TABLE 3.
Motif groups that have the largest number of Rfam loops that match them with a cutoff score above set thresholds, among Rfam families that are not mapped to a 3D structure
| Motif group | Description | # core | Cutoff | # matches |
|---|---|---|---|---|
| HL_53890.2 | Three conserved stacks, one or two bulged bases | 5 | 80 | 60 |
| HL_75660.5 | One conserved stack, multiple bulged bases | 3 | 80 | 47 |
| HL_32346.4 | One conserved stack, multiple bulged bases | 3 | 80 | 41 |
| HL_52953.3 | Four conserved stacks, occurs in riboswitches, ribozymes | 6 | 80 | 39 |
| HL_04783.2 | GNRA variation | 5 | 80 | 38 |
| HL_50006.2 | Two conserved stacks, multiple bulged bases | 4 | 80 | 28 |
| HL_37824.7 | GNRA hairpin | 6 | 80 | 28 |
| IL_87907.2 | Isolated noncanonical cWW pair | 6 | 80 | 1216 |
| IL_07785.1 | Isolated noncanonical cWW pair | 6 | 80 | 804 |
| IL_44465.1 | Isolated noncanonical GG cWW contact | 6 | 80 | 530 |
| IL_42997.3 | Isolated noncanonical cWW/cWS pair | 6 | 80 | 525 |
| IL_67095.2 | Isolated tWW turn | 6 | 80 | 504 |
| IL_08770.1 | Isolated noncanonical pair | 6 | 80 | 473 |
| IL_14688.1 | Isolated noncanonical cWW pair | 6 | 80 | 464 |
| IL_28037.2 | Isolated noncanonical cWW pair | 6 | 80 | 340 |
| IL_42771.1 | Multiple bulged bases | 4 | 80 | 327 |
| IL_10167.6 | Isolated cWH base pair, usually GG | 6 | 80 | 298 |
| IL_31737.3 | One conserved stack, one bulged | 5 | 80 | 286 |
| IL_57744.1 | Isolated noncanonical cWW pair | 6 | 80 | 212 |
| IL_82107.4 | Multiple bulged bases | 4 | 80 | 124 |
| IL_77658.1 | Tandem noncanonical cWW pairs | 8 | 80 | 87 |
| J3_07845.1 | Nearly minimal, one instance in the motif group | 7 | 60 | 4 |
| J3_41486.2 | Coaxial stacking, recurrent | 8 | 60 | 3 |
| J3_11375.2 | Coaxial stacking, recurrent | 10 | 60 | 2 |
| J3_70599.1 | Coaxial stacking, recurrent | 11 | 60 | 2 |
| J4_00691.2 | Minimal J4, two coaxial stacks, recurrent | 8 | 60 | 3 |
| J4_76096.5 | Minimal J4, two coaxial stacks, recurrent | 8 | 60 | 2 |
| J4_24280.2 | Minimal J4, two coaxial stacks, from LSU | 8 | 60 | 1 |
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Column 1 lists the motif group identifier, Column 2 gives a brief description of the instances in the motif group, Column 3 tells the number of core positions in the motif group (which does not count bulged bases), Column 4 tells the cutoff score threshold, and Column 5 tells the number of Rfam loops that match at or above the cutoff score threshold.
