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The resultant BESs were analyzed by utilizing the RepeatMasker program [ 47].
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We also utilized the RepeatMasker program [ 71] to recognize and mask interspersed repeat sequences from OR promoter regions.
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.
For construction of the phylogenetic trees, the intronic sequences were first run through the Repeatmasker program (http://www.repeatmasker.org), which masked evolutionarily non-neutral repeats.
Repeats were annotated with the RepeatMasker program [45] and the genomic positions of repeats were taken from UCSC Genome Browser [41] using the Table Browser [46].
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
To mask interspersed repeats and low complexity regions, the RepeatMasker program (http://www.repeatmasker.org) was used with the -xsmall option for each corresponding library.
The genome locations and identities of human TE sequences were taken from annotation generated by the RepeatMasker program (http://www.repeatmasker.org) [24].
Repeat sequences were masked with the RepeatMasker program (RepeatMasker at ).
The RepeatMasker program was used for finding Alu.
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