Chromatograms that inclued data outside of reference fasta leads to nonsensical results

[YDum]

I use forward and reverse sequencing on amplicons using M13 tails on degenerated primers (with inosine). This leads to my dendrograms including the degenerated primers regions. To avoid including this unreliable data in my next analysis, I use a reference fasta corresponding only to the region between the primers.

But if I upload a chromatogram that has data outside the reference, the results are none-sensical :

Removing this region resolves the problem.

I don't know if this is a bug. For me it is a issue since I must do a little more work to find and remove the primers' data in every chromatogram, and I was expecting the algorithm to understand that it must stick to the reference fasta when aligning the sequences, and not to the chromatograms. Also, it might mean that the alignment is perform only from one extremity of chromatogram. In this case, resolving the problem will mean a little more work...