This quick "one-liner" (actually a "six-liner") gives a rough implementation of the idea in my previous post:

$ perl -E '
> my @unique = (1, 20, 3, 4, 44, 55, 66, 77, 5, 10, 2, 11, 20, 42, 30,
+ 31, 32, 33, 34, 35, 36, 37, 40);
> my @in = (4, 3, 2, 2, 42, 40);
> my %lookup = map { $_ => 1 } @in;
> for my $i (0..$#unique) {
>     say $i if exists $lookup{$unique[$i]};
> }
> '
2
3
10
13
22
[download]

Of course, this does not deal with duplicates in either array, but you haven't said how they should be processed.