use strict;
use warnings;

my @instances  = qw ( AAAAA ATCGA ATAAA );
my @instances2 = qw ( AAAAA AACGA ATAAA ATAAA );

print consensus(@instances),"\n";        # ATAAA
print consensus(@instances2),"\n";       # ATAAA
exit;

sub consensus{
 my @mi = @_;
 chomp(@mi);
 my $motif_count=0;
 my @words =();

  my %H = ( A=>[], T=>[], C=>[], G=>[] );

  s/\s//g for @mi;
  my ($w) = sort {$b <=> $a} map {length} @mi;    # set w to the length of the longest element

    foreach my $j ( 0 .. $w-1 ){
        # Initialize the base counts.
        my %h = ( a=>0, t=>0, c=>0, g=>0 );
        foreach my $mi ( @mi ) {
            $h{ lc substr($mi,$j,1) }++;           # example:  $h{g}++;
        }
        push @{$H{ uc $_ }}, $h{$_} for keys %h;   # example:  push @{$H{G}}, $g;
    }

    my @cons = ();
    my %prefOrder = ( A=>1, T=>2, C=>3, G=>4 );
    foreach my $B ( 0 .. $w-1 ){
      push @cons, [ sort { $H{$b}->[$B] <=> $H{$a}->[$B] || $prefOrder{$b} <=> $prefOrder{$a} } qw/A T G C/ ]->[0];
    }

    return @cons;
}

##</code><code>##

  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)