We previously identified and modeled a principle of visual map alignment in the midbrain involving the mapping of the retinal projections and concurrent transposition of retinal guidance cues into the superior colliculus providing positional information for the organization of cortical V1 projections onto the retinal map (Savier et al., 2017). This principle relies on mechanisms involving Epha/Efna signaling, correlated neuronal activity and axon competition. Here, using the 3-step map alignment computational model, we predict and validate in vivo the visual mapping defects in a well-characterized mouse model. Our results challenge previous hypotheses and provide an alternative, although complementary, explanation for the phenotype observed. In addition, we propose a new quantification method to assess the degree of alignment and organization between maps, allowing inter-model comparisons. This work generalizes the validity and robustness of the 3-step map alignment algorithm as a predictive tool and confirms the basic mechanisms of visual map organization.