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Choices for Probe Design: Similarly for probes, when you choose Unique, AlleleID® designs one probe per sequence. When you choose the Minimal set option, AlleleID® designs the smallest number of probes required to identify the sequences.
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Species Identification: Minimal probes with Optimal primers
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Taxa Specific/Cross Species Identification: Conserved Probe with Optimal Primers
Conserved Probe with Optimal Primers: AlleleID® designs a primer pair that would amplify the maximum number of sequences possible in an alignment. There are two choices available for designing primers, Unique and Optimal. For "Unique", the program designs a primer pair to amplify each sequence. Each primer is completely homologous to its template. For "Optimal', the program minimizes the number of primers required to amplify all sequences; taking advantage of the fact that primers can bind to a sequence and amplify it even if they contain a limited number of mismatched bases especially towards the 5' end of the primer.
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Design qPCR and Microarray Assays for Related Organisms
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