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    my @site1 = qw( AATKKM aatkkm );
    my @site2 = qw( GGGGGG gggggg );
...
    );

    print Dumper(\%counts), "\n";

    my @site1 = qw( AATKKM aatkkm );
    my @site2 = qw( GGGGGG gggggg );
...
     }

    print Dumper \%counts;