By default, only one device is assumed to be in the JTAG scan chain. If you have multiple devices in the scan chain, you must properly configure it. To do so, you have to specify the exact position of the CPU that should be addressed. Configuration of the scan is done by the target application. A target application can be a debugger such as Atmel Studio, the IAR™ C-SPY® debugger, ARM’s AXD using RDI, a flash programming application such as SEGGER’s J-Flash, or any other application using J-Link/J-Trace. It is the application’s responsibility to supply a way to configure the scan chain. Most applications offer a dialog box for this purpose.