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#! perl -slw
use strict;
...

C:\test>888162 -N=3e6
Took: 25.244000 seconds

my @array_es = split ' ', $hash_es->{ $string_es };
 my $prob_es = ( @array_es ) / 6939873;

    my $n_array_es = $hash_es->{ $string_es } =~ tr[ ][ ];
    ++$n_array_es;

sub Intersection {
    my( $refA, $refB ) = @_;
...

    return $intersects;
}

#! perl -slw
use strict;
...

C:\test>888162 -N=3e6
Took: 15.616000 seconds