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Primer pR(3+4) consisted of two arms: the P4 arm was complementary to the insert and P3 arm annealed to the 3' sequence of insertion site.
It represents an attractive host for insertion of multiple genes or a sequence of insertion and deletion without the necessity for marker recycling.
Only the 3'-tagged sequence of insertion 17-2 was transcribed in the different tissues tested at 26°C and 8°C as shown by the expected RT-PCR signal of 165 bp, which corroborates the in silico analysis.
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Moreover, the R-tree index is non-deterministic as the tree structure differs based on the sequence of insertions, whereas the Hilbert R-tree does not suffer from this.
High sequence homogeneity of insertion sequence elements within F. tularensis strains but divergence between subspecies suggests a strong effect of this process in F. tularensis.
Sequencing of insertion sites indicates that each is inserted into a repetitive region which could impact expression of affected genes but direct alteration of floral homeotic gene sequences was not detected.
Cloning and sequencing of insertion sites were carried out by plasmid rescue techniques as described before [ 20] with the exception that the chromosomal DNA was digested with EcoRI and XbaI to clone either side of the insertion.
The generation of large collections of mutagenised lines and the concurrent sequencing of insertion sites to develop readily searchable databases for these populations has revolutionised gene characterisation by providing 'in silico' access to thousands of mutant alleles.
"Validation summary" contains information on whether the mutant allele (retrotransposon) and null allele were detected by PCR, the validation result, the sequences of insertion site primers (ISPs) and other primers (OPs), and the combination of these primers producing detectable amplification.
To do this, we first extract from reads the sequences of insertion that are at least 20 bp long and then align them to the reference genome using BLAT.
Structural inferences from NMR data suggest that each insertion site shows a reflex response to insertions: the sequence of the insertion has much less impact on structural adaptations than does the site of the insertion.
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