Cyclone V: PCIe x4 + XAUI.

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I'm not sure you are using which QII version.

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Sorry, I am using QII 13.0.0 Build 156.

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In CV Native PHY GUI, you should enable the "Use external PLL" option if you want to use fPLL a transmit PLL feature.

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Unfortunately, there is no such option In "XAUI PHY v13.0" and "Cyclone V Hard IP for PCI Express v13.0" Megacore functions.