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To evaluate whether annotated miRNAs are located on genomic repeats and to discover the nature of these repeats, novel and downloaded miRNA precursors from the miRBase release 20 were analyzed using the RepeatMasker script, version 3.2.8 (http://www.repeatmasker.org/).org/
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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].
ERVFRDE1 LTR borders limits were determined using the RepeatMasker software (www.repeatmasker.org).org
Repetitive sequences were identified by using the RepeatMasker program obtained from http://www.repeatmasker.org.org
We screened the unigenes for nine Heliconius repetitive elements using the RepeatMasker software [ 52, 56].
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