The prediction appropriated short or long primer (probe) annealing site is only one way for PCR product prediction. Primer can bind many predicted sequences in template(s), but only sequences with few mismatches (1 or 2 depends from place and nucleotide) at 3’end of primer can be used for polymerase extension. The last 10-12 bases at 3’end of primer are sensitive to initiation of polymerase extension and general primer stability on binding template site. Single mismatch at these last 10 bases at 3’end of primer depends from the position and the structure can slightly reduced the primer binding and PCR efficiency. This software allows simultaneously testing single primer or list of the individual primer or probe with any length thorough multiplex target sequences. This test control by primer complementarity to target sequence performed with fast no gap alignment.
Oligonucleotides with degenerated sequence are fine for performing this test.
Probe with not complemental tail on 5’end and on 3’end to target is not problem for performing this test.
The probable PCR product can found for linear and cycle molecular, for standard, inverted PCR and for multiplex PCR.
Web tool for in silico PCR.
User must specify a directory by click on any file within a directory. The program will be sequentially read and analyze each file individually and test primer pairs or the primers (probes) list. Files can contain one or more FASTA sequence with standard IUB/IUPAC nucleic acid codes characters. This software allows simultaneously testing single primer or list of the individual primer or probe with any length thorough multiplex target sequences.