We develop a detailed theory describing a non-trivial interplay between non-equilibrium effects and long-range quantum coherence in superconducting hybrid nanostructures exposed to a temperature gradient. We establish a direct relation between thermoelectric and Josephson effects in such structures and demonstrate that at temperatures exceeding the Thouless energy of our device both phase-coherent thermoelectric signal and the supercurrent may be strongly enhanced due to non-equilibrium low energy quasiparticles propagating across the system without any significant phase relaxation. By applying a temperature gradient one can drive the system into a well pronounced $pi$-junction state, thereby creating novel opportunities for applications of Andreev interferometers.
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