Single Molecule Sequencing technologies such as the Heliscope simplify the preparation of DNA for sequencing, while sampling millions of reads in a day. Simultaneously, the technology suffers from a significantly higher error rate, ameliorated by the ability to sample multiple reads from the same location. In this paper we develop novel rapid alignment algorithms for two-pass Single Molecule Sequencing methods. We combine the Weighted Sequence Graph (WSG) representation of all optimal and near optimal alignments between the two reads sampled from a piece of DNA with k-mer filtering methods and spaced seeds to quickly generate candidate locations for the reads on the reference genome. We also propose a fast implementation of the Smith-Waterman algorithm using vectorized instructions that significantly speeds up the matching process. Our method combines these approaches in order to build an algorithm that is both fast and accurate, since it is able to take complete advantage of both of the reads sampled during two pass sequencing.