No, his code clearly gives 0 and 6. If you want 0 and 2, try this:

#!/usr/bin/perl
use strict;

my $str = 'ATCGATCGAT';
my @sub = qw(ATCG CGAT);

my $id = 0;

foreach (@sub) {
    $id = index($str, $_, $id);
    print "$id\n";
    $id++;
}
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