See the attached archive. There are two sequences and one file with forward and reverse primers. The second (extended) sequence has additional 12 'T' characters at the beggining.
- Open a sequence.
- Open the "In Silico PCR" tab on the options panel.
- Input the forward and reverse primers from the third file.
- Set the number of mismatches for the forward primer to "27" (note that it is enough to set the value to "22" for the extended sequence).
- Click "Find product(s) anyway".
A product is found only in case of the extended sequence.
The product is found in both cases.
In the attached pictures you can see that in case of "not_extended" sequence the primers searching algorithm needs to insert additional gaps at the beginning of the sequence, but it doesn't do that. In case of "extended" sequence, the beginning is already filled with 'T' chars, so the algorithm can find the place correctly.
This issue was created according the following issue on GitHub: