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Some genes were assessed for multiple repeat regions.
Finally, regions that have multiple repeat regions can be broken up and sequenced separately (Liepelt et al., 2001).
Assembly of the initial shotgun sequences of the S. latifolia BAC lead to the identification of numerous relatively short contigs because of the presence of multiple repeat regions.
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Between the two Repeat A/B regions, multiple Repeat C regions exist in tandem, but the number of Repeat C regions varies between MITE464 copies, up to 14 repeats.
For example, Liepelt et al. (2001) noted that polymerase error can occur at a higher rate in regions containing multiple variable repeat regions.
For example multiple reads from repeat regions such as Long Interspersed Nuclear Elements (LINEs), Short Interspersed Nuclear Elements (SINEs), and ALUs in the untranslated regions of the transcriptome can distort the true expression level.
Multiple repeat elements within the region mediate a variety of rearrangements, including interstitial duplications, interstitial triplications, and supernumerary isodicentric marker chromosomes, as well as the deletions that cause Prader-Willi and Angelman syndromes.
The multiple alignment of these 3 repeat regions is shown in Figure 4B, demonstrating the strong similarity between these elements.
In cases where contigs had multiple accurate alignments, possibly due to repeat regions or shared sequences between genomes, we counted each contig's contribution for all the alignments.
While there is no obvious sequence similarity between the two repeat regions, both contain multiple copies of palindromic sequences, which are predicted to form stable stem-loop DNA structures [ 24].
Such an intensive interactive environment may increase the chance of aberrant DNA amplification, and thus form multiple copy number inverted repeats or tandem repeat regions on these chromosomes.
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