Dear community
Well, you are right, it was a typo. However, the problem I faced is still persistant (though I was not able to describe it due to my typo). It is also hard to reproduce. This is why I would like to show you a sample of my data. Please execute the script and look at the output:

You will see that there is the letter "V" in row number 19 AND 25 ... That is not correct, is it?

They should all be in 25 or even 28, depending on the situation with the 3 and the U...

I am really sorry for the amount of data, but I cannot really reproduce this behavior. With many smaller data sets (those i showed you), it worked ...
Greetings, Jan

#!/usr/bin/perl -w

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

my @seqs = (
[ qw ( A B C D E Z F G H I J K L M N O V W X Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E Z F G H I J K L M N O P Q V W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E Z F G H I J K L M N O P V W Y ) ],
[ qw ( A B C D E Z F G H I J K L M N O P V Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E Z F G H I J K L M N O P Q R S T V W Y ) ],
[ qw ( 3 W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W Y ) ],
[ qw ( A B C D E Z F G H I J K L M N O V W 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P V W Y ) ],
[ qw ( A B C D E Z F G H I J K L M N Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P V W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T V W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S W 2 4 ) ],
[ qw ( N O V Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( N O P Q R S V W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( 7 2 4 ) ],
[ qw ( A B C D E 1 F G H I J K L M N O P V 5 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T V W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E Z F G H I J K L M N O V W 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T U W 2 Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O V 5 ) ],
[ qw ( A B C D E Z F 6 G I J K V W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S W X 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T V W Y ) ],
[ qw ( A O P Q R V W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T V 5 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T V W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E Z F G H I J K L M N O V W 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E Z F G H I J K L M N O P Q V W 4 ) ],
[ qw ( A B C D E 1 F G H I J K L M 5 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S W 2 4 ) ],
[ qw ( A B C D E Z F G H I J K L M N Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E 1 Z F 6 G H I J K L M N O P Q R V W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T V W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S V W Y ) ],
[ qw ( A B C D E Z F G H I J K L M N O P V W Y ) ],
[ qw ( A B C D E 1 F G H I J K L M N O P V 5 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T U V W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T V W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T V W Y ) ],
[ qw ( 3 W 2 4 ) ],
[ qw ( 3 W 2 4 ) ],
[ qw ( A B C D E 1 F G H I J K L M N O P V 5 ) ],
[ qw ( A O P Q V W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E Z F 6 G I J K L M N P V W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T V W 2 4 ) ],
[ qw ( A B C D E Z F G H I J K L M N O P V X Y ) ],
[ qw ( A B C D E 1 F G H I J K L M N O P V 5 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T V W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T V W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( N O P V W Y ) ],
[ qw ( A B C D E 1 F G H I J K L M N O P V 5 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E Z F G H I J K L M N O V W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E Z F 6 G I J K L M N O P Q R V W Y ) ],
[ qw ( A O P Q V W Y ) ],
[ qw ( 3 W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P V W Y ) ],
[ qw ( A O P Q R V W Y ) ],
[ qw ( A B C D E Z F G H I J K L M N O P V X Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T U V W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T V W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O 5 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T U V W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( N O P V W Y ) ],
[ qw ( A B C D E Z F G H I J K L M N O P V W Y ) ],
[ qw ( A B C D E Z F G H I J K L M N O V W Y ) ],
[ qw ( A B C D E Z F 6 G I J K L M N P V W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P V W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T V W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T V W 2 4 ) ],
[ qw ( A B C D E Z F G H I J K L M N O P Q R S T U V W Y ) ],
[ qw ( A B C D E Z F G H I J K L M N O P V X Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S W 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A O P Q R V W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T V W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P V W Y ) ],
[ qw ( N O P V W Y ) ],
[ qw ( A B C D E Z F G H I J K L M N O V W 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T V W 2 4 ) ],
[ qw ( A B C D E Z F 6 G I J K L M N O P Q R V W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T V W 2 4 ) ],
[ qw ( A B C D E Z F G H I J K L M N O V W Y ) ],
[ qw ( A B C D E 1 F G H I J K L M N O P V 5 ) ],
[ qw ( A B C D E Z F G H I J K L M N O P Q R S T V W Y ) ],
[ qw ( N O P V Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S W X 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E Z F G H I J K L M N O P Q R S T U V W Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T V W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E Z F G H I J K L M N O P V Y ) ],
[ qw ( A B C D E Z F G H I J K L M N O P V W Y ) ],
[ qw ( A B C D E Z F G H I J K L M N O V W 4 ) ],
[ qw ( A B C D E Z F G H I J K L M N O P V Y ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T V W 2 4 ) ],
[ qw ( A B C D E 1 Z F G H I J K L M N O P Q R S T W 2 4 ) ],
[ qw ( A B C D E Z F G H I J K L M N O P Q V W 2 4 ) ],
[ qw ( A B C D E Z F G H I J K L M N O V W Y ) ],

);

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");
}
[download]

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