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We compute the effect of a non-zero lepton chemical potential on the structure of the three flavor Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) phase of QCD at finite temperature. We show that, as in the BCS case, the lepton chemical potential favors two-species color superconductivity and disfavors the three species pairing. We stress that this study could be relevant for the cooling of a proto-neutron star with a FFLO core, if the temperatures are higher than the un-trapping temperature.

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