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I believe the FTDI chip on the BeMicro gets all of its startup information from the little microchip EEPROM on the board.
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Yes, that can be expected. It's the same with USB Blaster.
It's clear, that FT2232 can be used as a JTAG adapter without additional logic (except for the configuration EEPROM). I wanted to know from someone, who owns the bemicro, if it's done there this way. The first question is about the exact FTDI chip type.
I only have the bemicro manual, and I can't clearly see from the assembly drawing if there's any PLD chip that could be possibly work as additional JTAG glue logic. Perhaps someone can share a high resolution photo of the board to identify the assembled parts.
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