The robbery happened just after 2:30 am Monday on Kings Canyon Road and Fowler Avenue.
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Investigators said the suspects entered the store and demanded cash from the register.
At one point, one of the men used his gun to hit the clerk on the head.
The clerk suffered minor injuries and is expected to recover.
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Both suspects took off in a white four-door car.
Police have not yet set said how much money they stole.