]

In reply to Re^2: manipulating alignment data by jwkrahn
in thread manipulating alignment data by AWallBuilder

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