The In-circuit Serial Programming (ISP) header is located on the edge of the board, next to the USB port.
Pin 1 (MISO) is in the top right corner in this picture.
Follow the instructions provided with your AVR programmer to connect it to the ISP header. If you are using the Bus Pirate, here are the connection instructions.
If your programmer has the option to choose between 3V and 5V, choose 5V.
Plug your AVR programmer into your computer.
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