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Primer deletion and GBLOCKS 5' and 3' trimming resulted in 235 bp of the initial 330 bp (71%).
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Sequences could be extended 520 bp upstream and 383 bp downstream of the initial fragments, yielding 1,221-bp 1,221-bps fragmentsgenetic analysis.
However, retention of intron 1 introduces a UAA stop codon 123 bp downstream of the initial AUG.
Based on the initial sequences, two new 5′ primers (F2 and F3) were designed to hybridize 60 80 bp downstream of the initial 5′ primer (F1).
Additionally, a transcription map with a 35 bp resolution of the initial 24 hours of development indicates that 30% of the transcribed regions are still unannotated.
The new 5′ primers and a 3′ primer (R2), which hybridized more than 200 bp downstream of the initial primer, were used for subsequent PCR amplifications [ 9, 10].
These sites are located at positions 4 and 6 bp downstream of the initial ATG (M1) start codon, indicating that the original sequence annotation for this gene is incorrect and that the second ATG (M11) most likely constitutes the translation start codon for SO2426.
The resulting complete mitochondrial sequence of 17,271 bp (the initial contig was 17,103 bp) was deposited in the GeneBank (accession number KP718940) and considered our reference mitogenome for A. charrua (Fig. 1).
528 829 bp (15.3%) of the initial target region were omitted due to reasons of specificity and uniqueness.
The transcription unit is made up of 7665 bp, and the transcription start site located at –197 bp from the initial ATG of the ORF.
A total of 4790 bp of the VvDXS locus, from the initial ATG start codon to the TAG stop codon, was resequenced corresponding to base pair numbers 3759954-3764743 of NC_012011.
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