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I know that there are USB port and External JTAG port, both for configuration.
Do they both support chipscope?
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Yes, both interfaces control the same JTAG chain on the board. The 14-pin JTAG connector is disabled if the USB-JTAG interface is connected (even if it's not in use; the 5V supplied by the PC switches a mux away from the 14-pin JTAG interface).
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