Help with the Primer match tool
The primer match form contains the following options:
Query - this field allows the user to choose specific loci/alleles to use as template for the primer design, separated by a comma or a carriage return character.
Select the type of sequence to be used - primers can be designed on the coding DNA or on the genomic DNA.
The sequence of forward primer - The sequence of the 5'-3' primer to be used as forward. Sequence can be degenerated
The sequence of reverse primer - The sequence of the 3'-5' primer to be used as reverse. Sequence can be degenerated
Maximum number of mismatches - The maximum number of mismatches allowed over the entire primer sequence.
Identity primer end - The portion of the primer in number of bases to be considered as 3' end. This portion needs to be identical to match the sequence.
Reverse complement rvs primer - If the reverse primer is privided in 5'-3' direction, this option allows to automatically reverse complement it.
Predicted product size - this option provides a range for the algorithm to exclute fragment bigger or smaller