Qpcr primer design software free

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DNA Barcoding. Cell Line Authentication. Need Help? In selecting the appropriate probe and primers, a variety of constraints on the probe, the primers and amplified product are already considered and taken as default values. You either can use the default constraint values or modify those values to customise the analysis. Line breaks and blank spaces are allowed.

The template sequence may contain ambiguous bases, but the design tool will not select primers or probes complementary to any ambiguous sites on the template sequence.

For PCR primer pairs, you can specify any required bases at the 3' end of the primer 3' clamp , and a maximum difference in primer melting temperatures. Sequence homopolymer stretches and 5' G are avoided by the software automatically and more Cs than Gs are considered to be present in the probe sequence.

The maximum primer length you can search for are bases. Primer melting temperatures is calculated by using the nearest-neighbor model of Borer, and thermodynamic parameters for DNA nearest-neighbor interactions and the salt dependence of oligonucleotides determined by SantaLucia [Proc.

For efficient priming, the design tool avoids primers with extensive self-dimer and cross dimer formations in order to minimize primer secondary structure and primer dimer formation.

Amplicon Criterias For PCR products, you can specify a range of acceptable product sizes and define the minum and maximum GC content and melting temperature Tm. The maximum product length to enter is 5, bases. PCR product melting temperatures are calculated by using the formula of Baldino, et al. Reaction Conditions Salt concentration specifies the mM salt concentration in the reaction. This value is used in the calculation of both primer and PCR product melting temperatures.

The default value is