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I have Micosemi/Actel ProASIC3 Nano A3P125,VQ100 Chip. I was looking for the PLL integrated CCC to connect 100MHz Clock and I have been through the manual ProASIC3 FPGA Fabric User’s Guide. where i have found, i have three options(3pins) like "GFA0, GFA1 or GFA2". It's clear from manual that 'Only one of the I/Os can be directly connected to a chip global at a time'.

what about the rest of two pins? Can I use them as output?

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Yes, you can use those pins for GPIO when you don't need their special functions.

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