The following pins are not used in the software packages:
Pin | Pin number | Direction | Type |
AVR_RXD | AW35 | IN | LVCMOS25 |
AVR_TXD | AY34 | OUT | LVCMOS25 |
E_KEY0_FPGA | D15 | INOUT | LVCMOS25 |
E_KEY1_FPGA | C15 | INOUT | LVCMOS25 |
E_KEY2_FPGA | G12 | INOUT | LVCMOS25 |
E_KEY3_FPGA | H13 | INOUT | LVCMOS25 |
CUSTOM0_FPGA_IO | F15 | OUT | LVCMOS25 |
CUSTOM1_FPGA_IO | AW16 | OUT | LVCMOS25 |
AVR_RXD and AVR_TXD are UART links RX and TX between the FPGA and the AVR.
The other pins are either GPIO pins or a SPI link between the FPGA and the AVR. There is also no code on the AVR that uses these pins.