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This study provides 154 high quality primer pairs targeting polymorphic repeats conserved in two Amynthas corticis mitochondrial lineages.
This program identifies SSRs, allows the control of many parameters to facilitate high quality primer construction, and can simultaneously process thousands of sequences.
Primer pairs could not be synthesized for about 40% of the SSR-containing EST sequences, as the microsatellite was located close to one of the ends of the sequence or flanking sequences were inappropriate for designing high quality primer pairs.
Use a high quality primer and apply it to the paneling using a paintbrush or a paint roller.
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To obtain high quality primers, many primer design constraints must be satisfied.
Moreover, high quality primers are essential for successful multiplex amplification reactions.
Sufficient flanking sequences existed to design high quality primers for 548 potentially amplifiable SSR loci.
Sufficient 60 bp flanking sequence on either side of the SNPs was obtained from paired end reads to effectively design high quality primers for SNP identification.
Forty-four paincludinguding three for housekeeping genes used for normalization) of high quality primers with amplification efficiencies in the range of 92.5% to 104.9% were selected for study.
The primers (Additional file 7) used for the ChIP assays were designed automatically to produce 90- to 140-base-pair amplicons that cover the Xic region spanning from position 100,532,247 to 100,832,343 on NCBI build 37. A program was written with the aim of producing high quality primers and maximizing coverage in this region (available upon request).
It is important to remark that MARs are not suitable targets for high-quality primer design, because their characteristic composition (richness of A-T tracks and repetitive DNA) prevents an acceptable design.
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CEO of Professional Science Editing for Scientists @ prosciediting.com