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I am wondering where the extra 5v output power on the Arduino uno come from. Is it directly from the atmega328 microcontroller or from the external power source (usb or 9v battery). Thanks.

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If you are connected to USB then it comes direct from the USB port's 5V.

If you have an external power supply connected (either to the barrel jack or to the VIN pin) then it comes from the onboard 5V regulator.

The only thing that ever comes from the ATMega chip is digital signals.

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