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To investigate IS structure, for each IS group, IS sequences along with 500 bp of 5′ and 3′ flanking genomic sequences were aligned.
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The Pathogen Genomics group is sequencing genomes of organisms that are relevant to human and animal health.
First, we studied non-overlapping weighted designs where the individuals are divided to disjoint groups of d individuals and each group is sequenced individually.
The third group are sequences that did not BLAST against our 13 target species as the closest hit.
Initially, all amplified targeting sequences were cloned into a pGEXT-vector and several clones per group were sequenced.
In the single instance of inconsistency, all isolates from the mixed emm group were sequenced, and all remaining isolates shared the initially identified emm type.
Individual clones from adrenals from 5 different animals in each treatment group were sequenced to determine the degree of methylation of the three CpG sites in the AT1b proximal promoter.
ospC amplicons that could not be classified to a major allelic group were sequenced.
Starting at Round 3, 6 12 phage clones per group were sequenced (Supporting Information Figure S2).
PCR products were then cloned, organised into groups by RFLP analysis and one clone from each group was sequenced.
Clones from each group were sequenced and primers specific to each type were designed (see Additional file 1).
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