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We examine symmetries of chiral four-dimensional vacua of Type IIB flux compactifications with vanishing superpotential . We find that the supersymmetric MSSM-like and Pati-Salam vacua possess enhanced discrete symmetries in the effective action below the mass scale of stabilized complex structure moduli and dilaton. Furthermore, a generation number of quarks/leptons is small on these vacua where the flavor, CP and metaplectic modular symmetries are described in the framework of eclectic flavor symmetry.

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