On many of my sequences it appears as a duplicate of the sequence about 15bp longer fades in at the end. Sometimes it becomes the hight of the “original” signal and ruins the sequence, its still readable for the last 15 or so bases when the shortest version of the sequence ends. Most often its about 15bp longer , sometimes about 2 or 3. Im sequencing short 16S about 150 bp. The template is from a DGGE-gel and is a single genotype for sure. Template has a GC-tail but the sequencing primer has not. What causes this problem?
You can get secondary products in the PCR templates. Normally they are at a low level and so you can’t notice them, but when main signal ends they come through as weak peaks that the KB basecaller then calls.
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