| Initial/Insertion (I) |
Variable-length insertions |
Length distribution, base distribution and independent bases |
Allow for extraneous bases before the first flanking pair of a motif |
| Basepair (B) |
Nested basepairs and adjacent variable-length insertions (bulged bases) |
4×4 probability score matrix for basepair; length and base distribution for insertions |
All loops with nested basepairs |
| Cluster (C) |
Base triples, crossing basepairs, basepairs on the same strand |
Markov Random Field |
S/R (base triple), C-loop (crossing basepairs) |
| Fixed (F) |
Unpaired core nucleotides |
1×4 probability score vector for base |
Conserved base stacked between basepairs |
| Hairpin (H) |
Hairpin loops, which can contain base triples, non-nested basepairs and basepairs on the same strand |
Markov Random Field |
T-loop, GNRA loop, UNCG loop |
