use strict;
use warnings;
use Algorithm::Diff qw( );

my @seqs = (
   [qw( A B C D E F G H I )],
   [qw( A D C X F G H I )],
#   [qw( A  )],
  # [qw( A B C )],
);

my @combined;
my @grid;

for my $col_idx (0..$#seqs) {
   my $seq = $seqs[$col_idx];

   my $diff = Algorithm::Diff->new(\@combined, $seq);

   my @new_combined;
   my @new_grid;
   while ($diff->Next()) {
      if ($diff->Same()) {
         for ($diff->Range(1)) {
            push @new_combined, $combined[$_];
            push @new_grid,     $grid[$_];

            $new_grid[-1][$col_idx] = 1;
         }
      } else {
         for ($diff->Range(1)) {
            push @new_combined, $combined[$_];
            push @new_grid,     $grid[$_];
         }

         for ($diff->Range(2)) {
            push @new_combined, $seq->[$_];
            push @new_grid,     [];

            $new_grid[-1][$col_idx] = 1;
         }
      }
   }

   @combined = @new_combined;
   @grid     = @new_grid;
}

for my $row_idx (0..$#combined) {
   my $ch = $combined[$row_idx];

   for my $col_idx (0..$#seqs) {
      print($grid[$row_idx][$col_idx] ? $ch : " ", " ");
   }

   print("\n");
}


##</code><code>##

A A
B
C
D D
E
  C
  X
F F
G G
H H
I I

##</code><code>##

A A
B B
C C
D
  X
E
F F
G G
H H
I I