| 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 7 2 | 5 7 I | 6 8 3 | 7 8 I | 8 8 4 | 9 7 I | 10 7 5 | 11 6 I | 12 5 6 | 13 4 I | 14 3 7 | 15 2 I | 16 2 8 | 17 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_08002.5_Instance_1 HL_08002.5_HL_6DN2_004_G88_C95 | G | U | A | G | A | G | U | C | ||||||||||||||
| HL_08002.5_Sequence_1 HL_08002.5_HL_6DN2_004_G88_C95 | G | U | A | G | A | G | U | C | true | 99 | 0 | 0 | 0.17 | |||||||||
| HL_08002.5_Instance_2 HL_08002.5_HL_3F2X_005_G88_C95 | G | U | A | G | A | G | U | C | ||||||||||||||
| HL_08002.5_Sequence_2 HL_08002.5_HL_3F2X_005_G88_C95 | G | U | A | G | A | G | U | C | true | 99 | 0 | 0 | 0.17 | |||||||||
| HL_08002.5_Instance_3 HL_08002.5_HL_5C45_004_G88_C95 | G | U | A | G | A | G | U | C | ||||||||||||||
| HL_08002.5_Sequence_3 HL_08002.5_HL_5C45_004_G88_C95 | G | U | A | G | A | G | U | C | true | 99 | 0 | 0 | 0.17 | |||||||||
| HL_08002.5_Instance_4 HL_08002.5_HL_4FRG_003_G58_C66 | G | U | U | A | U | A | C | U | C | |||||||||||||
| HL_08002.5_Sequence_4 HL_08002.5_HL_4FRG_003_G58_C66 | G | U | U | A | U | A | C | U | C | true | 83 | 0 | 0 | 2.44 | ||||||||
| HL_08002.5_Instance_5 HL_08002.5_HL_5C45_002_G36_C43 | G | U | A | U | A | G | U | C | ||||||||||||||
| HL_08002.5_Sequence_5 HL_08002.5_HL_5C45_002_G36_C43 | G | U | A | U | A | G | U | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| HL_08002.5_Instance_6 HL_08002.5_HL_3F2X_002_G36_C43 | G | U | A | U | A | G | U | C | ||||||||||||||
| HL_08002.5_Sequence_6 HL_08002.5_HL_3F2X_002_G36_C43 | G | U | A | U | A | G | U | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| HL_08002.5_Instance_7 HL_08002.5_HL_4FRN_007_G56_C64 | G | U | U | A | U | A | C | U | C | |||||||||||||
| HL_08002.5_Sequence_7 HL_08002.5_HL_4FRN_007_G56_C64 | G | U | U | A | U | A | C | U | C | true | 83 | 0 | 0 | 2.44 | ||||||||
| HL_08002.5_Instance_8 HL_08002.5_HL_6DN2_002_G36_C43 | G | U | A | U | A | G | U | C | ||||||||||||||
| HL_08002.5_Sequence_8 HL_08002.5_HL_6DN2_002_G36_C43 | G | U | A | U | A | G | U | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| HL_08002.5_Instance_9 HL_08002.5_HL_4WF9_012_G370_C378 | G | U | A | A | U | A | A | U | C | |||||||||||||
| HL_08002.5_Sequence_9 HL_08002.5_HL_4WF9_012_G370_C378 | G | U | A | A | U | A | A | U | C | true | 81 | 0 | 0 | 2.61 | ||||||||
| HL_08002.5_Instance_10 HL_08002.5_HL_5J7L_144_G327_C335 | G | U | G | A | C | A | G | C | C | |||||||||||||
| HL_08002.5_Sequence_10 HL_08002.5_HL_5J7L_144_G327_C335 | G | U | G | A | C | A | G | C | C | true | 83 | 0 | 0 | 2.46 | ||||||||
| HL_08002.5_Instance_11 HL_08002.5_HL_7A0S_012_G338_C346 | G | U | G | A | G | A | G | U | C | |||||||||||||
| HL_08002.5_Sequence_11 HL_08002.5_HL_7A0S_012_G338_C346 | G | U | G | A | G | A | G | U | C | true | 97 | 0 | 0 | 0.48 | ||||||||
| HL_08002.5_Instance_12 HL_08002.5_HL_4Y4O_114_G327_C335 | G | U | G | A | A | A | G | C | C | |||||||||||||
| HL_08002.5_Sequence_12 HL_08002.5_HL_4Y4O_114_G327_C335 | G | U | G | A | A | A | G | C | C | true | 79 | 0 | 0 | 2.97 | ||||||||
| HL_08002.5_Instance_13 HL_08002.5_HL_4V9F_012_G334_C342 | G | U | G | A | C | A | A | C | C | |||||||||||||
| HL_08002.5_Sequence_13 HL_08002.5_HL_4V9F_012_G334_C342 | G | U | G | A | C | A | A | C | C | true | 75 | 0 | 0 | 3.46 | ||||||||
