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The resulting spretus sequence assembly was analyzed for repeat content using the RepeatMasker algorithm (; Institute for Systems Biology, Seattle).
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Repeat elements were masked using the RepeatMasker [ 51].
Transposon sequences were searched using the RepeatMasker and RepeatProteinMasker softwares.
Genome wide repeats were analysed using the RepeatMasker programme [ 96].
To find SINEs among these sequences, we aligned these sequences using CLUSTAL X [ 97] and performed a RepeatMasker search using the RepeatMasker software (Smit & Green, Repeat Masker at http://ftp.genome.Washington.edu/RM/RepeatMasker.html).html
Identification and classification of TE sequences in the genome of C. heterostrophus were performed using the RepeatMasker program (A.F.A. Smit, R. Hubley & P. Green RepeatMasker at http://repeatmasker.org).org
The identification and classification of the repetitive element sequences in the genome of M. fijiensis was performed using the RepeatMasker software (A.F.A. Smit, R. Hubley & P. Green, RepeatMasker at http://repeatmasker.org).org
The conventional approaches are based on similarity searching using the RepeatMasker program [ 17].
We compared the sequences between pairs of NUMTs manually or using the RepeatMasker program.
We screened the unigenes for nine Heliconius repetitive elements using the RepeatMasker software [ 52, 56].
Vole Oct4 locus was analyzed for the presence of repeated sequences using the RepeatMasker program [ 29].
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