Oligo design tool for detection of precise insertions using Guide-it screening assays

Each insert screening assay performed using the Guide-it Knockin Screening Kit involves the application of oligos designed to detect seamless 5' and 3' junctions between the inserted sequence and the surrounding genomic target locus. To simplify the oligo design process, we have developed the software tool below. You will need to input (in the 5'→3' orientation) four sequence fragments corresponding to the 5' and 3' junctions of the inserted sequence and target site following successful editing. (Please see figure below for further clarification.)

• To generate the oligos to detect the 5' junction:
  • Enter the wild type sequence 5' upstream of the insertion (1)
  • Enter 5' terminal sequence of the insert (2)
• To generate the oligos to detect the 3' junction:
  • Enter the 3' terminal sequence of the insert (3)
  • Enter the wild type sequence 3' downstream of the insertion (4)

Following submission of the four sequences, the tool will output displacement, flap-probe, wild-type control, and knockin control oligos for analysis of both the 5' and 3' junctions.