| 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 4 I | 8 5 4 | 9 6 I | 10 7 5 | 11 8 I | 12 9 6 | 13 9 I | 14 10 | 15 9 I | 16 9 7 | 17 4 I | 18 4 8 | 19 3 I | 20 3 9 | 21 2 I | 22 2 10 | 23 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_96332.5_Instance_1 IL_96332.5,IL_8K85_001,G4_C53 | G | A | C | G | G | U | C | G | G | G | C | |||||||||||||||||
| IL_96332.5_Sequence_1 IL_96332.58K85_G4_C53 | G | A | C | G | G | U | C | * | G | G | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_96332.5_Instance_2 IL_96332.5,IL_8K85_012,G4_C53 | G | A | C | G | G | U | C | G | G | G | C | |||||||||||||||||
| IL_96332.5_Sequence_2 IL_96332.58K85_G4_C53 | G | A | C | G | G | U | C | * | G | G | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_96332.5_Instance_3 IL_96332.5,IL_8K7W_001,G3_C47 | G | A | C | G | G | U | C | G | G | G | C | |||||||||||||||||
| IL_96332.5_Sequence_3 IL_96332.58K7W_G3_C47 | G | A | C | G | G | U | C | * | G | G | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_96332.5_Instance_4 IL_96332.5,IL_4TS2_005,G22_C77 | G | A | A | G | G | A | C | G | A | G | C | |||||||||||||||||
| IL_96332.5_Sequence_4 IL_96332.54TS2_G22_C77 | G | A | A | G | G | A | C | * | G | A | G | C | true | 99 | 0 | 0 | 0.13 | |||||||||||
| IL_96332.5_Instance_5 IL_96332.5,IL_4KZD_004,G19_C66 | G | A | A | G | G | A | C | G | A | G | C | |||||||||||||||||
| IL_96332.5_Sequence_5 IL_96332.54KZD_G19_C66 | G | A | A | G | G | A | C | * | G | A | G | C | true | 99 | 0 | 0 | 0.13 | |||||||||||
| IL_96332.5_Instance_6 IL_96332.5,IL_7L0Z_002,G12_C58 | G | A | G | G | G | U | C | G | G | G | C | |||||||||||||||||
| IL_96332.5_Sequence_6 IL_96332.57L0Z_G12_C58 | G | A | G | G | G | U | C | * | G | G | G | C | true | 91 | 0 | 0 | 1.61 | |||||||||||
| IL_96332.5_Instance_7 IL_96332.5,IL_3NPQ_006,C26_G19 | C | C | C | A | G | G | C | A | A | G | ||||||||||||||||||
| IL_96332.5_Sequence_7 IL_96332.53NPQ_C26_G19 | C | C | C | A | G | G | * | C | A | A | G | true | 61 | 0 | 0 | 6.64 |
1 2 s35 1 10 cWW 2 3 s35 2 9 cWW 3 8 cWW 4 5 s35 4 6 s53 6 7 cWW 6 8 s55 7 8 s35 8 9 s35 9 10 s35JAR3D SCFG/MRF model for IL_96332.5:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [10] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009252003,0.018892763,0.010549706,0.191568511,0.000000000],[0.016731454,0.009121701,0.203695325,0.012732248,0.000000000],[0.010465893,0.254442413,0.001991715,0.025065205,0.000000000],[0.189814218,0.013075076,0.022815388,0.009786380,0.000000000],[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 [10] // Basepair G4 - C53 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.027927600,0.013680095,0.393365084,0.016383004,0.000000000],[0.038025646,0.009098313,0.017695249,0.039762803,0.000000000],[0.324054816,0.017893971,0.003372903,0.014884762,0.000000000],[0.016351114,0.042012656,0.014565881,0.010926104,0.000000000],[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 [9] // Basepair A5 - G52 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.242329585,0.019554064,0.024112449,0.119259274,0.000000000],[0.045263942,0.009132029,0.152932728,0.017221854,0.000000000],[0.019925147,0.121857365,0.030651698,0.023568003,0.000000000],[0.120395959,0.018162068,0.022152059,0.013481776,0.000000000],[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 [8] // Basepair C6 - G51 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.055555556,0.722222222,0.055555556,0.000000000] | Position [1] | Left Index [4] | Right Index [7] // Fixed node on left for 8K85|1|A|G|7 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 [7] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.055555556,0.833333333,0.055555556,0.000000000] | Position [1] | Left Index [5] | Right Index [7] // Fixed node on left for 8K85|1|A|G|8 InitialNode | Left Length Distribution [0.146977400,0.846630090,0.006090502,0.000302008] | Left Letter Distribution [0.312500000,0.062500000,0.062500000,0.562500000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009117787,0.016733999,0.010467584,0.189844861,0.000000000],[0.018895995,0.009236003,0.254474892,0.013077223,0.000000000],[0.010551423,0.203726527,0.001992038,0.022818912,0.000000000],[0.191599712,0.012734286,0.025069445,0.009659312,0.000000000],[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 C10 - G50 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_96332.5:
> IL_96332.5 8K85 G 4 C 53 GACGGUC*GGGC > IL_96332.5 8K85 G 4 C 53 GACGGUC*GGGC > IL_96332.5 8K7W G 3 C 47 GACGGUC*GGGC > IL_96332.5 4TS2 G 22 C 77 GAAGGAC*GAGC > IL_96332.5 4KZD G 19 C 66 GAAGGAC*GAGC > IL_96332.5 7L0Z G 12 C 58 GAGGGUC*GGGC > IL_96332.5 3NPQ C 26 G 19 CCCAGG*CAAG