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I think of buying an AVR Dragon or an AVR JTAG ICE MKIII. But before I do this, I need to know what side effects the reduced debug frequency has on an ATMEGA328P while debugging. I make heavy use of UART, Timer0 and Timer1 at a frequency of 16 MHz.

In particular the UART should work while debugging. Is this ensured?

Which debug device do you prefer? Does it work with Atmel Studio 6? I am fimiliar with the PicKit2 as a debugger.

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The UART hardware part will send and receive while you debug. However, the isr will of course not fire when you have stopped the execution of your program. So if the code hits a breakpoint, the UART will drop characters as long as the program execution is halted.

Having the debugger attached (in debugWire mode) does not reduce the performance of the microcontroller.

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