We compute the structure of flux vortices in a d-wave superconductor which emerges from a higher temperature pseudogap metal. Such a transition is described by a continuum theory of the Higgs condensation of 2 flavors of charge bosons which are fundamentals of an emergent SU(2) gauge field. Period-2 charge order is present near the vortex center. Upon coupling the electrons to the superconducting and charge order parameters, we find that the electronic local density of states does not have a zero-bias peak, in contrast to BCS theory. But there are sub-gap peaks at positive and negative bias, and these exhibit anti-phase periodic spatial modulations, similar to observations in scanning tunneling microscopy experiments in the underdoped cuprates (K. Matsuba et al., J. Phys. Soc. Jpn. 76, 063704 (2007)).

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