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This paper proposes a technique based on Physical Unclonable Functions (PUFs), obfuscation, and Dynamic Partial Self Reconfiguration (DPSR) to protect partial FPGA configuration bitstreams from cloning and reverse engineering. With the aid of this technique, we are able to do the equivalent of partial bitstream encryption on low-cost FPGAs, which is only featured on high-end FPGAs. Low-cost FPGAs do not even have built-in support for encrypted (full) bitstreams. Through DPSR, our PUF implementation does not steal real estate from the encrypted design. We also present a new DPSR flow for Xilinx FPGAs, which is difference-based but still allows modular design. It works regardless of the amount of difference between Partial Reconfiguration (PR) modules and is called DPSR-LD, where LD stands for Large-Difference. DPSR-LD is an enabler especially for Spartan-6 FPGA family, as Xilinx currently supports PR on Spartan-6 only through the difference-based flow and only for small differences. Our DPSR-LD also includes a controller that interfaces to the ICAP and can process compressed bitstreams. It is called ICAP+ and occupies only 1% of Spartan-6 slices.