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Multiple sequence alignments of all selected clusters are generated using limited alignments produced by greedy clustering.
Previous studies that examined limited alignments in the 3' end of the ELN locus in five species noted particularly dense accumulations of repetitive sequences immediately downstream of the gene [ 4, 5] that contribute to rearrangements in the primate lineage.
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Pairwise nucleotide sequence alignments of human and chimpanzee, human and rhesus monkey (Maca mulatta) and human and mouse orthologs were constructed using ClustalW [ 60] and edited to limit alignments to the B and A domains only, which were then concatenated.
Of note, heuristics applied in short read aligners limit alignment of pairs within a given distance range.
Regions of sequence ambiguity and breaks between contigs in the BN genome form 876,652 gaps that limit alignment with DA and F344 reads.
In both cases, we limited the alignments to at most 3 mismatches using the Bowtie '–v 3' setting.
Because STXM based XANES utilizes a stack of STXM images taken at various energies, the achievable spatial resolution can be limited by alignment imperfections.
DEXA analysis, performed on 15 cases, showed a good calcar loading and stimulation, but there was significant lateral load transfer to R3 R4 zones, giving to the distal part of the stem a function not simply limited to alignment.
A DEXA analysis of 15 of these patients 3 years after implantation, performed as part of a comparative study between different femoral designs [10], showed a good calcar stimulation but a prevalence of distal stress transfer along the stem to the lateral femoral cortex and tip of the stem (R3 R4) giving to the distal segment of the component a function apparently not limited to alignment (1).
We computationally scanned the coverage in the WT 109J data to identify hyper-mutated regions, which limited the alignment of the short sequencing reads obtained for the HI clone.
Even the resolution of the reconstruction of the 20S proteasome with a total mass of 700 kDa does not appear to be limited by alignment errors at exposures of 12.6 e−/Å and higher (see previous section).
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