use strict;
use warnings;

my $clu_align=$ARGV[0];
open(IN,">",$clu_align) or die "can't open file $clu_align";

my @consensus;

while(my $line=<IN>){
chomp($line);
next if ($line =~ /^CLUSTAL/); # header row
next if ($line=~ /^$/); # a few blank rows
if ($line =~ /\*/){
        push (@consensus,$line);
}
}
close(IN);

chomp(@consensus);
#foreach my $c (@consensus){ just for debugging
#       print "consensus\n";
#       print "$c\t";
#       print "\n";
#}


my( @index )= grep { $consensus[$_] eq "*" } 0..$#consensus;
my $outfile="$clu_align.VarPositions";
open (OUT,">",$outfile);

foreach my $i (@index) {
        print OUT "$i\tis not conserved\n";
}