To put a Shimano Di2 system into pairing mode, you'll need to activate the Bluetooth connection.
For 12-speed Di2, this is done by pressing and holding the button on the rear derailleur for 0.5-2 seconds. The LED on the rear derailleur will then flash blue, indicating it's ready to pair.
For 11-speed Di2, you'll need the Shimano Wireless Unit (EW-WU110/EW-WU111) and will need to press the button on the junction box (or rear derailleur for 12-speed) for about two seconds until the red/green lights start flashing.
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