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Totally, 8 and 9 primers which produced highly readable, reproducible and polymorphic band patterns were selected for R. acetosa and C. communis, respectively (Additional file 2: Table S7).
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To show them in one analysis, selected DNA fragments corresponding to unique band patterns were denatured, subjected to MSSCP analysis and visualized by silver staining.
The band patterns were compared visually.
Band patterns were analyzed to determine clonal identity.
Band patterns were compared using Gelcompar II (Applied Maths, Belgium).
Band patterns were visualized with a silver staining method [ 54].
Band patterns were evaluated using the Dice similarity coefficient with a 4% band tolerance and 1% of optimization.
The correlation between band patterns was calculated with dice coefficient.
One individual per nest and the samples that had a deviating banding pattern on SSCP were selected for further sequencing.
Ten of the 38 primer pairs yielded distinct bands in the expected size range; consistent amplification patterns and fewer stutter bands were selected for characterization in 40 individuals that were sampled at El Comitán and 40 that were sampled at Punta Prieta, Ensenada, Baja California (29.063°N, 114.155°W).
A total of twenty six common bands were selected after band matching between different growth stages and twenty two of these bands were positively identified.
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