A core challenge in probabilistic mapping is to extract meaningful uncertainty information from data registration methods. While this has been investigated in ICP-based scan matching methods, other registration methods have not been analyzed. In this paper, an uncertainty analysis of a Fourier Mellin based image registration algorithm is introduced, which to our knowledge is the first of its kind involving spectral registration. A covariance matrix is extracted from the result of a Phase-Only Matched Filter, which is interpreted as a probability mass function. The method is embedded in a pose graph implementation for Simultaneous Localization and Mapping (SLAM) and validated with experiments in the underwater domain.