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In conclusion, we identified 1457 putative TSSs with promoter elements or with multiple identical sequences upstream of the coding region.
In women with chronic HIV-1 infection multiple identical sequences suggest proliferation of HIV-1-infected cells, and low diversity tissue-specific phylogenetic clades are consistent with bursts of viral replication.
In cases multiple identical sequences resulted from cloned PCR products of one accession, only one sequence was included in the data set.
Nonetheless, in cases where multiple identical sequences were found within a site, only one of these was included in the analysis.
The phylogenies of these latter five families show multiple identical sequences, consistent with their current transposition (supplementary fig. S4 I K, M, and P, Supplementary Material online).
Next, shotgun reads from each data set were checked for sequencing artifacts generated by the presence of multiple beads and a single template in emPCR drops, which can potentially produce multiple identical sequences that can skew estimates of repeat element abundance (Gomez-Alvarez et al. 2009; Niu et al. 2010).
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First, sequence differences of less than 3 bp when compared to multiple identical sequence replicates from different clones within individuals were considered to be PCR or cloning artifacts and removed from the alignment.
However, this method leaves a loxP scar sequence and creates multiple identical loxP sequences throughout the genome if additional deletions are constructed (16).
The tRNA isodecoder consensus approach was undertaken as there are over 640 predicted tRNA genes in A. thaliana, originating from the nuclear, mitochondrial and chloroplast genomes often with multiple identical isodecoder sequences that makes assigning IIlumina sequences to individual transcribed tRNA loci challenging.
Each list was sorted, and where a sequence from one species had multiple best matches from the other species (which can happen when there are multiple identical protein sequences), all but one of the matching pairs were deleted.
The alignment of high coverage short reads along with an adequate number of informative long reads provides an extremely effective strategy for efficient closing and finishing of genomes containing multiple long identical sequences, regardless of size.
More suggestions(15)
several identical sequences
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multiple identical rows
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