I am trying to sequence a gene that appears to have a duplication and the duplication is 20-70 bp less than the original. I've tried three genus specific primer sets and observe the double band every time, so I know it isn't contamination or mispriming.
Attached is an image of the PCR product visualized on a 3% agarose gel after 45 minutes. The bands are too close together to extract for sequencing. I ran the gel again for 150 minutes but the bands became very weak and still were'nt seperated enough to confidently remove them.
Is there any way to get these bands separated? Any suggestions are welcome and appreciated.