2.4 | Annotation of repetitive sequences
Both homology-based and de  novo- based approaches were used to search for TEs. Tandem Repeat was extracted using TRF (http://tandem.bu.edu/trf/trf.html) by ab initio prediction. The homolog prediction used Repbase (http://www.girinst.org /repbase) database employing RepeatMasker (http://www.repeatmasker.org/) software and its in-house scripts (RepeatProteinMask) with default parameters to extract repeat regions. For the de novo-based approach, we used LTR_FINDER (http://tlife.fudan.edu.cn/ltr_finder/), RepeatScout (http://www.repeatmasker.org/), and RepeatModeler (http://www.repeatmasker.org/RepeatModeler.html) to build the de novo repeat library. All the repeats identified by different methods were combined into the final repeat annotation after removing the redundant repeats.