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A circular 23 kb mercury resistance plasmid (23,319 bp; G+C content, 68%) was also detected (Fig. 1B) and shown to have a nucleotide sequence 99.9% identical to that of the 23 kb pMM23 mercury resistance plasmid from Mycobacterium marinum (strain ATCC BAA-535) [30].
As was found in TaEP1, there was a significant conservation of the non-coding sequence between TaZFN1 and BdZFN1, especially in introns 3, 5 and 6 which all have a nucleotide sequence coverage of >62%.
In this study, EV71 subgenotype C4 was shown to have a nucleotide sequence divergence of 18.1% (17 20%), which exceeded the average threshold divergence of 14.95% for EV71 subgenotyping when comparing with EV71 subgenotypes C1 C5.
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Similarly, the B region of strain M22 has a nucleotide sequence identical to that inserted into chromosome XII of EC1118 (EC1118_XII), but the two forms differ in terms of their insertion site.
BlastN analysis revealed a 1.56 kb region of pKF3-70 that included a region containing 10 direct repeats followed by ORF1 and ORF2; this region had a nucleotide sequence that is almost identical (1535/1564 identities) to that of parA partition system in IncFII plasmids R1 and R100 [15], [15].
Although the RANTES (CCL5) sample had extra bands of unknown origin, the band at the expected size of 205 bp had a nucleotide sequence that matched RANTES.
One isolate (233) tested positive for the ECII marker by PCR, but yielded a mixed pattern by MVLST, because the gene inlB showed a sequence identical to ECIV, whereas the remaining five genes had a nucleotide sequence consistent with ECII.
This second isolate has a nucleotide sequence that was 100% identical to that of AWRIB429, indicating that these two strains most likely both represent Lalvin VP41 and that the observed phylogeny is in fact a true representation.
The HMM stochastically enters a state, stochastically emits a single nucleotide (if the state is bg) or a single site (if in a motif state), and repeats this process until it has emitted a nucleotide sequence of the predetermined length, that is, length of x or y.
Although human cells express minor sequence variants of the U1 snRNA (Kyriakopoulou et al, 2006), direct RNA sequencing of 3′-end labelled TAF15-associated U1 snRNA has revealed a nucleotide sequence identical to the Gly41 Gly164 3′-terminal portion of the most abundant U1A sequence variant of U1 snRNA (data not shown).
Author response: The criteria which we used for the prediction of miRNA precursors are very stringent, since we selected as putative miRNAs only those sequences which have a nucleotide identity greater than 95% with a known precursor.
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