Hi Jan, I am afraid that Atmega MCUs do not have an unique ID. But you can store some hidden magic number into EEPROM (by another sketch) and then check it from your sketch. This thread may help you.
Not possible in CONTROLLINO because the USB is handled by another microcontroller Atmega16U2 (like on Arduino MEGA or UNO). As far as I know the sketch is not able to directly communicate with this chip.
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