In addition to base pairs, DSSR also automatically detects higher-order base associations. They are generally termed multiplets, consisting of three or more co-planar bases arranged together via H-bonding interactions. The simplest multiplets are base triplets. For example, the yeast phenylalanine tRNA (PDB entry 1ehz) contains four base triplets, as shown below:

The well-known (types I and II) A-minor motifs are also multiplets of three bases. Similarly, the G-tetrad where four guanine bases associate via Hoogsteen H-bonding to form a square planar structure is also a special multiplet. The G-tetrad is the building block of the G-quadruplexes. As of v1.7.0-2017oct19, DSSR can automatically identify and characterize G-quadruplexes (see the DSSR User Manual).

The DSSR algorithm for detecting multiplets is generally applicable. It can identify as many co-planar bases as available in a given structure. Shown below is an octad, consisting of a G-tetrad in the middle and four Us on the peripheries. The octad is derived from PDB entry 1j8g using atomic coordinates from biological assembly 1 and 3.