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It is just a gigantic storm. Spots form on Jupiter all of the time, this one just happens to be the largest. It has decreased in size over the past decade, however.
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Mattforte has provided the answer, but just as a cheeky extra I'll add that the spot is big enough to fit three earths into its boundaries.
As mattforte says its a giant storm system that has existed for centuries, it's so huge you could fit 3 Earths inside it.
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