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I do know for a fact, following a ticket submitted to Altera, that there is no internal protection on the Stratix III JTAG interface
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Very simple, the I/O pin voltage maximum ratings are valid for the JTAG pins as well. In my opinion it's obvious, that they don't have additional internal protection.
Unlike other connectors designed for hot-plug, e.g. USB, the 10 pin JTAG connector has no leading ground pin, so there's basically a high risk to apply an illegal voltage level to a signal pin, particularly if part of the equipment, e.g. a notebook is powered from a SMPS without protective earth connection.
I can report, that I never observed a JTAG interface related device damage with boards, that utilize series resistors and schottky clamp diodes for the JTAG interface, even in a rough power electronics enviroment.
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