| 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 11 6 | 13 12 I | 14 13 7 | 15 13 I | 16 14 | 17 13 I | 18 13 8 | 19 2 I | 20 2 9 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_88017.1_Instance_1 IL_88017.1,IL_7JRT_002,G24_C51 | G | A | A | C | U | A | C | G | C | |||||||||||||||||
| IL_88017.1_Sequence_1 IL_88017.17JRT_G24_C51 | G | A | A | C | U | A | C | * | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_88017.1_Instance_2 IL_88017.1,IL_7JRT_006,G24_C51 | G | A | A | C | U | A | C | G | C | |||||||||||||||||
| IL_88017.1_Sequence_2 IL_88017.17JRT_G24_C51 | G | A | A | C | U | A | C | * | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_88017.1_Instance_3 IL_88017.1,IL_3P59_001,G52_C111 | G | A | A | C | U | A | C | G | C | |||||||||||||||||
| IL_88017.1_Sequence_3 IL_88017.13P59_G52_C111 | G | A | A | C | U | A | C | * | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_88017.1_Instance_4 IL_88017.1,IL_7JRT_004,G91_C118 | G | A | A | C | U | A | C | G | C | |||||||||||||||||
| IL_88017.1_Sequence_4 IL_88017.17JRT_G91_C118 | G | A | A | C | U | A | C | * | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_88017.1_Instance_5 IL_88017.1,IL_7JRT_008,G91_C118 | G | A | A | C | U | A | C | G | C | |||||||||||||||||
| IL_88017.1_Sequence_5 IL_88017.17JRT_G91_C118 | G | A | A | C | U | A | C | * | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_88017.1_Instance_6 IL_88017.1,IL_2PN3_002,G52_C111 | G | A | A | C | U | A | C | G | C | |||||||||||||||||
| IL_88017.1_Sequence_6 IL_88017.12PN3_G52_C111 | G | A | A | C | U | A | C | * | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_88017.1_Instance_7 IL_88017.1,IL_6DVK_003,G28_C62 | G | A | A | C | U | A | C | G | C | |||||||||||||||||
| IL_88017.1_Sequence_7 IL_88017.16DVK_G28_C62 | G | A | A | C | U | A | C | * | G | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 9 cWW 2 3 s35 2 9 s55 3 4 s35 5 6 s35 6 7 s35 7 8 cWW 9 8 7BPh 6 4 7BRJAR3D SCFG/MRF model for IL_88017.1:
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 [9] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003645200,0.053141532,0.004150910,0.075393230,0.000000000],[0.006402894,0.025021395,0.076032072,0.004974767,0.000000000],[0.004104812,0.613115256,0.000782421,0.010023372,0.000000000],[0.074428341,0.036143291,0.008785937,0.003854569,0.000000000],[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 [9] // Basepair G24 - C51 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.833333333,0.055555556,0.055555556,0.055555556,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // Fixed node on left for 7JRT|1|A|A|25 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 [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.833333333,0.055555556,0.055555556,0.055555556,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left for 7JRT|1|A|A|26 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 [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.833333333,0.055555556,0.055555556,0.000000000] | Position [1] | Left Index [4] | Right Index [8] // Fixed node on left for 7JRT|1|A|C|27 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 [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.055555556,0.055555556,0.833333333,0.000000000] | Position [1] | Left Index [5] | Right Index [8] // Fixed node on left for 7JRT|1|A|U|28 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 [6] | Right Index [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.959459459,0.013513514,0.013513514,0.013513514,0.000000000] | Position [1] | Left Index [6] | Right Index [8] // Fixed node on left for 7JRT|1|A|A|29 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 [7] | Right Index [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009090944,0.016302246,0.010451159,0.189500131,0.000000000],[0.019328903,0.009258863,0.264630806,0.013146218,0.000000000],[0.010568529,0.193583350,0.001992102,0.022369654,0.000000000],[0.191956811,0.012666128,0.025520256,0.009633898,0.000000000],[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 C30 - G50 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_88017.1:
> IL_88017.1 7JRT G 24 C 51 GAACUAC*GC > IL_88017.1 7JRT G 24 C 51 GAACUAC*GC > IL_88017.1 3P59 G 52 C 111 GAACUAC*GC > IL_88017.1 7JRT G 91 C 118 GAACUAC*GC > IL_88017.1 7JRT G 91 C 118 GAACUAC*GC > IL_88017.1 2PN3 G 52 C 111 GAACUAC*GC > IL_88017.1 6DVK G 28 C 62 GAACUAC*GC