use strict;
use warnings;

my $consensus = 'abc*def*ghi';
my( @index_c, @index_n );
my $idx = 0;
my $len = length( $consensus );

push( @{ substr( $consensus, $idx, 1 ) eq '*' ? \@index_c : \@index_n }, $idx++ )
    while $idx < $len;

print "C: @index_c\n";
print "N: @index_n\n";