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The methodologies are exemplary demonstrated by modeling and optimizing a typical tunnel lining structure, which contains many repetitive elements.
Another challenge in extracting copy number information from sequence data is that the genome contains many repetitive elements, and aligning reads to these positions is impossible using current short-read technologies.
Besides the well-classified sequences, many repetitive elements could not be assigned to a superfamily or even class.
For example, many agriculturally important plants (e.g., sunflower, wheat) have enormous genomes containing many repetitive elements and large intergenic regions.
It is known that over the course of S. latifolia sex chromosome evolution, many repetitive elements have accumulated on the Y chromosome [ 21].
In addition, we observed a high level of methylation in many repetitive elements, which is also in agreement with the patterns observed in mice [ 49, 50].
Similar(44)
Although many repetitive element regions are distinctive enough to permit unique mapping of 35 or 50 bp sequence reads, underrepresentation of repetitive elements in the "mappable" genome may also contribute to the lower than expected overlap between DMEs and several repeat classes.
Many repetitive element insertions, including those of L1 and Alu [ 30], are found in the introns of genes.
Many repetitive element families were differentially expressed in prostate tumors, with most of the changes occurring within LINE, LTR, and DNA class elements.
The presence of many repetitive DNA elements in the W chromosome, especially non-LTR retrotransposons, has been reported [ 46, 47].
Indeed, in the self-comparative-plot analysis of sequence similarity among large SD regions (Additional file 10), we found that most of the SDs comprised unique repetitive sequences, although all of the SDs share many known repetitive elements.
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