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Adaptase™ technology, used in the xGen™ Broad-Range RNA Library Prep Kit, adds a low complexity polynucleotide tail with a median length of eight bases to the 3’ end of each fragment during the addition of the first NGS adapter molecule. Considering this, it is normal and expected to observe them at the beginning of Read 2 (R2).
When read length is close to fragment size, the tail may also be observed toward the end of Read 1 (R1). We recommend using the STAR aligner (Dobin et al. 2013) to soft clip the synthetic tail sequence and provide efficient mapping without extra processing of your sequencing data.
For more details, you can refer to the Appendix section of the xGen Broad-Range RNA Library Prep Kit Protocol pertaining to Data Analysis and Informatics.