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Modern alignment methods designed to work rapidly and efficiently with large datasets often do so at the cost of method sensitivity. To overcome this, we have developed a novel alignment program, GRAT, built to accurately align short, highly similar DNA sequences. The program runs rapidly and requires no more memory and CPU power than a desktop computer. In addition, specificity is ensured by statistically separating the true alignments from spurious matches using phred quality values. An efficient separation is especially important when searching large datasets and whenever there are repeats present in the dataset. Results are superior in comparison to widely used existing software, and analysis of two large genomic datasets show the usefulness and scalability of the algorithm.