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Identification of intact LTR retroelements (Step 1 in Figure 7) consists of three steps. (a) Pairs of maximal exact direct repeats (> 40 bp) were found; (b) Repeats were merged if they were proximal in the genome locations, if the length of the merged repeats is greater than 100 bp and the identity is greater than 80%; (c) If the segment capped by repeats contain frequent protein domains (RT, RNaseH, or IN), or an ORF (>700 bp), they were retained.
