In Arria® 10 devices, the CLKUSR pin can be used for Active Serial (AS) configuration and transceiver calibration simultaneously.
For transceiver calibration, the CLKUSR pin must be connected to a free-running 100MHz – 125MHz clock at device power-up. Transceiver calibration first utilizes CLKUSR during configuration and continues to use CLKUSR into user-mode.
If you intend to use CLKUSR for 100MHz AS configuration, then the CLKUSR pin will drive both the configuration circuitry as well as the transceiver calibration logic that executes during device configuration.