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The occurrence of incomplete PMUs only may indicate that the AT genome is also less prone to insertion and recombination events.
There were 88 indels relative to Illumina data; these were mostly single nucleotide insertions in the PacBio sequence, and were located in homopolymeric tracts, regions that are known to be prone to insertion errors in PacBio sequencing [ 28, 29].
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However, based on our studies with A2UCOE-like dual divergently transcribed housekeeping gene promoters (Williams et al; M.A. et al), we would predict that CpG island associated single promoters such as PGK1 and EF1α would be prone to insertion-site position effects and silencing, as has recently been found to be the case following in vivo transplantation of transduced cells.
The 1-bp insertion of an adenine into an existing tract of seven adenines in the BoxG1 element is likely to have occurred more often, because homopolymeric tracts are very prone to insertions and deletions resulting from strand slippage during replication [ 50, 51].
These observations suggest that in xanthomonads genomes, loci flanking the hrp cluster on both sides are prone to the insertion of mobile genetic elements carrying virulence genes, especially T3Es and behave as PAIs [ 150].
The slight overrepresentation may actually result from the known enrichment of tandem repetitive sequences in transcription factors [ 23], which are therefore more prone to frequent insertions and deletions.
At present, it is unclear why some gene-rich regions, but not others are prone to L1 element insertion.
The relationship between the coverage obtained using IS-seq (reads per RFLP band) and the difference between observed and expected sites showed that our method was prone to identify fewer insertion sites than number of bands identified by RFLP when the coverage was below 100 reads per RFLP band, hence decreasing the sensitivity (Additional file 3: Figure S 2).
They then measured the length of a stretch of noncoding DNA that is prone to environmentally induced insertions and deletions, which allows for an easy determination of the mutation rate.
The ubiquitin gene is prone to duplications and insertions, leading to the formation of new fusion proteins [52], [53].
However, indels seem to be more prone to homoplasy than insertions of transposable elements [cf. [ 31, 33].
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