| 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 5 3 | 7 6 I | 8 7 4 | 9 8 I | 10 9 5 | 11 10 I | 12 17 6 | 13 17 I | 14 18 7 | 15 18 I | 16 19 | 17 18 I | 18 18 8 | 19 17 I | 20 17 9 | 21 16 I | 22 15 10 | 23 14 I | 24 13 11 | 25 12 I | 26 11 12 | 27 2 I | 28 2 13 | 29 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_54177.4_Instance_1 IL_54177.4,IL_8P9A_404,G562_C583 | G | U | G | C | C | A | G | C | G | G | U | A | A | UU | C | |||||||||||||||||||
| IL_54177.4_Sequence_1 IL_54177.48P9A_G562_C583 | G | U | G | C | C | A | G | * | C | G | G | U | A | A | UU | C | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_54177.4_Instance_2 IL_54177.4,IL_8CRE_423,G560_C581 | G | U | G | C | C | A | G | C | G | G | U | A | A | UU | C | |||||||||||||||||||
| IL_54177.4_Sequence_2 IL_54177.48CRE_G560_C581 | G | U | G | C | C | A | G | * | C | G | G | U | A | A | UU | C | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_54177.4_Instance_3 IL_54177.4,IL_5J7L_025,G515_C536 | G | U | G | C | C | A | G | C | G | G | U | A | A | UA | C | |||||||||||||||||||
| IL_54177.4_Sequence_3 IL_54177.45J7L_G515_C536 | G | U | G | C | C | A | G | * | C | G | G | U | A | A | UA | C | true | 96 | 0 | 0 | 0.96 | |||||||||||||
| IL_54177.4_Instance_4 IL_54177.4,IL_4LFB_021,G515_C536 | G | U | G | C | C | A | G | C | G | G | U | A | A | UA | C | |||||||||||||||||||
| IL_54177.4_Sequence_4 IL_54177.44LFB_G515_C536 | G | U | G | C | C | A | G | * | C | G | G | U | A | A | UA | C | true | 96 | 0 | 0 | 0.96 |
1 2 s35 1 13 cWW 2 3 s35 3 11 s35 3 12 s55 4 9 s53 4 10 s35 5 6 s35 6 7 s35 6 9 tHS 7 8 cWW 7 9 s55 7 13 perp 8 9 s35 12 13 s35 3 10 2BPh 4 10 7BPh 3 12 6BPh 11 3 7BR 5 9 7BR 13 12 7BR 7 13 2BRJAR3D SCFG/MRF model for IL_54177.4:
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 [13] // Initial node BasepairNode | Deletion Probability [0.0000000006078908] | Pair Probability [[0.004701945,0.048962338,0.005354260,0.097249743,0.000000000],[0.008259094,0.023053645,0.098073785,0.006416952,0.000000000],[0.005294798,0.543084038,0.001009245,0.012929150,0.000000000],[0.096005132,0.033300885,0.011332982,0.004972009,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.000000000,0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.250000000,0.050000000,0.050000000,0.650000000,0.000000000] | Left Index [1] | Right Index [13] // Basepair G562 - C583 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000] | Position [1] | Left Index [2] | Right Index [12] // Fixed node on left for 8P9A|1|sR|U|563 InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.002525253,0.002525253,0.992424242,0.002525253,0.000000000] | Position [1] | Left Index [3] | Right Index [12] // Fixed node on left for 8P9A|1|sR|G|564 InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.016666667,0.950000000,0.016666667,0.016666667,0.000000000] | Position [1] | Left Index [4] | Right Index [12] // Fixed node on left for 8P9A|1|sR|C|565 InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.022727273,0.931818182,0.022727273,0.022727273,0.000000000] | Position [1] | Left Index [5] | Right Index [12] // Fixed node on left for 8P9A|1|sR|C|566 InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [6] | Right Index [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [2] | Left Index [6] | Right Index [12] // Fixed node on right for 8P9A|1|sR|A|579 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Left Index [6] | Right Index [11] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.022727273,0.022727273,0.022727273,0.931818182,0.000000000] | Position [2] | Left Index [6] | Right Index [11] // Fixed node on right for 8P9A|1|sR|U|578 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.083333333,0.750000000,0.083333333,0.000000000] | Position [2] | Left Index [6] | Right Index [10] // Fixed node on right for 8P9A|1|sR|G|577 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.110577593,0.111399105,0.171202567,0.123434124,0.000000000],[0.117061285,0.116790218,0.001327410,0.116159705,0.000000000],[0.001327410,0.001327410,0.006489287,0.001327410,0.000000000],[0.006256089,0.001327410,0.112665566,0.001327410,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair A567 - G576 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.004738018,0.009867595,0.005395338,0.097995839,0.000000000],[0.008322457,0.004646102,0.098826203,0.006466183,0.000000000],[0.026677098,0.546955482,0.005084939,0.065141709,0.000000000],[0.096741680,0.006711274,0.011419928,0.005010154,0.000000000],[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 G568 - C575 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_54177.4:
> IL_54177.4 8P9A G 562 C 583 GUGCCAG*CGGUAAUUC > IL_54177.4 8CRE G 560 C 581 GUGCCAG*CGGUAAUUC > IL_54177.4 5J7L G 515 C 536 GUGCCAG*CGGUAAUAC > IL_54177.4 4LFB G 515 C 536 GUGCCAG*CGGUAAUAC