The Atmel AVR's A/D converter needs a reference voltage to set its converting range. Atmel STK600 can supply two of these voltages, AREF0 and AREF1.
For all Atmel tinyAVR and Atmel megaAVR devices, only the AREF0 is connected trough the routing card, whilst for Atmel AVR XMEGA devices, AREF0 is connected to ArefA and AREF1 is connected to ArefB.
For AVR XMEGA devices the AREF pins is also general purpose I/O pins. Hence, to use the pins as GPIO the Aref jumpers must be removed.
Note
For routingcard "STK600-RC100X-13" revision A and revision B the AREF1 is connected to PA1. These cards are marked "A0607.3.1213.A" and "A0607.3.1213.B"
If the AREF0/AREF1 jumpers are mounted, the on-board
Analog Reference Voltage sources are connected to the target AVR’s AREF
pins. The On-board Analog Reference Voltages can be adjusted from the PC
software in the range 0 to 5.5V, but not above VTARGET. The resolution and
accuracy is 10mV.
The AREF0 and AREF1 generated voltages can also be connected to the analog comparator.
The target AVR’s AREF signals are accessible on the AUX header. The figure below shows the connection of the AREF signals, the target section and the AREF sources.



