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and if you meant JTAG, it can be used for in circuit debugging of your software (when you have a JTAG programmer). This means that you can debug the software while it's running on the microcontroller and set breakpoints, ...
It's interesting when you got some hardware which is difficult to simulate in the AVR Studio simulator.
www.olimex.com sells JTAG programmers for AVR which aren't as expensive as the original one from atmel. Perhaps there are others.
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