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...Clunk like I have been rear ended? It only does this when when I stop. I don't have any other problems upon acceleration or just driving. Everytime I come to a complete stop a second or two I feel a thump. Like someone behind me just bumped my car

 
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Check your shocks or struts, and have you front end check could be a number of problems. Controll arms, drive shaft, to name a few. Your best bet is to have it checked out.