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We then developed the TEdenovo pipeline, a tool combining several different programs, including procedures for the clustering of interspersed repeats, into a single framework, the REPET package (http://urgi.versailles.inra.fr/index.php/repet).inra.fr/index.php/repet
To avoid merging repeats into a single genomic sequence, the overlapping unique sequence contigs were merged if the rate of polymorphism did not exceed 2% and if the resulting sequence coverage of the overlap did not exceed 150% of the average coverage (see Text S1).
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As a means to directly examine the status of meiotic homologous pairing in vivo, we built a strain, AV221, that carries a transgene insertion (meIs1 ) expressing GFP-LacI using the germline-specific pie-1 promoter (Praitis et al. 2001; Yuen et al. 2011) and a large array of lacO repeats integrated into a single genomic locus on chromosome III (meIs4 ).
No cue letters were repeated in a single experimental run.
To help disambiguate the true relationships between the reads from those induced by different copies of repeats, it is useful to construct a graph where all the copies of a repeat are collapsed into a single segment.
This finding of parallel pathways differs from results from kinetic studies of repeat-proteins composed of sequence-variable repeats, where modest repeat-to-repeat energy variation coalesces folding into a single, dominant channel.
This is especially true of phages with non-permuted terminal repeats: during sequence assembly, reads from each identical repeat are usually collapsed into a single region in the middle of the assembled contig, resulting in what can appear to be a circularly permuted genome.
If the corresponding two-sequence alignment of two overlapping repeats align at a pair of identical indices, then they will be combined into a single repeat.
Based on a periodic hyperspace description, the non-periodic structure can be described by the Aubry hull function, which plots atomic relaxations at the core of the boundary relative to an unrelaxed structure, folded into a single repeat unit of the neighboring grain.
The bits and pieces of photography are then reworked into a single, repeating short that makes beauty of the artistic process.
Finally, we must be aware that the same effect can be produced by repeated introductions of a pathogen into a single population.
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