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Several maize centromeres contain only limited amounts of the centromeric satellite repeats, and represent some of the best sequenced centromeres in multicellular eukaryotes (Wolfgruber et al. 2009).
In summary, we found that the important Notch opa repeats are best sequenced and assembled using sequence reads >140 bp long (3 bp × 40 triplet repeats + 10 bp × 2 anchor sequences).
Despite the possibility of underestimating LSDs in low-coverage strains, we are able to detect a large number of LSDs in the majority of strains for both species: the mean for the best sequenced S. cerevisiae and S. paradoxus strains is 80 and 75, respectively.
As Clostridia and Proteobacteria are the best sequenced groups of Bacteria, we also applied weighted measures to find the most frequent donors outside the best sequenced groups.
We chose the six species in this paper because they are in independent lineages at varying phylogenetic distances, are among the best sequenced genomes, and have high fractions of aligned sequence that includes several thousand repeats per chromosome even in the genomes with the least data available.
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