#!/usr/bin/env perl

use strict;
use warnings;

my %list = (1 => [qw{a b c}], 2 => [qw{a b d}], 3 => [qw{b c d}]);
my (%align, %seen);

%{$align{$_}} = map { ++$seen{$_}; $_ => undef } @{$list{$_}} for keys %list;

for my $char (sort keys %seen) {
    for my $list (sort keys %align) {
        print exists $align{$list}{$char} ? $char : '-', ' ';
    }
    print "\n";
}