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This is more than twice the value using Plain insert at the same flow condition.
However the elements do not insert at the same sites in the two species.
Although they were found to insert at the same target sequence (ATTTT), their relative genomic locations were different.
In total we identified 127 inserts at unique locations in the genome (Additional file 1 Table S1) and we have not identified any insert at the same location from two different parent populations, suggesting that there is no strong bias in preferred insertion sites between different experiments.
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The 42,445-bp φSa3(MSHR1132) prophage is inserted at the same site as φSa3 insertions in other S. aureus strains within the phospholipase C precursor gene (SAMSHR1132_17840).
Most elements were found to have inserted at unique sites, although three pairs of elements inserted at the same sites were found (insertions 12.4 and 14.22, 22.1 and 14.18, and 14.1 and 14.15).
Given this number of potential Zorro3 insertion sites it is interesting that in our sample of 30 new insertions we identified three pairs of elements that had independently inserted at the same sites.
Prophages have specific characteristics, including protein length, transcription strand directionality, AT/GC skews, phage-specific oligonucleotides and phage insertion points (even though different strains can have different prophages inserted at the same chromosomal integration site), that can be used for identification.
ICE 6013 insertions are found in several locations in S. aureus, and ICE 6013MSHR1132 is inserted at the same location as ICE 6013 in several sequenced strains (fig. 1).
A close analysis of 41 dissected cadavers found that the A.L.L. was, indeed, a ligament that consistently appeared in the same place, originated and inserted at the same spots and measured approximately the same length in all of the bodies studied.
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