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Insert-containing clones were identified by standard colony-PCR using above primer combinations.
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Since Tetracystis intermedia (TEL170), T. pulchra (TEL173) and Tetracystis texensis (TEL175) from the Dunaliellinia clade did not show a clear TRAP pattern using the primer combinations mentioned above, TRAP products were cloned from reactions utilizing the primer set CAMV × T3AG2-C (fig. 5 E ).
All the experimental AFLP profiles were generated using the protocol described above, and using the same primer combinations described in the in silico analyses.
The mitochondrial adenosine triphosphatase subunit 6 (ATP6) was amplified using the primer combinations ATP6-3/ATP6-4 ATP6-3/ATP6-4 ATP6-3/ATP6-4 Taq Porymerase sATP6-3/ATP6-4 sATP6-3/ATP6-4 sATP6-3/ATP6-4ed andve and the cycling profiles described by Kretzer and Bruns [ 26].
PCR was performed using the primer combinations: sense, 5'-TGTGTGCGGAAAGTATGCTGTC-3' and antisense 3'-RACE AAGCAGTGGTATCAACGCAGAGT.
Using four primer combinations we scored 451 polymorphic loci.
No amplification could be obtained with MtCBF13-specific primers from both accessions despite using different primer combinations and PCR conditions.
Initially, our results on twenty-five clinical isolates showed 0 3 polymorphic bands per primer pair while using ten primer combinations.
Genomic DNA sequences of H1, H7 and H16 were obtained by amplifying two overlapping fragments using primer combinations HcPsy1-CDS3F/HcPsy1-5ER HcPsy1-CDS3F/HcPsy1-5ER HcPsy1-CDS3F/HcPsy1-5ER cloning and HcPsy1-2EF/HcPsy1-CDS5R HcPsy1-2EF/HcPsy1-CDS5R HcPsy1-2EF/HcPsy1-CDS5R
Cytochrome oxidase 1 sequences were obtained using the primer combination of universal primers FishF1-5' TCACCCC AAC CAC AAA GAC ATT GGC and3' and FishR1-5' TACTACTCTCT GGG TGG CCA AAG AAT CA.-3' described in Ward et al., (2005) with the same PCR profiles and sequencing procedures as described above.
All primer sequences used above are listed in Additional file 1.
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