• You need to find the value at which to start.
• You need to find the value at which to stop.
• You need some way of determining if a value is present in an array. (I used a hash rather than grepping the entire array over and over again.)

use strict;
use warnings;

my @arrays = (
   [0,1,2,3,4,5,6,7,8,9],
   [1,2,3,4,6,8,10,12,14],
   [1,2,3,5,7,9,11,13,15],
);

my $min = my $max = $arrays[0][0];

my @lkups;
for (0..$#arrays) {
   my $array = $arrays[$_];
   my $lkup = \%{ $lkups[$_] };
   for (@$array) {
      $min = $_ if $_ < $min;
      $max = $_ if $_ > $max;
      ++$lkup->{$_};
   }
}

for my $i ($min..$max) {
   print(join("\t", $i, map { $_->{$i} ? 'yes' : '' } @lkups), "\n");
}
[download]

Alternatively, you could take advantage of the fact that the numbers are sorted and do something like a merge sort.

Update: Oops, I thought you wanted continuous indexes, but I doubt that now. Fix:

• You need to find which values are present in any array.
• You need some way of determining if a value is present in an array. (I used a hash rather than grepping the entire array over and over again.)

use strict;
use warnings;

my @arrays = (
   [0,1,2,3,4,5,6,7,8,9],
   [1,2,3,4,6,8,10,12,14],
   [1,2,3,5,7,9,11,13,15],
);

my %global_lkup;
my @lkups;
for (0..$#arrays) {
   my $array = $arrays[$_];
   my $lkup = \%{ $lkups[$_] };
   for (@$array) {
      ++$lkup->{$_};
      ++$global_lkup{$_};
   }
}

for my $i ( sort { $a <=> $b } keys(%global_lkup) ) {
   print(join("\t", $i, map { $_->{$i} ? 'yes' : '' } @lkups), "\n");
}
[download]