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To address questions of species delimitation and relationships, AFLP data generated from multiple primer combinations are generally combined into one large matrix and analyzed together to produce a phylogenetic tree.
For CNVs where the breakpoints were not clear, multiple primer combinations were tested.
Third, the ProPneumo-1 assay is a multiplex assay, which allows for multiple primer combinations in one reaction, instead of multiple monoplex reactions.
For some genes with previously described sequence diversity, such as ggt and ansB, multiple primer combinations were tested to exclude false-negative results and to ensure that the absence of the gene is not due to the sequence diversity.
No difference in size or exon content for scn4ab transcripts was detected when using multiple primer combinations, restriction enzyme digests and sequencing (supplementary material Fig. S8C and Table S1).
Despite the fact that the longer cDNA is likely the functional cox3 mRNA, a genomic copy corresponding to it could not be amplified from genomic DNA using multiple primer combinations (all of which successfully amplified the corresponding fragments in RT-PCRs; data not shown).
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It was therefore necessary to test multiple primer pair combinations for some targets, rejecting those that generated profile collapse or extensive plateau drifting as indicated by LRE analysis (see [ 18] for details about these anomalies).
That this single type was found from multiple different PCR primer combinations with varying conditions also argues against it being a PCR artifact caused by polymerase slippage between poly-T regions.
The remaining 16 primer combinations either produced multiple bands or did not amplify in either H. sect.
A hair sample (OMModCl, table 1) from a living muskox was amplified, products cloned, and multiple sequences determined using several of the primer combinations used in this study.
The combination of 16S rRNA gene amplification using multiple primer sets and the subsequent sequencing of the PCR products by Roche 454 pyrosequencing should therefore be a powerful method to assess the diversity of the microbiota in the GI tract of common carp.
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