| 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 3 3 | 7 3 I | 8 3 4 | 9 3 I | 10 3 5 | 11 3 I | 12 3 6 | 13 4 I | 14 5 | 15 4 I | 16 3 7 | 17 2 I | 18 2 8 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_40892.1_Instance_1 IL_40892.1_IL_3U5H_101_A2520_U2587 | A | U | G | A | A | G | C | G | GG | U | ||||||||||||||
| IL_40892.1_Sequence_1 IL_40892.1_IL_3U5H_101_A_2520_U_2587 | A | U | G | A | A | G | C | * | G | GG | U | true | 100 | 0 | 0 | 0.00 | ||||||||
| IL_40892.1_Instance_2 IL_40892.1_IL_4A1B_099_G2515_C2576 | G | U | G | A | A | G | A | U | UG | C | ||||||||||||||
| IL_40892.1_Sequence_2 IL_40892.1_IL_4A1B_099_G_2515_C_2576 | G | U | G | A | A | G | A | * | U | UG | C | true | 95 | 0 | 0 | 0.85 |
1 2 s35 1 8 cWW 2 3 cWS 3 8 s35 6 7 cWWJAR3D SCFG/MRF model for IL_40892.1:
Character Definition | A,C,G,U,* // Define characters here InitialNode | 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 [1] | Right Index [8] // Initial node A2520 - U2587 from junction BasepairNode | Deletion Probability [0.0000000005912491] | Pair Probability [[0.009722986,0.022602524,0.010807110,0.213946067,0.000000000],[0.018642384,0.008854915,0.200306720,0.011770232,0.000000000],[0.010724456,0.213953122,0.002148800,0.027678057,0.000000000],[0.199554445,0.012136228,0.023684855,0.013467100,0.000000000],[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 [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.083333333,0.083333333,0.583333333,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair A2520 - U2587 cWW ClusterNode | Deletion Probability [0.000000000000000077146797411633740000000000000000000000000000] | Num Left Bases [5] | Num Right Bases [1] | Left Index [2] | Right Index [7] | Norm Constant [1.000000000000000] // Cluster node U2521:C2526 and G2584:G2584 Interaction | Interacting Bases [5,6] | Pair Probability [[0.009640843,0.020820542,0.010733993,0.213406915,0.000000000],[0.020428208,0.008935347,0.213416622,0.012101297,0.000000000],[0.010799946,0.200886051,0.002149018,0.025786435,0.000000000],[0.200132635,0.011807914,0.025581673,0.013372561,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C2526 - G2584 cWW Interaction | Interacting Bases [1,2] | Pair Probability [[0.007512069,0.008360159,0.007186863,0.008188381,0.000000000],[0.014137583,0.014479854,0.010969251,0.014468650,0.000000000],[0.010578210,0.009148700,0.008845779,0.007931851,0.000000000],[0.327000080,0.177983196,0.181398224,0.191811151,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2521 - A2523 cWS Interaction | Interacting Bases [3,3] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A2524 Interaction | Interacting Bases [4,4] | 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 G2525 Insertion | Location [1] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000]// Insertion after nucleotide 2, position 1 in cluster node InitialNode | 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 [6] // New Initial node after Cluster 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_40892.1:
> IL_40892.1 IL_3U5H_101 A 2520 U 2587 AUGAAGC*GGGU > IL_40892.1 IL_4A1B_099 G 2515 C 2576 GUGAAGA*UUGC