| 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 7 I | 10 10 5 | 11 10 I | 12 11 6 | 13 11 I | 14 12 | 15 11 I | 16 11 7 | 17 10 I | 18 10 8 | 19 9 I | 20 8 9 | 21 3 I | 22 3 10 | 23 2 I | 24 2 11 | 25 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_79083.3_Instance_1 IL_79083.3_IL_3U5H_139_U3332_G3371 | U | G | U | A | A | G | C | U | G | A | G | |||||||||||||||||||
| IL_79083.3_Sequence_1 IL_79083.3_IL_3U5H_139_U_3332_G_3371 | U | G | U | A | A | G | * | C | U | G | A | G | true | 96 | 0 | 0 | 0.63 | |||||||||||||
| IL_79083.3_Instance_2 IL_79083.3_IL_4A1B_130_U3290_G3327 | U | G | U | A | A | G | C | U | G | A | G | |||||||||||||||||||
| IL_79083.3_Sequence_2 IL_79083.3_IL_4A1B_130_U_3290_G_3327 | U | G | U | A | A | G | * | C | U | G | A | G | true | 96 | 0 | 0 | 0.63 | |||||||||||||
| IL_79083.3_Instance_3 IL_79083.3_IL_4IOA_103_U2822_G2844 | U | G | C | A | C | G | U | U | C | A | G | |||||||||||||||||||
| IL_79083.3_Sequence_3 IL_79083.3_IL_4IOA_103_U_2822_G_2844 | U | G | C | A | C | G | * | U | U | C | A | G | true | 84 | 0 | 0 | 2.83 | |||||||||||||
| IL_79083.3_Instance_4 IL_79083.3_IL_2QBG_109_U2847_G2869 | U | G | U | A | A | G | U | U | G | A | G | |||||||||||||||||||
| IL_79083.3_Sequence_4 IL_79083.3_IL_2QBG_109_U_2847_G_2869 | U | G | U | A | A | G | * | U | U | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_79083.3_Instance_5 IL_79083.3_IL_3V2F_106_U2847_G2869 | U | G | U | A | A | G | U | U | G | A | G | |||||||||||||||||||
| IL_79083.3_Sequence_5 IL_79083.3_IL_3V2F_106_U_2847_G_2869 | U | G | U | A | A | G | * | U | U | G | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 11 cWW 2 3 s35 2 10 tSH 3 9 perp 3 10 s55 4 5 s35 5 6 s35 5 8 tHH 6 7 cWW 7 8 s33 10 11 s35 8 4 6BPh 10 4 2BR 2 9 6BR 3 9 6BRJAR3D SCFG/MRF model for IL_79083.3:
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 [11] // Initial node U3332 - G3371 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.012646166,0.014364762,0.015110345,0.037632857,0.000000000],[0.307921916,0.015603035,0.043960978,0.016966392,0.000000000],[0.015452329,0.037921065,0.003427306,0.015046324,0.000000000],[0.044331362,0.015314258,0.390349627,0.013951278,0.000000000],[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 [11] // Basepair U3332 - G3371 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.106770229,0.024890874,0.000257289,0.001225177,0.000000000],[0.107720164,0.022581288,0.000257289,0.000257289,0.000000000],[0.514059910,0.000932882,0.004519616,0.077597028,0.000000000],[0.116055460,0.022360926,0.000257289,0.000257289,0.000000000],[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 [2] | Right Index [10] // Basepair G3333 - A3370 tSH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.018518519,0.203703704,0.018518519,0.759259259,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Position [1] | Left Index [4] | Right Index [9] // Fixed node on left InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.214285714,0.642857143,0.071428571,0.000000000] | Position [2] | Left Index [5] | Right Index [9] // 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 [5] | Right Index [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.015321660,0.003151887,0.049920537,0.528611003,0.000000000],[0.003399205,0.000747565,0.004119347,0.350157565,0.000000000],[0.003239678,0.014889424,0.000747565,0.005232956,0.000000000],[0.003459265,0.011021822,0.000747565,0.005232956,0.000000000],[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 [5] | Right Index [8] // Basepair A3336 - U3368 tHH BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.013578915,0.188924424,0.013662582,0.101216274,0.000000000],[0.015121168,0.009998321,0.103243806,0.014148428,0.000000000],[0.013403983,0.128391209,0.002848221,0.240583182,0.000000000],[0.096847870,0.015374978,0.018078655,0.024577984,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [6] | Right Index [7] // Basepair G3337 - C3367 cWW HairpinNode | Num Bases [1] | Left Index [7] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node type * Interaction | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncationSequences of instances from IL_79083.3:
> IL_79083.3 IL_3U5H_139 U 3332 G 3371 UGUAAG*CUGAG > IL_79083.3 IL_4A1B_130 U 3290 G 3327 UGUAAG*CUGAG > IL_79083.3 IL_4IOA_103 U 2822 G 2844 UGCACG*UUCAG > IL_79083.3 IL_2QBG_109 U 2847 G 2869 UGUAAG*UUGAG > IL_79083.3 IL_3V2F_106 U 2847 G 2869 UGUAAG*UUGAG