use strict;
use warnings;

my %hoa1 = (
            'key1' => ["A","B","C","D"],
            'key2' => ["A","C","D","B"],
            'key3' => ["C","A","D","H"],
            'key4' => ["A","B","I","C"],
           );

my %hoa2 = (
            'key1' => ["A","D"],
            'key2' => ["A","B"],
            'key3' => ["C","H"],
           );

print_aoa( 'AoA1', align_array( %hoa1 ) );
print_aoa( 'AoA2', align_array( %hoa2 ) );

sub align_array {

  my %h = @_;
  my @keys = sort keys %h;      # huh?  why should sort order
                                # dictate the reference array?
  my $ref = $h{ $keys[ 0 ] };
  my @ret = map [ $_ ], @$ref;

  for my $i ( 0 .. $#{ $ref } ) { # $i determines the row in @ret
    my $elem = $ref->[ $i ];

    for my $j ( 1 .. $#keys ) { # $j determines the col in @ret
      my $arr = $h{ $keys[ $j ] };
      $ret[ $i ][ $j ] = '-';

      for my $k ( 0 .. $#{ $arr } ) {
        if ( $elem eq $arr->[ $k ] ) {
          $ret[ $i ][ $j ] = $elem;
          splice @$arr, 0, $k + 1;
          last;
        }
      }
    }
  }
  return \@ret;
}

sub print_aoa {
  my ( $name, $aoa ) = @_;
  print '@', $name, ' = (', $/;
  for my $arr ( @$aoa ) {
    print '  [', join( ',', @$arr ), ']', $/;
  }
  print ')', $/;
}
__END__
@AoA1 = (
  [A,A,A,A]
  [B,B,-,B]
  [C,-,-,C]
  [D,-,D,-]
)
@AoA2 = (
  [A,A,-]
  [D,-,-]
)