Hi, I have Sanger-Sequencing results, so a 1000bp fa file. I want to map these to my circular plasmid, which was sequenced. This works fine with normal pattern search or SW-algorithm. However, if the fa file contains the start=end of the circular plasmid file, the search does not work with either of the two algorithms.

Any suggestions, how to cope with this problem?

Randolf, the feature you asked is implemented for the standard pattern search in UGENE 1.14. Support of other algorithms is planned for 1.15.