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Both programs, but especially LTRharvest, return overlapping and nested elements.
All TEs were scanned using Censor [ 35], to identify the presence of nested elements.
A total of 78 putative clusters of nested elements was found in the M. graminicola genome.
Finally the nested elements (elements inserted in each other as Russian dolls) are separated and reconstructed separately.
Only 16 REs (6.30%) were flanked at both sides by transposon fragments, possibly representing loci with nested elements.
Relative chromosomal locations of the elements and their family annotations were used to identify clusters of nested elements.
Similar(38)
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.
A total of 78 putative nested element clusters was identified in the M. graminicola genome, with 69 888%) clusters present on the core chromosomes.
From a genome wide collection of annotated retroposed elements we extracted all 1,978 cases of nested CR1 elements.
However, we did not employ such design since it may become necessary in the future to define more deeply nested XML elements and multiple items with the same names under the same elements to integrate PDBML with other database resources.
Thus, an analysis of the patterns of nested CR1 elements (transpositions in transpositions that we call the TinT method, Figure 1) provides a relative timetable of active CR1 elements.
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