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A total of 78 putative nested element clusters was identified in the M. graminicola genome, with 69 888%) clusters present on the core chromosomes.
They arise, for instance, when i) a transposable element nesting an unrelated element is mobilised, transducing the nested element; or ii) recombination between TE or ERV sequences leads to a new replication-competent element.
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Both programs, but especially LTRharvest, return overlapping and nested elements.
A total of 78 putative clusters of nested elements was found in the M. graminicola genome.
All TEs were scanned using Censor [ 35], to identify the presence of nested elements.
The default values are typically defined in the primary elements, and changes are defined as needed in the nested elements.
Finally the nested elements (elements inserted in each other as Russian dolls) are separated and reconstructed separately.
Relative chromosomal locations of the elements and their family annotations were used to identify clusters of nested elements.
Only 16 REs (6.30%) were flanked at both sides by transposon fragments, possibly representing loci with nested elements.
The 995 nested elements from the 917,008 dimeric Alu elements detected in the Tarsius genomic sequences comprise only the two known AluJ elements.
The 2,132 nested elements from the 1,057,994 Alu elements detected in the New World marmoset also show a distribution comparable to those of human and rhesus monkey.
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