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The wheel has Thru axles so definitely seated properly and my 700c wheels are perfectly aligned so sounds like the 650 wheel needs re-dishing.
motman-
One other thing to check is that the tyre is seated perfectly evenly on the rim.
Although to be brutally honest, I don't think you've got satisfactory clearance even if you can get the wheel to sit evenly, especially for use off road. There will be absolutely zero clearance for any mud/dirt and the occasional branch/twig. Why not drop down tyre size to a 35 or 38mm CX size? c.35mm is honestly plenty big enough for general offroad use.
Jameo
With the bike standing on the floor, open and then close the rear QR to check that the axle is fully seated into both dropouts.
Now if your rim is still sitting off centre then either
a) something is wrong with your frame, or
b) you must re-dish the wheel.
You can test the frame by grabbing a different, healthy wheel (if you have one) and seeing if that sits straight in the frame.