| 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 3 2 | 5 3 I | 6 3 3 | 7 3 I | 8 3 4 | 9 3 I | 10 3 5 | 11 3 I | 12 3 6 | 13 3 I | 14 3 7 | 15 3 I | 16 3 8 | 17 2 I | 18 2 9 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_17926.4_Instance_1 HL_17926.4_HL_4WF9_002_U87_A95 | U | G | U | A | A | G | U | A | A | |||||||||||||||
| HL_17926.4_Sequence_1 HL_17926.4_HL_4WF9_002_U87_A95 | U | G | U | A | A | G | U | A | A | true | 90 | 0 | 0 | 1.14 | ||||||||||
| HL_17926.4_Instance_2 HL_17926.4_HL_4Y4O_104_C87_G95 | C | G | G | U | A | G | C | G | G | |||||||||||||||
| HL_17926.4_Sequence_2 HL_17926.4_HL_4Y4O_104_C87_G95 | C | G | G | U | A | G | C | G | G | true | 85 | 0 | 0 | 1.74 | ||||||||||
| HL_17926.4_Instance_3 HL_17926.4_HL_4QLM_002_U72_G81 | U | A | C | U | C | C | U | U | C | G | ||||||||||||||
| HL_17926.4_Sequence_3 HL_17926.4_HL_4QLM_002_U72_G81 | U | A | C | U | C | C | U | U | C | G | true | 57 | 0 | 0 | 4.92 | |||||||||
| HL_17926.4_Instance_4 HL_17926.4_HL_5J7L_135_U87_A95 | U | G | A | U | A | U | G | A | A | |||||||||||||||
| HL_17926.4_Sequence_4 HL_17926.4_HL_5J7L_135_U87_A95 | U | G | A | U | A | U | G | A | A | true | 82 | 0 | 0 | 1.99 | ||||||||||
| HL_17926.4_Instance_5 HL_17926.4_HL_6UFJ_004_G33_C41 | G | C | U | C | A | A | A | G | C | |||||||||||||||
| HL_17926.4_Sequence_5 HL_17926.4_HL_6UFJ_004_G33_C41 | G | C | U | C | A | A | A | G | C | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_17926.4_Instance_6 HL_17926.4_HL_5K7D_002_G33_C41 | G | C | C | C | U | A | A | G | C | |||||||||||||||
| HL_17926.4_Sequence_6 HL_17926.4_HL_5K7D_002_G33_C41 | G | C | C | C | U | A | A | G | C | true | 83 | 0 | 0 | 1.95 |
1 9 cWW 2 3 s35 3 4 s35 4 5 s35 5 6 s35 6 7 s35 7 8 s35 8 9 s35JAR3D SCFG/MRF model for HL_17926.4:
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 [9] // Initial node U87 - A95 from junction BasepairNode | Deletion Probability [0.0000097596267952] | Pair Probability [[0.009353012,0.017115225,0.010782073,0.165404832,0.000000000],[0.064326949,0.012255484,0.178046090,0.012586828,0.000000000],[0.010818665,0.186779082,0.002191230,0.022094170,0.000000000],[0.194304352,0.012235239,0.091370254,0.010336514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.826344012,0.171868555,0.001718686,0.000068747] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | 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 [9] // Basepair U87 - A95 cWW HairpinNode | Num Bases [7] | Left Index [2] | Right Index [8] | Norm Constant [1.000000000000000] // Hairpin node G88:A94 Interaction | Interacting Bases [1,1] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.437500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.437500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G88 Interaction | Interacting Bases [2,2] | Pair Probability [[0.187500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.187500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.437500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U89 Interaction | Interacting Bases [3,3] | Pair Probability [[0.187500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.437500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.312500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A90 Interaction | Interacting Bases [4,4] | Pair Probability [[0.562500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.187500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A91 Interaction | Interacting Bases [5,5] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.312500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.312500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G92 Interaction | Interacting Bases [6,6] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.187500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.312500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U93 Interaction | Interacting Bases [7,7] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.437500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A94Sequences of instances from HL_17926.4:
> HL_17926.4 HL_4WF9_002 U 87 A 95 UGUAAGUAA > HL_17926.4 HL_4Y4O_104 C 87 G 95 CGGUAGCGG > HL_17926.4 HL_4QLM_002 U 72 G 81 UACUCCUUCG > HL_17926.4 HL_5J7L_135 U 87 A 95 UGAUAUGAA > HL_17926.4 HL_6UFJ_004 G 33 C 41 GCUCAAAGC > HL_17926.4 HL_5K7D_002 G 33 C 41 GCCCUAAGC