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Sequences that are supposed to be in the reaction mixture. Its important primers do not have unwanted connections to these sequences, so it will be checked that there are no hairpins, self- or hetero-dimers between the resulting primer and any sequence from the "Other sequences in PCR reaction" file.
Result
The search result is from 1 to 4 pairs of primers. The results should be as close as possible to the amplified fragment. That means, that the searching process starts from the edge of the amplified fragment to the 5' direction on the direct strand in case of forward primer and to the 3' direction of the reverse-complementary strand in case of reverse primer. The results are defined with special names:
- A - the pair of primers closest to the amplified fragment, corresponding to the entire set of parameters.
- B1 - the pair of primers closest to the amplified fragment, corresponding to the entire set of parameters, if B2 and / or B3 exist.
- B2 - the pair of primers corresponding to the entire set of parameters, which has a 4-nucleotide intersection with B1.