| 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 4 I | 6 7 3 | 7 7 I | 8 8 4 | 9 8 I | 10 9 5 | 11 9 I | 12 10 6 | 13 10 I | 14 11 7 | 15 11 I | 16 12 | 17 11 I | 18 11 8 | 19 10 I | 20 10 9 | 21 9 I | 22 9 10 | 23 8 I | 24 8 11 | 25 7 I | 26 7 12 | 27 6 I | 28 5 13 | 29 2 I | 30 2 14 | 31 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_44067.4_Instance_1 IL_44067.4_IL_3V2F_001_G24_C516 | G | U | G | G | A | U | G | C | U | G | A | A | A | C | ||||||||||||||||||||||
| IL_44067.4_Sequence_1 IL_44067.4_IL_3V2F_001_G24_C516 | G | U | G | G | A | U | G | * | C | U | G | A | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| IL_44067.4_Instance_2 IL_44067.4_IL_4IOA_001_G24_C526 | G | U | G | G | A | U | G | C | U | G | A | A | A | C | ||||||||||||||||||||||
| IL_44067.4_Sequence_2 IL_44067.4_IL_4IOA_001_G24_C526 | G | U | G | G | A | U | G | * | C | U | G | A | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| IL_44067.4_Instance_3 IL_44067.4_IL_2QBG_006_G24_C516 | G | U | G | G | A | U | G | C | U | G | A | A | A | C | ||||||||||||||||||||||
| IL_44067.4_Sequence_3 IL_44067.4_IL_2QBG_006_G24_C516 | G | U | G | G | A | U | G | * | C | U | G | A | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| IL_44067.4_Instance_4 IL_44067.4_IL_3U5H_016_A13_U410 | A | C | G | G | A | U | C | G | U | G | A | A | A | U | ||||||||||||||||||||||
| IL_44067.4_Sequence_4 IL_44067.4_IL_3U5H_016_A13_U410 | A | C | G | G | A | U | C | * | G | U | G | A | A | A | U | true | 90 | 0 | 0 | 1.96 | ||||||||||||||||
| IL_44067.4_Instance_5 IL_44067.4_IL_1S72_001_G21_U522 | G | U | G | G | A | U | U | A | U | G | A | A | A | U | ||||||||||||||||||||||
| IL_44067.4_Sequence_5 IL_44067.4_IL_1S72_001_G21_U522 | G | U | G | G | A | U | U | * | A | U | G | A | A | A | U | true | 95 | 0 | 0 | 1.04 |
1 2 s35 1 14 cWW 2 3 s35 3 4 s35 3 11 s33 3 12 tSH 4 5 s35 4 10 s33 4 11 tSH 5 6 s35 5 10 tHS 5 11 s55 6 7 s35 6 9 cWW 7 8 cWW 7 9 s55 8 9 s35 9 10 s35 11 12 s35 12 13 s35 13 14 s35 9 8 7BPh 3 11 6BPh 4 11 6BPh 14 13 7BPh 12 3 6BR 13 3 6BR 10 4 6BR 4 10 6BR 5 10 6BRJAR3D SCFG/MRF model for IL_44067.4:
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 [14] // Initial node G24 - C516 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003849789,0.050954645,0.004205623,0.179999416,0.000000000],[0.006121463,0.014587489,0.063201629,0.013952603,0.000000000],[0.004152707,0.385104148,0.000824854,0.157082684,0.000000000],[0.060630465,0.023681555,0.007901793,0.023749136,0.000000000],[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 [14] // Basepair G24 - C516 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.214285714,0.071428571,0.642857143,0.000000000] | Position [1] | Left Index [2] | Right Index [13] // 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 [3] | Right Index [13] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.944444444,0.018518519,0.018518519,0.018518519,0.000000000] | Position [2] | Left Index [3] | Right Index [13] // 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 [3] | Right Index [12] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.042467188,0.049500945,0.000511675,0.002436533,0.000000000],[0.042845019,0.044907828,0.000511675,0.000511675,0.000000000],[0.405791869,0.003581728,0.017352721,0.297927871,0.000000000],[0.046160330,0.044469591,0.000511675,0.000511675,0.000000000],[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 [3] | Right Index [12] // Basepair G26 - A514 tSH BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.042467188,0.049500945,0.000511675,0.002436533,0.000000000],[0.042845019,0.044907828,0.000511675,0.000511675,0.000000000],[0.405791869,0.003581728,0.017352721,0.297927871,0.000000000],[0.046160330,0.044469591,0.000511675,0.000511675,0.000000000],[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 [4] | Right Index [11] // Basepair G27 - A513 tSH BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.064373739,0.064946473,0.330650278,0.069971976,0.000000000],[0.075035834,0.068073375,0.002830312,0.067409074,0.000000000],[0.000775621,0.000775621,0.013712268,0.000775621,0.000000000],[0.003693410,0.000775621,0.235425154,0.000775621,0.000000000],[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 [10] // Basepair A28 - G512 tHS BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003391032,0.035734817,0.003264180,0.055013013,0.000000000],[0.004188811,0.004263654,0.004929479,0.025191782,0.000000000],[0.003200983,0.005020856,0.001027476,0.073233431,0.000000000],[0.006599491,0.003906482,0.004182469,0.766852045,0.000000000],[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 [6] | Right Index [9] // Basepair U29 - U511 cWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009662245,0.019360521,0.011052990,0.190423231,0.000000000],[0.018822386,0.008416510,0.210415236,0.012452350,0.000000000],[0.010998513,0.231797422,0.002089006,0.025286298,0.000000000],[0.201082692,0.012694357,0.024632354,0.010813889,0.000000000],[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 [7] | Right Index [8] // Basepair G30 - C510 cWW HairpinNode | Num Bases [1] | Left Index [8] | Right Index [8] | 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_44067.4:
> IL_44067.4 IL_3V2F_001 G 24 C 516 GUGGAUG*CUGAAAC > IL_44067.4 IL_4IOA_001 G 24 C 526 GUGGAUG*CUGAAAC > IL_44067.4 IL_2QBG_006 G 24 C 516 GUGGAUG*CUGAAAC > IL_44067.4 IL_3U5H_016 A 13 U 410 ACGGAUC*GUGAAAU > IL_44067.4 IL_1S72_001 G 21 U 522 GUGGAUU*AUGAAAU