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NTM isolates are 5'-16S rDNA sequenced, which, in most cases, results in the unequivocal identification of a known or sometimes unknown mycobacterial species.
Moreover, Alastruey-Izquierdo et al. (2010) studied species boundaries in Lichtheimia using genealogical concordance phylogenetic species recognition and established that the ITS region is the marker of choice for molecular identification of species in Lichtheimia because of its high degree of variability and the possibility of direct sequencing in most cases.
Nevertheless, for the other ones, we identified an adenine-rich sequence in most cases.
Such substitution is "conservative," which minimally affects the unique structure of parent sequences in most cases.
Comparison with the published sequence showed that 454 sequence contigs were joined correctly by ABI-Sanger sequences in most cases.
These findings confirm that the scaffolds produced from our contig joining procedure successfully recapitulate cDNA sequences in most cases.
A very small percentage of reads aligned to rRNA sequences in most cases, ranging from 0.2 to 12%%.
Microsatellites or simple sequence repeats (SSRs) are tandemly repeated DNA sequences (in most cases 1 6 bases in length) highly abundant throughout prokaryotic and eukaryotic genomes [ 43].
It is likely then, that in the context of WGS assembly, retrotransposon sequences in most cases will not affect assembly of genic regions.
Authors' response: It has been reported that the phylogeny tends to be stable when K = 5 for protein sequences in most cases [ 10, 13].
The mature sequences of miRNA genes within families showed ≥85% sequence identity in most cases (i.e., the number of nucleotide differences between the sequences was ≤3), whereas the sequences between different gene families were mostly unalignable.
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