| 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 9 I | 12 9 6 | 13 9 I | 14 9 7 | 15 9 I | 16 9 8 | 17 9 I | 18 9 9 | 19 10 I | 20 11 | 21 10 I | 22 9 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_19897.3_Instance_1 IL_19897.3,IL_7EOG_003,C28_G15 | C | C | A | A | U | C | G | U | A | U | G | |||||||||||||||||||
| IL_19897.3_Sequence_1 IL_19897.37EOG_C28_G15 | C | C | A | A | U | C | G | U | A | * | U | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_19897.3_Instance_2 IL_19897.3,IL_7SZU_004,C9_G60 | C | C | A | A | U | C | G | U | A | U | G | |||||||||||||||||||
| IL_19897.3_Sequence_2 IL_19897.37SZU_C9_G60 | C | C | A | A | U | C | G | U | A | * | U | G | true | 100 | 0 | 0 | 0.00 |
1 9 s35 1 11 cWW 2 3 s35 3 4 s35 4 5 s35 5 8 tWH 6 7 s35 7 8 s35 9 10 cWW 9 11 s55 10 11 s35JAR3D SCFG/MRF model for IL_19897.3:
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 [0.0000229437914523] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [11] // Basepair C28 - G15 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [2] | Right Index [10] // Fixed node on left for 7EOG|1|A|G|15 InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left for 7EOG|1|A|C|28 InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [4] | Right Index [10] // Fixed node on left for 7EOG|1|A|C|29 InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 ClusterNode | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [5] | Num Right Bases [1] | Left Index [5] | Right Index [10] | Norm Constant [1.000000000000000] // Cluster node 7EOG|1|A|U|32:7EOG|1|A|A|36 and 7EOG|1|A|U|14:7EOG|1|A|U|14 Interaction | Interacting Bases [5,6] | Pair Probability [[0.008439024,0.020009585,0.009013060,0.294293647,0.000000000],[0.015925609,0.008709326,0.176514522,0.009417127,0.000000000],[0.008995516,0.178802856,0.001855592,0.048376163,0.000000000],[0.178203292,0.010025601,0.020920558,0.010498523,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7EOG|1|A|A|36 - 7EOG|1|A|U|14 cWW Interaction | Interacting Bases [1,4] | Pair Probability [[0.019059668,0.003911733,0.033938098,0.003911733,0.000000000],[0.338291337,0.045646942,0.003911733,0.003911733,0.000000000],[0.003911733,0.012240000,0.025155457,0.036900503,0.000000000],[0.038529923,0.003911733,0.015986500,0.410781171,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7EOG|1|A|U|32 - 7EOG|1|A|U|35 tWH Interaction | Interacting Bases [2,2] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.625000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 7EOG|1|A|C|33 Interaction | Interacting Bases [3,3] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 7EOG|1|A|G|34 InitialNode | Left Length Distribution [0.973871734,0.024940618,0.001187648] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.973871734,0.024940618,0.001187648] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [9] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [10] | Right Index [10] | 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_19897.3:
> IL_19897.3 7EOG C 28 G 15 CCAAUCGUA*UG > IL_19897.3 7SZU C 9 G 60 CCAAUCGUA*UG