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In case of insertion, the newly inserted sequence would be composed of segments of different RUs.
However, the exact size of larger insertions cannot be determined when the inserted sequence is longer than a sequence read.
For each test genome, 100 new IS insertions were simulated with the newly inserted sequence randomly chosen from existing IS element copies.
The algorithm relies on the presence of read pairs that span the TE insertion (TEI) site on either side of the inserted sequence.
Generally, NGS reads help identify insertion breakpoints, but additional assembly is required to identify the inserted sequence.
Each node that is traversed during the insertion process will have placed the sequence ID of the inserted sequence into its internal list.
These primers bound the insertion junction, with the two 3′-most bases binding to the inserted sequence.
Each line represents one strain, and the insertions are color coded according to the most likely origin of the inserted sequence.
Successful insertion of eGFP was detected by PCR using primers embedded in the inserted sequence and genomic sequences (Fig. 3A,C; supplementary material Fig. S6).
When the inserted sequence is larger than the deletion, we call it a type-A insertion associated with deletion.
Although it is unclear whether this phenomenon occurred consequent upon a nearby insertion of transposable element, the existence of this phenomenon supports the suggestion that inserted sequence is not the only source of CpG sequences and that inserted sequence itself is not necessarily CpG-rich.
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