| 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 4 3 | 7 5 I | 8 6 4 | 9 6 I | 10 6 5 | 11 6 I | 12 6 6 | 13 6 I | 14 6 7 | 15 6 I | 16 6 8 | 17 6 I | 18 6 9 | 19 6 I | 20 6 10 | 21 5 I | 22 4 11 | 23 4 I | 24 4 12 | 25 3 I | 26 3 13 | 27 2 I | 28 2 14 | 29 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_28843.1_Instance_1 HL_28843.1_HL_3IGI_002_U47_A61 | U | G | A | A | G | G | C | A | G | A | A | G | U | A | A | |||||||||||||||||||
| HL_28843.1_Sequence_1 HL_28843.1_HL_3IGI_002_U47_A61 | U | G | A | A | G | G | C | A | G | A | A | G | U | A | A | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 14 cWW 2 11 s33 2 12 s33 2 13 tSH 2 14 s55 3 12 tHW 3 13 s55 4 5 s35 5 6 s35 6 7 s35 7 8 s35 8 9 s35 9 10 s35 10 11 s35 10 12 s35 11 12 cSH 12 13 s35 13 14 s35 11 3 6BPh 2 12 6BPh 13 2 6BRJAR3D SCFG/MRF model for HL_28843.1:
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 [14] // Initial node U47 - A61 from junction BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009123784,0.017718471,0.010008206,0.198264936,0.000000000],[0.022262210,0.009929018,0.198931998,0.011154256,0.000000000],[0.010027726,0.196386049,0.002064490,0.023275738,0.000000000],[0.216349992,0.010477281,0.053822220,0.010203624,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Basepair U47 - A61 cWW BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.044130649,0.046718239,0.000529759,0.002496756,0.000000000],[0.044458508,0.046610059,0.000529759,0.000529759,0.000000000],[0.380732303,0.003708313,0.018128765,0.314747597,0.000000000],[0.049261589,0.046358426,0.000529759,0.000529759,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [13] // Basepair G48 - A60 tSH ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [3] | Right Index [12] | Norm Constant [0.259025769291484] // Cluster node A49:A49 and G58:U59 Interaction | Interacting Bases [1,3] | Pair Probability [[0.018961504,0.042198433,0.004196211,0.429522110,0.000000000],[0.004196211,0.338134433,0.010058595,0.004196211,0.000000000],[0.019694625,0.004196211,0.031911832,0.024345914,0.000000000],[0.004196211,0.004196211,0.018663303,0.041331983,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A49 - U59 tHW Interaction | Interacting Bases [2,3] | Pair Probability [[0.031413984,0.032009409,0.001759976,0.031282354,0.000000000],[0.023452592,0.035343467,0.000389689,0.031347933,0.000000000],[0.192125245,0.002727821,0.234360049,0.282683054,0.000000000],[0.031901402,0.031709893,0.000389689,0.037103443,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G58 - U59 cSH 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 [4] | Right Index [10] // New Initial node after Cluster HairpinNode | Num Bases [7] | Left Index [4] | Right Index [10] | Norm Constant [0.999999999999998] // Hairpin node G51:A57 Interaction | Interacting Bases [1,1] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G51 Interaction | Interacting Bases [2,2] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G52 Interaction | Interacting Bases [3,3] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C53 Interaction | Interacting Bases [4,4] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A54 Interaction | Interacting Bases [5,5] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G55 Interaction | Interacting Bases [6,6] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A56 Interaction | Interacting Bases [7,7] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A57Sequences of instances from HL_28843.1:
> HL_28843.1 HL_3IGI_002 U 47 A 61 UGAAGGCAGAAGUAA