| 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 7 3 | 7 8 I | 8 9 | 9 8 I | 10 7 4 | 11 7 I | 12 7 5 | 13 6 I | 14 5 6 | 15 2 I | 16 2 7 | 17 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_90133.3_Instance_1 IL_90133.3_IL_3U5F_028_G516_C536 | G | U | A | U | A | A | C | |||||||||||||||
| IL_90133.3_Sequence_1 IL_90133.3_IL_3U5F_028_G516_C536 | G | U | A | * | U | A | A | C | true | 80 | 0 | 0 | 1.93 | |||||||||
| IL_90133.3_Instance_2 IL_90133.3_IL_3V2F_031_G875_C902 | G | C | U | A | A | A | C | |||||||||||||||
| IL_90133.3_Sequence_2 IL_90133.3_IL_3V2F_031_G875_C902 | G | C | U | * | A | A | A | C | true | 84 | 0 | 0 | 1.52 | |||||||||
| IL_90133.3_Instance_3 IL_90133.3_IL_2AW7_006_C67_G102 | C | G | G | C | G | A | G | |||||||||||||||
| IL_90133.3_Sequence_3 IL_90133.3_IL_2AW7_006_C67_G102 | C | G | G | * | C | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_90133.3_Instance_4 IL_90133.3_IL_1S72_053_A1465_U1478 | A | C | C | G | A | C | U | |||||||||||||||
| IL_90133.3_Sequence_4 IL_90133.3_IL_1S72_053_A_1465_U_1478 | A | C | C | * | G | A | C | U | true | 77 | 0 | 0 | 2.17 | |||||||||
| IL_90133.3_Instance_5 IL_90133.3_IL_3U5F_068_U1276_A1436 | U | G | G | U | CU | G | U | G | A | |||||||||||||
| IL_90133.3_Sequence_5 IL_90133.3_IL_3U5F_068_U_1276_A_1436 | U | G | G | * | U | CU | G | U | G | A | true | 59 | 0 | 0 | 3.93 | |||||||
| IL_90133.3_Instance_6 IL_90133.3_IL_4BPP_066_U1248_A1407 | U | G | G | U | CU | G | U | G | A | |||||||||||||
| IL_90133.3_Sequence_6 IL_90133.3_IL_4BPP_066_U_1248_A_1407 | U | G | G | * | U | CU | G | U | G | A | true | 59 | 0 | 0 | 3.93 |
1 2 s35 1 7 cWW 2 3 s35 2 7 s55 3 4 cWW 3 5 tSH 5 6 s35 6 7 s35JAR3D SCFG/MRF model for IL_90133.3:
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 [7] // Initial node G516 - C536 from junction BasepairNode | Deletion Probability [0.0000040507541457] | Pair Probability [[0.009286488,0.019798872,0.010378792,0.203290480,0.000000000],[0.019928641,0.008620290,0.203764573,0.011464360,0.000000000],[0.010357661,0.214071747,0.002069606,0.024700235,0.000000000],[0.213844488,0.011558359,0.024769722,0.012095683,0.000000000],[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 [0.661815186,0.335026775,0.003020733,0.000137306] | Right Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair G516 - C536 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.312500000,0.437500000,0.187500000,0.000000000] | Position [1] | Left Index [2] | Right Index [6] // Fixed node on left 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 [6] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.437500000,0.187500000,0.062500000,0.312500000,0.000000000] | Position [2] | Left Index [3] | Right Index [6] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | 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 [3] | Right Index [5] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.0000000034668202] | Num Left Bases [1] | Num Right Bases [2] | Left Index [3] | Right Index [5] | Norm Constant [0.271490520016192] // Cluster node A518:A518 and U533:A534 Interaction | Interacting Bases [1,2] | Pair Probability [[0.011482008,0.112765157,0.011905390,0.153344322,0.000000000],[0.017883524,0.009447760,0.151510989,0.012622831,0.000000000],[0.011794866,0.153462523,0.002487231,0.146131042,0.000000000],[0.151182686,0.013156782,0.021350858,0.019472030,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A518 - U533 cWW Interaction | Interacting Bases [1,3] | Pair Probability [[0.083316030,0.057750357,0.002817434,0.213979904,0.000000000],[0.097281044,0.044047618,0.002817434,0.002817434,0.000000000],[0.059598005,0.002817434,0.257800837,0.030806940,0.000000000],[0.076365633,0.062149028,0.002817434,0.002817434,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A518 - A534 tSH Insertion | Location [2] | Length Distribution [0.659069065,0.008238363,0.329809145,0.002746121,0.000137306] | Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000]// Insertion after nucleotide 4, position 2 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 [4] | Right Index [3] // New Initial node after Cluster 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_90133.3:
> IL_90133.3 IL_3U5F_028 G 516 C 536 GUA*UAAC > IL_90133.3 IL_3V2F_031 G 875 C 902 GCU*AAAC > IL_90133.3 IL_2AW7_006 C 67 G 102 CGG*CGAG > IL_90133.3 IL_1S72_053 A 1465 U 1478 ACC*GACU > IL_90133.3 IL_3U5F_068 U 1276 A 1436 UGG*UCUGUGA > IL_90133.3 IL_4BPP_066 U 1248 A 1407 UGG*UCUGUGA