How Did the Clones Know Anakin Wasn't a Jedi During Order 66? Star Wars Explained

During Order 66, the Clone Troopers were set out to annihilate all Jedi.

The 501st Legion was sent with Anakin (later become Vader's Fist) to raid the Jedi Temple...so why didn't they just shoot Anakin? What piece from the films are we missing? I hope this episode puts it all together.

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