| HL_08002.5_Instance_14 HL_08002.5_HL_5TBW_007_G216_C224 | G | U | G | A | G | A | A | U | C | |||||||||||||
| HL_08002.5_Sequence_14 HL_08002.5_HL_5TBW_007_G216_C224 | G | U | G | A | G | A | A | U | C | true | 89 | 0 | 0 | 1.48 |
1 2 s35 1 8 cWW 2 5 tWH 3 4 perp 5 8 s35 6 7 s35 8 7 7BPhJAR3D SCFG/MRF model for HL_08002.5:
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 [8] // Initial node G88 - C95 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003421372,0.049878455,0.003896030,0.070763821,0.000000000],[0.006009733,0.023484994,0.071363436,0.004669298,0.000000000],[0.003852762,0.636871337,0.000734378,0.009407902,0.000000000],[0.069858180,0.033923966,0.008246450,0.003617885,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair G88 - C95 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.031250000,0.218750000,0.031250000,0.718750000,0.000000000] | Position [2] | Left Index [2] | Right Index [7] // 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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [6] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.218750000,0.156250000,0.593750000,0.031250000,0.000000000] | Position [2] | Left Index [2] | Right Index [6] // 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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [5] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000011805868568] | Pair Probability [[0.016670989,0.003689317,0.017315551,0.003689317,0.000000000],[0.037100939,0.297288410,0.003689317,0.003689317,0.000000000],[0.003689317,0.008843535,0.028056941,0.016408810,0.000000000],[0.498434800,0.003689317,0.021404972,0.036339155,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.428133005,0.569660385,0.002105156,0.000101453] | Left Letter Distribution [0.150000000,0.050000000,0.550000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [5] // Basepair U89 - A92 tWH HairpinNode | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A90:G91 Interaction | Interacting Bases [1,1] | Pair Probability [[0.906250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.031250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.031250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A90 Interaction | Interacting Bases [2,2] | Pair Probability [[0.093750000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.156250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.343750000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.406250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G91Sequences of instances from HL_08002.5:
> HL_08002.5 HL_6DN2_004 G 88 C 95 GUAGAGUC > HL_08002.5 HL_3F2X_005 G 88 C 95 GUAGAGUC > HL_08002.5 HL_5C45_004 G 88 C 95 GUAGAGUC > HL_08002.5 HL_4FRG_003 G 58 C 66 GUUAUACUC > HL_08002.5 HL_5C45_002 G 36 C 43 GUAUAGUC > HL_08002.5 HL_3F2X_002 G 36 C 43 GUAUAGUC > HL_08002.5 HL_4FRN_007 G 56 C 64 GUUAUACUC > HL_08002.5 HL_6DN2_002 G 36 C 43 GUAUAGUC > HL_08002.5 HL_4WF9_012 G 370 C 378 GUAAUAAUC > HL_08002.5 HL_5J7L_144 G 327 C 335 GUGACAGCC > HL_08002.5 HL_7A0S_012 G 338 C 346 GUGAGAGUC > HL_08002.5 HL_4Y4O_114 G 327 C 335 GUGAAAGCC > HL_08002.5 HL_4V9F_012 G 334 C 342 GUGACAACC > HL_08002.5 HL_5TBW_007 G 216 C 224 GUGAGAAUC