my $num_cols = @{ $AoA[0] };

for my $col (0..$num_cols-1) {
   for my $row (0..$#AoA) {
      ...
   }
}

##</code><code>##

my $num_cols = @{ $AoA[0] };

for my $col (0..$num_cols-1) {
   my @col = map $_->[$col], @AoA;
   ...
}

##</code><code>##

sub consensus {
   my %counts;
   $counts{$_}++ for @_;

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

   return ( $counts{$consensus} / @_ >= 0.6
      ? $consensus
      : 'A'
   );
}

{
   my $num_cols = @{ $AoA[0] };

   my @combined;
   for my $col (0..$num_cols-1) {
      push @combined, consensus( map $_->[$col], @AoA );
   }

   print(join(', ', @combined), "\n");
}