| 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 5 I | 8 5 4 | 9 6 I | 10 7 | 11 6 I | 12 5 5 | 13 2 I | 14 2 6 | 15 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_39980.1_Instance_1 IL_39980.1_IL_4A1B_004_A144_U122 | A | A | UU | G | U | A | U | |||||||||||||
| IL_39980.1_Sequence_1 IL_39980.1_IL_4A1B_004_A144_U122 | A | A | UU | G | U | * | A | U | true | 100 | 0 | 0 | 0.00 | |||||||
| IL_39980.1_Instance_2 IL_39980.1_IL_3U5H_007_A144_U124 | A | G | UU | G | U | A | U | |||||||||||||
| IL_39980.1_Sequence_2 IL_39980.1_IL_3U5H_007_A144_U124 | A | G | UU | G | U | * | A | U | true | 92 | 0 | 0 | 0.85 | |||||||
| IL_39980.1_Instance_3 IL_39980.1_IL_1S72_009_C260_G249 | C | A | AU | G | U | A | G | |||||||||||||
| IL_39980.1_Sequence_3 IL_39980.1_IL_1S72_009_C260_G249 | C | A | AU | G | U | * | A | G | true | 87 | 0 | 0 | 1.44 | |||||||
| IL_39980.1_Instance_4 IL_39980.1_IL_4BPP_061_A1197_U1230 | A | A | GG | G | A | U | U | |||||||||||||
| IL_39980.1_Sequence_4 IL_39980.1_IL_4BPP_061_A_1197_U_1230 | A | A | GG | G | A | * | U | U | true | 86 | 0 | 0 | 1.47 |
1 2 s35 1 6 cWW 3 4 cSH 4 5 cWW 4 6 perpJAR3D SCFG/MRF model for IL_39980.1:
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 [6] // Initial node A144 - U122 from junction BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009264210,0.022192915,0.010074369,0.234029155,0.000000000],[0.019865957,0.008943928,0.203731184,0.010973984,0.000000000],[0.010098514,0.193326205,0.002107237,0.026270642,0.000000000],[0.199529587,0.010865754,0.024111426,0.014614932,0.000000000],[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 [1] | Right Index [6] // Basepair A144 - U122 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.583333333,0.083333333,0.250000000,0.083333333,0.000000000] | Position [1] | Left Index [2] | Right Index [5] // Fixed node on left InitialNode | Left Length Distribution [0.000000000,0.012187690,0.975015235,0.012187690,0.000609385] | Left Letter Distribution [0.150000000,0.050000000,0.250000000,0.550000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [3] | Right Index [5] | Norm Constant [0.259243905872397] // Cluster node G148:U149 and A121:A121 Interaction | Interacting Bases [2,3] | Pair Probability [[0.008973807,0.020802927,0.009627934,0.214768857,0.000000000],[0.022945963,0.009293412,0.189732133,0.010152995,0.000000000],[0.009636163,0.189182448,0.002110966,0.024208445,0.000000000],[0.237966914,0.010117212,0.026275422,0.014204402,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U149 - A121 cWW Interaction | Interacting Bases [1,2] | Pair Probability [[0.076779974,0.079320859,0.012294084,0.010181688,0.000000000],[0.074799046,0.092378832,0.002581015,0.088429265,0.000000000],[0.192506263,0.010059924,0.020642474,0.156176861,0.000000000],[0.013567760,0.076991426,0.002581015,0.090709515,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G148 - U149 cSH 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 [5] | Right Index [4] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [5] | Right Index [5] | 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_39980.1:
> IL_39980.1 IL_4A1B_004 A 144 U 122 AAUUGU*AU > IL_39980.1 IL_3U5H_007 A 144 U 124 AGUUGU*AU > IL_39980.1 IL_1S72_009 C 260 G 249 CAAUGU*AG > IL_39980.1 IL_4BPP_061 A 1197 U 1230 AAGGGA*UU