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Probably USB considering the microcontroller on it has USB device support. Simplest way to interface custom hardware to a PC I would think. Or simple serial. But I'd say USB along with a few I/O pins that connect to the mobos power/reset lines. This is backed up by the two differential traces you can see going from the connector to the two USB pins on the micro (check the datasheet) in the image of the custom board.
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