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The PCR products were sequenced directly with the use of Boα6-F, Boα6-R and two more internal primers (Boα6F1: 5′-ATGAATCGGAATATGGAG-3′ and Boα6R1: 5′-AACGGATTTAATCCAAGG-3′). No multiple peaks were observed in the obtained sequences, indicating the absence of sequence polymorphism in the pools.
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We followed the laboratory protocol of [ 31] and designed more specific and/or internal primers where required (detailed in Additional file 3).
The initial internal sequence was sometimes extended with an additional degenerate primer outside the initial sequence and a B. betularia-specific primer from within (cds extension primers in Table S2), or alternatively, two additional degenerate primers targeting a non-overlapping fragment were used to cover more internal sequence (cds additional primers in Table S2).
For some large PCR fragments that were more than 1600 bp, specific internal primers were designed to obtain their complete sequences.
They suggested that these loci be split into two (or more, if necessary) loci by designing internal primers to increase DNA polymerase fidelity; this solution would also remove issues with size homoplasy by insuring that all variation is produced by a single variable region.
This was likely due to mispriming from the internal primers of the earlier analysis and highlights the advantage of survey sequencing for a more accurate inspection of repetitive DNA.
No more rhythms, no more internal rhythms.
PCs have scads more internal memory.
The entire mitogenomes were amplified and sequenced by primer walking using newly designed specific internal primers.
The PCR product was cloned and sequenced using the forward, reverse and internal primers.
(DOCX 12 KB) 12284_2013_75_MOESM2_ESM.doc Additional file 2: Table S2: Primer combinations used to amplify the Waxy alleles and internal primers used for amplicons sequencing.
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