saving sequence exports "reference only" bases

[YDum]

I aligned two chromatograms of the same amplicon (forward and reverse), with a reference fasta from another source to observe the covering of my sequencing and to exclude the PCR primers (the sequencing was performed using M13 tails).

When using "Save user sequence (FA)" to retrieve the sequence after treating the conflicts, I realized that the exported sequence include a part that was only determined by the reference fasta I used. Even if there is some supporting data in one of the chromatograms (see image below), it was not included in the analysis (maybe it is also a problem).

Strangely this does not happened in 3' of the sequence (see image below), were there is also supporting data but no reference-only bases in the exported sequence.

I hardly understand how the trimming is done, by the way. Quality remains rather high after the reverse chromatograms that is problematic.

As a temporary work-around, I manually deleted the undesired bases using "Treat as not sequenced", but it is a bit long...