Running multiple PCR experiments in a single tube is referred to as multiplex PCR. Typically the experiment involves amplifying multiple targets on the same strand of DNA at the same time, which is useful if multiple amplicons need to be expressed from the same strand and is essential if the amount of sample is very limited. Typically the amplicons are designed so that they are all different lengths and can be separated by conventional gel techniques. The multiplex PCR technique is very powerful for running repeated multiple assays, but in practice it is difficult to set up the primers for an assay the first time and may take extensive trials to find primers and probes which do not have any problems with cross-hybridization with each other or mis-hybridization to unintended locations on the target.
Visual OMPTM allows the experimenter to simultaneously design primers and probes for multiple specific sites while checking each primer and probe to make sure it does not hybridize anywhere it is not intended to. The program is also capable of then simulating the multiplex experiment and predicting the equilibrium concentration of each product. It can also display a matrix of all the free energies of each possible product (indented or not) which is very helpful in the experimental design.