| aphased | Predicting A-phased DNA repeat(s) |
| gquad | Predicting G quadruplexes |
| gquadO | Predicting G quadruplexes including overlaps |
| hdna | Predicting intramolecular triplexes (H-DNA) |
| hdnaO | Predicting intramolecular triplexes (H-DNA) including overlaps |
| slipped | Predicting slipped motif(s) |
| str | Predicting short tandem repeats |
| tfo | Predicting triplex forming oligonucleotide(s) |
| zdna | Predicting Z-DNA motif(s) |