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Transposable elements (TEs) are segments of DNA that self-replicate in a genome. DNA segments that originated from TE duplications may or may not remain transpositionally active but are herein referred to simply as TEs. TEs form vast families of interspersed repeats and constitute large parts of eukaryotic genomes, for example, over half of the human genome (Lander et al., 2001; de Koning et al., 2011; Wheeler et al., 2013) and over four fifths of the maize genome (Schnable et al., 2009). The repetitive nature of TEs confounds many types of studies, such as gene prediction, variant calling (i.e., the identification of sequence variants such as SNPs or indels), RNA-Seq analysis, and genome alignment. Source text: Hoen et al., 2015.