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Verifying Configuration Memory after Programming

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I'm working on an application for a high EMI environment and need to constantly verify the configuration of an FPGA to ensure that the circuit isn't being damaged/altered by the noise. I know I can do it prior to programming the device, but how do I go about reading/verifying the configuration of a chip that's already been programmed? Is there a way to access the LUTs from the JTAG header? I don't need to know where the problem occurs, only whether something's been altered. A go/no go scenario, where any change causes me to halt the chip. If not JTAG, is there any other way for me to accomplish this?

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