It seems that the sequening primer is binding also with high affinity somehere inside your target region.

You should use PCR primers with an extension, which you can use as target for universal sequencing primers. Then you are able to separate primary PCR from subsequent Sanger sequencing and avoid any further problems.

@Marcus A Koch

So many thanks for your precious contribution.

Best Regards

Marcus A Koch

This is the list of universal sequencing primers. Would you please let me know, which do you suggest to use for Brassicaceae?

https://www.lslabs.com/resources/universal-primer-list