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Homology of the clones with LINE-1 sequence was systematically verified using the RepeatMasker program (http://repeatmasker.genome.washington.edu).edu
Apart from stems, we studied the composition of repetitive elements within large introns using the RepeatMasker program.
To explore whether transposons are components of the ALDH genes in rice, we screened all 21 unique ALDH genes using the RepeatMasker program (http://www.repeatmasker.org).org
Classification of L1 subfamilies was carried out using the RepeatMasker program (provided by Ensembl) and a customised version of the monomer search modules of L1Xplorer [16], which uses Matcher from the EMBOSS package and template sequences from published reports.
The conventional approaches are based on similarity searching using the RepeatMasker program [ 17].
Repetitive sequences were identified by using the RepeatMasker program obtained from http://www.repeatmasker.org.org
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To identify genomic repeats, we used the RepeatMasker program (http://www.repeatmasker.org/) to scan the black grouse draft genome sequence.
We used the RepeatMasker program (Smit, Hubley, and Green, unpublished data; RepeatMasker open-3.0.8 at [ 65]) to detect and classify interspersed repeats in the clone database.
To identify new isoforms, we used the RepeatMasker program version 3.2.9 and the NCBI/RMBLAST that is part of the program as search engine.
Because NUMTs are associated with repetitive elements, we used the RepeatMasker program (http://www.repeatmasker.org/) to identify repetitive elements in these extracted fragments.
Genome wide repeats were analysed using the RepeatMasker programme [ 96].
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