| Column number: Node in JAR3D model: Insertion positions indicated by I: Position in motif group: | 1 1 I | 2 2 1 | 3 3 I | 4 4 2 | 5 5 I | 6 6 3 | 7 6 I | 8 7 | 9 6 I | 10 6 4 | 11 3 I | 12 2 5 | 13 2 I | 14 2 6 | 15 2 I | 16 2 7 | 17 2 I | 18 2 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_21639.1_Instance_1 IL_21639.1_IL_3U5F_075_C1389_G1412 | C | U | A | U | G | G | A | A | G | |||||||||||||||||
| IL_21639.1_Sequence_1 IL_21639.1_IL_3U5F_075_C_1389_G_1412 | C | U | A | * | U | G | G | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_21639.1_Instance_2 IL_21639.1_IL_4BPP_074_C1359_G1383 | C | U | A | U | G | G | A | A | G | |||||||||||||||||
| IL_21639.1_Sequence_2 IL_21639.1_IL_4BPP_074_C_1359_G_1383 | C | U | A | * | U | G | G | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 9 cWW 2 9 perp 3 4 cWW 3 5 s55 3 9 s53 4 5 s35 5 6 s35 5 9 tWH 6 9 s55 7 8 s35 6 9 6BPh 8 6 7BR 2 9 7BRJAR3D SCFG/MRF model for IL_21639.1:
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 [9] // Initial node C1389 - G1412 from junction ClusterNode | Deletion Probability [0.000000000000015625000000000003000000000000000000000000000000] | Num Left Bases [1] | Num Right Bases [5] | Left Index [1] | Right Index [9] | Norm Constant [0.267118703471320] // Cluster node C1389:C1389 and G1408:G1412 Interaction | Interacting Bases [1,6] | Pair Probability [[0.010030806,0.017205487,0.011658168,0.192396585,0.000000000],[0.020773653,0.008567443,0.234601962,0.013925571,0.000000000],[0.011806790,0.208424324,0.002149941,0.023787799,0.000000000],[0.193514041,0.013266124,0.027576622,0.010314686,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1389 - G1412 cWW Interaction | Interacting Bases [2,6] | Pair Probability [[0.054517083,0.004401161,0.043297051,0.004401161,0.000000000],[0.030062838,0.020071606,0.021369465,0.004401161,0.000000000],[0.004401161,0.004401161,0.459723974,0.030471216,0.000000000],[0.051507409,0.004401161,0.236641445,0.025930945,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1408 - G1412 tWH Interaction | Interacting Bases [3,3] | Pair Probability [[0.031250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.031250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.906250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G1409 Interaction | Interacting Bases [4,4] | 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]] // Right strand conserved insertion A1410 Interaction | Interacting Bases [5,5] | Pair Probability [[0.875000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A1411 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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [4] // Initial node U1390 - U1407 from junction FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.041666667,0.041666667,0.041666667,0.875000000,0.000000000] | Position [1] | Left Index [2] | Right Index [4] // Fixed node on left 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 [4] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009250880,0.024435597,0.009809818,0.234417244,0.000000000],[0.020082763,0.009303252,0.192231283,0.010277023,0.000000000],[0.009793103,0.193347778,0.002148094,0.027785070,0.000000000],[0.206751230,0.010349703,0.023586724,0.016430437,0.000000000],[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 [3] | Right Index [4] // Basepair A1391 - U1407 cWW HairpinNode | Num Bases [1] | Left Index [4] | Right Index [4] | 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_21639.1:
> IL_21639.1 IL_3U5F_075 C 1389 G 1412 CUA*UGGAAG > IL_21639.1 IL_4BPP_074 C 1359 G 1383 CUA*UGGAAG