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Generally, a hypothesis is the prediction of the outcome of an experiment. A theory is a statement that is somewhat of an explanation of a set of observations. <---- well kind of not really.
A hypothesis is the start of a theory, in the scientific process you form a hypothesis, or an educated guess, based on an obeservation you make. You then test that hypothesis to see if it is true, if through repeated testing your hypothesis rings true, you can turn that hypothesis into a theory. A theory is basically an oberserved and tested hypothesis, meaning that a theory will generally be true, though its not fail safe. Evolution for example is a theory, there is obviously a whole bunch of evidence for evolution, but one can not say without a doubt that evolution, or evolution as we know it is true (new ideas are constantly coming out about evolution, I am not endorsing or discrediting evolution so please don't start going on a pro or anti religious rant here).