Search for Highly Divergent SINE repeats in the Rice Genome

In this article, we present a new method for searching for highly divergent copies of SINE elements in a genome. The method is based on the correlation of neighboring symbols both in constructing a positional weight matrix for a sequence of interest and in the genome scanning procedure. This makes possible to increase the alphabet size and, accordingly, the resolution capacity of the method. Using it, we found new copies of SINE repeats in the rice genome that have not been annotated before. The method was tested and compared with the RepeatMasker program; false positives were evaluated. SINE elements, retrotransposons, alignment-based methods, sequence similarity The work was partly supported by the RFBR Grant no. 20-016-00057.