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Pin1 (pink wire) lines up with the JTAG label on the board.
The other end of the JTAG connector must go into the SAM port on the Atmel ICE.
To test whether you have connected correctly open up Device Programmer in Atmel Studio (Tools->Device Programmer or Ctrl+Shift+P).
Use the methods mentioned above to connect to the board using the Atmel ICE.
To program the board's flash memory: