Flashing binary file directly to on-chip

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It wants to know which pins of the EPM 3064a is connected to the flash chips CE, WE , OE ,A0> a31 and D0 > D31 pins.

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Your questions are very unclear. You didn't mention before, that you are dealing with a hardware which circuit is apparently unknown. This problem hasn't anything to do with Altera CPLDs or programming tools.