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In this paper we establish that the singularities of the universal compactified Jacobian are canonical if the genus is at least four. As a corollary we determine the Kodaira dimension and the Iitaka fibration of the universal compactified Jacobian for every degree and genus. We also determine the birational automorphism group for every degree if the genus is at least twelve. This extends work of G. Farkas and A. Verra, as well as that of G. Bini, C. Fontanari and the third author.

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