| Column number: Node in JAR3D model: Insertion positions indicated by I: Position in motif group: | 1 1 I | 2 2 1 | 3 2 I | 4 5 2 | 5 5 I | 6 6 3 | 7 5 I | 8 5 4 | 9 4 I | 10 3 5 | 11 2 I | 12 2 6 | 13 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_96776.2_Instance_1 HL_96776.2_HL_4WF9_007_A228_U233 | A | A | A | A | U | U | ||||||||||||
| HL_96776.2_Sequence_1 HL_96776.2_HL_4WF9_007_A228_U233 | A | A | A | A | U | U | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_96776.2_Instance_2 HL_96776.2_HL_5TBW_002_C69_G74 | C | A | A | C | C | G | ||||||||||||
| HL_96776.2_Sequence_2 HL_96776.2_HL_5TBW_002_C69_G74 | C | A | A | C | C | G | true | 97 | 0 | 0 | 0.28 | |||||||
| HL_96776.2_Instance_3 HL_96776.2_HL_4V88_189_C190_G195 | C | C | U | U | U | G | ||||||||||||
| HL_96776.2_Sequence_3 HL_96776.2_HL_4V88_189_C190_G195 | C | C | U | U | U | G | true | 96 | 0 | 0 | 0.39 |
1 2 s35 1 6 cWW 2 3 s35 2 4 cSW 4 6 s35JAR3D SCFG/MRF model for HL_96776.2:
Character Definition | A,C,G,U,* // Define characters here InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Initial node A228 - U233 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009360260,0.018555845,0.010510723,0.208326134,0.000000000],[0.019169057,0.009574703,0.221475475,0.012523923,0.000000000],[0.010585638,0.198991965,0.002053422,0.033057966,0.000000000],[0.197647789,0.012412375,0.025270620,0.010484105,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair A228 - U233 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.300000000,0.100000000,0.500000000,0.000000000] | Position [2] | Left Index [2] | Right Index [5] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [4] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.091501253,0.108423963,0.020384970,0.077338991,0.000000000],[0.077411456,0.092811797,0.002352171,0.097488279,0.000000000],[0.078964272,0.002352171,0.022281808,0.069399138,0.000000000],[0.078895507,0.094378085,0.009774210,0.076241928,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [4] // Basepair A229 - A231 cSW HairpinNode | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node A230:A230 Interaction | Interacting Bases [1,1] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A230Sequences of instances from HL_96776.2:
> HL_96776.2 HL_4WF9_007 A 228 U 233 AAAAUU > HL_96776.2 HL_5TBW_002 C 69 G 74 CAACCG > HL_96776.2 HL_4V88_189 C 190 G 195 CCUUUG