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Manual tracing of the CC was performed by a single rater, BW, with a high intra-rater reliability (ICC >0.95 for repeated area measures).
If fewer repeated area measures are needed to explain more of the variation in usual long-term exposures as compared with personal measures, this could have far-reaching impacts on costs, participation, and other logistical concerns of long-term intervention studies.
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It yields highly reliable contigs and it is not so affected by repeated areas between contigs.
Gene duplications and repeated areas are prevalent in the SLY genome.
In genome data, there are many highly repeated areas, which are full of the same or similar sequences.
Repeated areas in the Giardia genome contain pseudogenes, retro-transposons and low complexity repeats and they could constitute areas of increased genomic plasticity or sites where recombination occurs, which is indicated by their associations with discontinued synteny.
Because Velvet and other de Bruijn graph-based programs cannot build across repeated areas (such as the inverted repeat regions in angiosperm plastomes), the plastome is assembled in segments, which need to be manually joined.
For the genome alignment classes, NM indicates reads that could not be mapped to the genome, R* reads that were mapped to repeat areas and U0-U2, reads that were mapped with either no, one or two mismatches to the genome.
The MIB6 segments available for phylogenetic analysis, which excluded the repeat area but included informative mutations within the repeat, was too short to resolve phylogenetic relationships for all MIB sequences (Fig. 3).
There are also CRISPR-associated (CAS) genes and a leader sequence before the repeat area.
However, gaps can occur if reads that would typically be assembled into one contig cannot span a large repeat area.
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