my %H = ( A=>[], T=>[], C=>[], G=>[] );
  my @mi_letters = map { [split '', uc $_] } @mi;
  foreach my $j ( 0 .. $w-1 ){
    $H{ $_->[$j] }->[$j]++ for @mi_letters;
  }

  # note: to avoid warnings, change the sort further down to include this (the '||0'):
  #    ($H{$b}->[$B]||0) <=> ($H{$a}->[$B]||0)