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This assay subjected each sample to both an empty site assay (stage 1) and an internal primer test (stage 2).
(2) An internal primer test was conducted to verify the presence of novel L1 inserts and verify that they were full length.
After the initial double-repeated primer test screening using our protocol, 19 markers were selected out of the initial 22 markers set, for their clear reproducible amplification pattern.
The sites of the possible primers were selected visually and evaluated using Primer test option of Primer Express software (Applied Biosystems®, USA).
The inefficient marker conversion can largely be attributed to low passing rates in the primer and probe tests, i.e. 32.4% failed the primer test and 18% failed the probe test.
The specificity of primers was checked through regular PCR amplification followed by agarose gel electrophoresis, as well as by the primer test in a Mx3000P quantitative real time PCR machine by examining the melting curve.
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For primer testing and identity confirmation, the fragments from preliminary PCR were cloned and sequenced.
Genomic DNA derived from human placenta was used to generate standard curves for each primer tested.
Primer testing and sequencing resulted in 88 gene sequences (Table 2).
Six individuals of P. gonoacantha were screened during primer testing, resulting in amplicons for 15 primer pairs (Table 1).
Initial primer testing included 12 samples of B. integrifolia from three populations in the Hunter Valley region, Australia (Appendix 1).
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