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In this article we study the second variation of the energy functional associated to the Allen-Cahn equation on closed manifolds. Extending well known analogies between the gradient theory of phase transitions and the theory of minimal hypersurfaces, we prove the upper semicontinuity of the eigenvalues of the stability operator and consequently obtain upper bounds for the Morse index of limit interfaces which arise from solutions with bounded energy and index without assuming any multiplicity or orientability condition on these hypersurfaces. This extends some recent results of N. Le and F. Hiesmayr.

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