All I/O port pins on the target Atmel AVR mounted on the Atmel STK600 are available on port pin connectors. These are labeled PORTA, PORTB, PORTC etc.
Depending to the AVR in use, different ports will be available.
The picture below shows PORTA. Here, all port pins PA0 to PA7 are available, in addition to the target voltage VTG and GND.
The other port connectors are identical, only with different signal names.
Cables can be mounted between the port connectors and the other peripherals on the board, or to external hardware.