Hi,
The clocks on your board are derived from the Si5338 Oscillator . The pins that are connected to the FPGA are : Y26, AF14, AA16, K14. These are the 50MHz clocks that are connected from the Si5338 to the FPGA. You could try any of these. These are the clock assignments from the QSF file for the board..
set_location_assignment PIN_Y26 -to clk_100m_fpga
set_location_assignment PIN_K14 -to clk_50m_fpga
set_location_assignment PIN_AA16 -to clk_top1
set_location_assignment PIN_AF14 -to clk_bot1
set_location_assignment PIN_AA26 -to hsmc_clkin_p[1]
set_location_assignment PIN_H15 -to hsmc_clkin_p[2]
set_location_assignment PIN_E7 -to hsmc_clkout_p[1]
set_location_assignment PIN_A11 -to hsmc_clkout_p[2]
set_location_assignment PIN_J14 -to hsmc_clk_in0
set_location_assignment PIN_AD29 -to hsmc_clk_out0
After making the pin assignments, you need to make sure that the PLL in your design is using the clock from the mentioned pins. Also check if there are any Jumpers/ settings for clock selection on the board.