indCAPS: A tool for designing screening primers for CRISPR/Cas9 mutagenesis events
Fig 2
Algorithm for generation of oligonucleotide primers useful for CAPS and dCAPS assays.
Two user-supplied sequences are analyzed, with one end near the predicted mutation site. Shared and unshared regions are identified in each sequence. A sub-sequence near the last shared base from each direction is isolated and compared to a library of restriction enzyme recognition motifs (https://www.neb.com/tools-and-resources/selection-charts/alphabetized-list-of-recognition-specificities). If a diagnostic site is detected, determined by an exact or close motif match in only one sequence, a primer is generated. The primer disrupts any exact matches present in the shared regions and is checked to ensure the mismatch number is less than the specified maximum.