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Usually Terasic puts protective diodes on their boards to make the I/O 5V tolerant. I know my DE2 has them, and I believe the DE1 has them as well. (BAT54S) I looked up the manual for the DE0, and it appears they forgot to include the schematic for the protective circuits, but they do mention that they exist. Might be worth a follow-up email with Terasic to verify - or just check the board for a whole bunch of 3-terminal diodes near the connectors.
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I'm going to email them to double check, but I don't think they are there.
I just looked at the board, and there are definitely not a bunch of 3-terminal diodes that I can see. Should there be (1) per pin to protect? aka 72 of them for my board?
Thanks
Keith