The Atmel-ICE is equipped with two 50-mil 10-pin JTAG connectors. Both connectors are directly electrically connected, but conform to two different pinouts; the AVR JTAG header and the Arm Cortex Debug header. The connector should be selected based on the pinout of the target board, and not the target MCU type - for example, a SAM device mounted in an AVR STK600 stack should use the AVR header.
Various cabling and adapters are available in the different Atmel-ICE kits. An overview of connection options is shown.
Figure 1. Atmel-ICE Connection Options
The red wire marks pin 1 of the 10-pin 50-mil connector. Pin 1 of the 6-pin
100-mil connector is placed to the right of the keying when the connector is seen from
the cable. Pin 1 of each connector on the adapter is marked with a white dot. The figure
below shows the pinout of the debug cable. The connector marked A plugs into the debugger while the B
side plugs into the target board.
Figure 2. Debug Cable Pinout