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We consider D3 branes at orbifolded conifold singularities which are not quotient singularities. We use toric geometry and gauged linear sigma model to study the moduli space of the gauge theories on the D3 branes. We find that topologically distinct phases are related by a flop transition. It is also shown that an orbifold singularity can occur in some phases if we give expectation values to some of the chiral fields.

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