Ikegami, thanks again... Here is what I have added to what you wrote beforehand:

sub consensus {
   $rest='-';
   my %counts;
   $counts{$_}++ for @_;

   my ($consensus) = sort { $counts{$b} <=> $counts{$a} }
                     keys(%counts);

   return ( $counts{$consensus} / @_ >= 0.7
     ? $consensus
    : $rest
   );
}


while(<>)
{
    $consensus = '';
    @total_seqs=();

    $seq=$_; push @total_seqs,$seq;

       for $i (0..length($seq)-1) 
    {
          $consensus.= consensus( map substr($_, $i, 1), @total_seqs )
+;
       }

       
}print("CON:$consensus\n");
[download]