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The amplified microsatellites were separated and analyzed on denaturing polyacrylamide gels, and were detected with a LI-COR Model 4200L automated DNA sequencer (LI-COR Inc., Lincoln, NE, USA).
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In this work, microsatellites being separated by less than a maximum threshold d max were classified as compound microsatellite.
SSR-couples are each two adjacent microsatellites being separated by less than 10 bp (d max ), which can be part of a more complex compound microsatellite.
Microsatellite amplicons were separated on 3% agarose gels (Sigma).
After PCR amplification, microsatellite markers were separated by PAGE.
The microsatellite amplicons were separated on 8% polyacrylamide gels and visualized by ethidium bromide staining.
Microsatellite alleles were separated by capillary electrophoresis using an ABI 3730 DNA Analyzer (Applied Biosystems) at AGRF.
For fragment analysis, 10 μl of HiDi and 0.1 μl of GSL600 LIZ size standard (Life Technologies. Norwalk, CT, USA) were mixed with 2 μl of the pooled PCR multiplex dilution (see details in Additional file 1), and microsatellite fragments were separated using an ABI 3130xl Prism Genetic Analyzer.
Microsatellite PCR products were separated by polyacrylamide electrophoresis (PAGE) and detected using a Licor 4200 semi-automated sequencer.
In contrast, C. pinima and C. piquiti each showed haplotypes that were separated by long branches in the mtDNA tree, and their microsatellite clusters were clearly separated in the second step of the Structure analyses, as well as by Structurama (Additional file 7: Figure S4, Column 1).
Amplified PCR products were separated on a 6% polyacrylamide gel with a labelled marker for minisatellites, and on a urea gel for microsatellites.
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