in reply to Re: manipulating alignment data
in thread manipulating alignment data

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

Another way to do that:

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

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

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