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foreach my $key1 (sort keys %hash){
    foreach my $key2 (sort keys %{$hash{$key1}}){
        print "$key1\t$key2\t$hash{$key1}{$key2}\n";
    }
}

foreach my $key1 (sort keys %hash){    
    foreach my $key2 (sort keys %{$hash{$key1}} ){
...
        }
    }
}