| 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 13 6 | 13 13 I | 14 14 7 | 15 14 I | 16 15 | 17 14 I | 18 14 8 | 19 13 I | 20 13 9 | 21 12 I | 22 11 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_97697.1_Instance_1 IL_97697.1,IL_5M0I_002,A4_U22 | A | A | C | U | G | A | A | U | A | C | A | U | U | |||||||||||||||||
| IL_97697.1_Sequence_1 IL_97697.15M0I_A4_U22 | A | A | C | U | G | A | A | U | * | A | C | A | U | U | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_97697.1_Instance_2 IL_97697.1,IL_5M0J_002,A4_U22 | A | A | C | U | G | A | A | U | A | C | A | U | U | |||||||||||||||||
| IL_97697.1_Sequence_2 IL_97697.15M0J_A4_U22 | A | A | C | U | G | A | A | U | * | A | C | A | U | U | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_97697.1_Instance_3 IL_97697.1,IL_5M0J_001,A4_U22 | A | A | C | U | G | A | A | U | A | C | A | U | U | |||||||||||||||||
| IL_97697.1_Sequence_3 IL_97697.15M0J_A4_U22 | A | A | C | U | G | A | A | U | * | A | C | A | U | U | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_97697.1_Instance_4 IL_97697.1,IL_5M0I_001,A4_U22 | A | A | C | U | G | A | A | U | A | C | A | U | U | |||||||||||||||||
| IL_97697.1_Sequence_4 IL_97697.15M0I_A4_U22 | A | A | C | U | G | A | A | U | * | A | C | A | U | U | true | 100 | 0 | 0 | 0.00 |
1 10 s35 1 11 cWW 2 10 s53 3 4 perp 4 5 s35 5 6 s35 6 7 s35 6 9 bif 7 8 cWW 8 9 s35 10 11 s55 2 10 6BRJAR3D SCFG/MRF model for IL_97697.1:
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 [11] // Initial node BasepairNode | Deletion Probability [0.0000001215781528] | Pair Probability [[0.009104408,0.021587263,0.009723705,0.238651416,0.000000000],[0.017181282,0.009396023,0.190432013,0.010159631,0.000000000],[0.009704777,0.192900773,0.002001899,0.052190437,0.000000000],[0.192253936,0.010816081,0.022570064,0.011326291,0.000000000],[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 [0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000] | Left Index [1] | Right Index [11] // Basepair A4 - U22 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.931818182,0.022727273,0.022727273,0.022727273,0.000000000] | Position [1] | Left Index [2] | Right Index [10] // Fixed node on left for 5M0I|1|F|A|5 InitialNode | Left Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Left Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left for 5M0I|1|F|C|6 InitialNode | Left Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Left Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [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 [1] | Left Index [4] | Right Index [10] // Fixed node on left for 5M0I|1|F|U|7 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 [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [5] | Right Index [10] // Fixed node on left for 5M0I|1|F|G|8 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 [10] // 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 [10] // Fixed node on right for 5M0I|1|F|C|19 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 [[0.027946128,0.720346789,0.006818853,0.006818853,0.000000000],[0.031393902,0.079858018,0.006818853,0.006818853,0.000000000],[0.006818853,0.006818853,0.028613102,0.006818853,0.000000000],[0.006818853,0.006818853,0.043653536,0.006818853,0.000000000],[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 A10 - C19 bif BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008860598,0.017207362,0.009719508,0.192545756,0.000000000],[0.021620030,0.009642604,0.193193575,0.010832498,0.000000000],[0.009738465,0.190721067,0.002004937,0.022604323,0.000000000],[0.238955281,0.010175052,0.052269656,0.009909289,0.000000000],[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 U11 - A18 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_97697.1:
> IL_97697.1 5M0I A 4 U 22 AACUGAAU*ACAUU > IL_97697.1 5M0J A 4 U 22 AACUGAAU*ACAUU > IL_97697.1 5M0J A 4 U 22 AACUGAAU*ACAUU > IL_97697.1 5M0I A 4 U 22 AACUGAAU*ACAUU