The Atmel-ICE Probe has two 50-mil 10-pin Joint Test Action Group (JTAG) connectors accessible on the front of the tool's enclosure. Both connectors are directly electrically connected, but conform to two different pinouts:
1) AVR® JTAG header
2) 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.
JTAG Interface Basics
When designing an application PCB which includes an AVR with the JTAG interface, it is recommended to use the pinout as shown. The Atmel-ICE can connect to both 100-mil and 50-mil variants of this pinout.
AVR JTAG Header Pinout
When designing an application PCB which includes a SAM device with the JTAG interface, it is recommended to use the pinout shown. The Atmel-ICE can connect to both 100-mil and 50-mil variants of this pinout.
SAM JTAG Header Pinout
Atmel-ICE Connection Options
The chart shows the pinouts for each connector type and a description of each pin.