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What are Tandem Repeats and Mask Tandems in RealTimeDesign?

April 26, 2017mask repeats tandem tandems

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What are Tandem Repeats and Mask Tandems in RealTimeDesign?

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When using Custom Mode, Tandem Repeats is the toggle that instructs the RealTimeDesign (RTD) Software to automatically mask or unmask the tandems repeats that the software has identified on the inputted sequence. Tandem Repeats are defined by the software as all identified mono, di, tri, tetra and penta nucleotide repeats. Masking Tandems converts the repeat bases to an N. N is the IUPAC ambiguity code that represents any of the the four nucleotide bases A, T, C or G. The RTD Software will eliminate all primers and probes that contain a certain number of ambiguity codes. Unmasking tandems repeats will allow the RTD Software to consider the repeat regions within the inputted sequence with designs primers and probes. Note: Custom Mode will allow the user to determine which tandem repeat to mask by checking or unchecking the box next to each repeat region. Users can also choose to “Mask All” or “Unmask All” as well.