Assuming your example contains some typos, you may want to go for:

use 5.010;

use strict;
use warnings;

use List::Util 'max';

my (%data, %all, @keys);
while (<DATA>) {
    chomp;
    my @chunks = split;
    my $key = shift @chunks;
    push @keys, $key unless exists $data{$key};
    foreach my $chunk (@chunks) {
        $data{$key}{$chunk}++;
        $all{$chunk} = 1;
    }
}

my @fields = sort {$a <=> $b} keys %all;
my $l = max map {length} @fields;

foreach my $key (@keys) {
    while (keys %{$data{$key}}) {
        print $key, " ";
        foreach my $field (@fields) {
            if ($data{$key}{$field}) {
                printf "%${l}s ", $field;
                delete $data{$key}{$field} unless --$data{$key}{$field
+};
            }
            else {
                printf "%${l}s ", "-";
            }
        }  
        print "\n";
    }
}


__DATA__
0. 1 1 7 2 2 9 4 6 8 10 2
1. 10 1 6 3 4 9
2. 5 8 59 77 81 3
3. 16 17 19 23 3
[download]

The result:

0.  1  2  -  4  -  6  7  8  9 10  -  -  -  -  -  -  - 
0.  1  2  -  -  -  -  -  -  -  -  -  -  -  -  -  -  - 
0.  -  2  -  -  -  -  -  -  -  -  -  -  -  -  -  -  - 
1.  1  -  3  4  -  6  -  -  9 10  -  -  -  -  -  -  - 
2.  -  -  3  -  5  -  -  8  -  -  -  -  -  - 59 77 81 
3.  -  -  3  -  -  -  -  -  -  - 16 17 19 23  -  -  -
[download]

Changing the sorting of fields if you have non-numeric fields is left as an exercise to the reader.