Given a sequence, all the substrings of length sizePrimer (default value = 25) are considered as potential primers and are processed through a serie of filters. The primers which pass sucessfully all the filters are selected.
Select primers with a minimum of nbGCMin (default value = 11) and a maximum of nbGCMax (default value = 13) G or C nucleotides.
Dismiss primers with nbRepeat (default value = 4) successive identical nucleotides.
Dismiss primers having hairpins with the following features:
C A G G A T G T T G | | | C | | | C loop A A G A C C C A A T duplex length
Check the 5' and 3' extremities (4 nucleotides) and select primers satisfying:
|1er nt / 2nd nt||dA||dC||dG||dT|
Dismiss primers having a potential secondary fixation site on its neighboring. The length of the scaning zone is equal to sizeScan (default value = 20000) upstream and downstream the primer site. A secondary site exists if the number of matches between the primer and this site is equal to or greater than maxSimMatch matches (default value = 15), with a maximum of maxSimGap gaps (default value = 0).