| 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 4 I | 10 5 5 | 11 5 I | 12 5 6 | 13 5 I | 14 5 7 | 15 6 I | 16 7 | 17 6 I | 18 5 8 | 19 4 I | 20 3 9 | 21 3 I | 22 3 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_38807.3_Instance_1 IL_38807.3_IL_3V2F_039_C1018_G1144 | C | U | A | A | G | U | G | C | U | U | A | A | G | |||||||||||||||||
| IL_38807.3_Sequence_1 IL_38807.3_IL_3V2F_039_C_1018_G_1144 | C | U | A | A | G | U | G | * | C | U | U | A | A | G | true | 97 | 0 | 0 | 0.51 | |||||||||||
| IL_38807.3_Instance_2 IL_38807.3_IL_1S72_041_U1115_A1248 | U | U | A | A | G | U | G | C | U | C | A | A | A | |||||||||||||||||
| IL_38807.3_Sequence_2 IL_38807.3_IL_1S72_041_U_1115_A_1248 | U | U | A | A | G | U | G | * | C | U | C | A | A | A | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_38807.3_Instance_3 IL_38807.3_IL_4IOA_035_C1029_G1155 | C | U | C | A | G | U | G | C | U | C | A | A | G | |||||||||||||||||
| IL_38807.3_Sequence_3 IL_38807.3_IL_4IOA_035_C_1029_G_1155 | C | U | C | A | G | U | G | * | C | U | C | A | A | G | true | 94 | 0 | 0 | 1.04 | |||||||||||
| IL_38807.3_Instance_4 IL_38807.3_IL_2QBG_039_U1018_A1144 | U | U | A | A | G | U | G | C | U | A | A | A | ||||||||||||||||||
| IL_38807.3_Sequence_4 IL_38807.3_IL_2QBG_039_U_1018_A_1144 | U | U | A | A | G | U | G | * | C | U | A | A | A | true | 98 | 0 | 0 | 0.37 |
1 2 s35 1 11 cWW 2 10 tWH 2 11 s55 3 4 s55 3 9 s53 3 10 s55 4 6 s35 4 9 tHW 4 10 tWW 5 6 cSH 5 7 s35 5 8 s33 5 9 s55 6 7 s35 7 8 cWW 10 11 s35 4 2 2BR 6 5 7BR 3 9 6BR 7 11 2BRJAR3D SCFG/MRF model for IL_38807.3:
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 [11] // Initial node C1018 - G1144 from junction BasepairNode | Deletion Probability [0.0000001215781528] | Pair Probability [[0.009389328,0.018311644,0.010532081,0.196004232,0.000000000],[0.022201629,0.008876226,0.219726245,0.011917651,0.000000000],[0.010613182,0.196724789,0.002110478,0.023262344,0.000000000],[0.219745044,0.011558533,0.027184577,0.011842020,0.000000000],[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 [0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Left Index [1] | Right Index [11] // Basepair C1018 - G1144 cWW ClusterNode | Deletion Probability [0.000000000000056748929858366210000000000000000000000000000000] | Num Left Bases [3] | Num Right Bases [2] | Left Index [2] | Right Index [10] | Norm Constant [0.360205348511261] // Cluster node U1019:A1021 and U1141:A1142A Interaction | Interacting Bases [3,4] | Pair Probability [[0.033115265,0.068984957,0.006945048,0.732966383,0.000000000],[0.002457439,0.020402667,0.002457439,0.002457439,0.000000000],[0.012054279,0.016312099,0.028759757,0.030316299,0.000000000],[0.002457439,0.002457439,0.011463236,0.026392811,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1021 - U1141 tHW Interaction | Interacting Bases [1,5] | Pair Probability [[0.025472342,0.005342148,0.026204408,0.005342148,0.000000000],[0.053063396,0.044352700,0.035460347,0.005342148,0.000000000],[0.005342148,0.005342148,0.062519909,0.024919560,0.000000000],[0.572676343,0.005342148,0.065903626,0.057374481,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1019 - A1142A tWH Interaction | Interacting Bases [3,5] | Pair Probability [[0.633374642,0.055859126,0.005949131,0.028182839,0.000000000],[0.018190876,0.007495204,0.005886151,0.007392232,0.000000000],[0.001934929,0.005882949,0.182786709,0.010588182,0.000000000],[0.009168390,0.007392376,0.010598000,0.009318263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1021 - A1142A tWW Interaction | Interacting Bases [2,2] | Pair Probability [[0.704545455,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.022727273,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.022727273,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A1020 Insertion | Location [4] | Length Distribution [0.253667482,0.736552567,0.009321516,0.000458435] | Letter Distribution [0.100000000,0.500000000,0.100000000,0.300000000,0.000000000]// Insertion after nucleotide 9, position 4 in cluster node InitialNode | 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 [5] | Right Index [8] // New Initial node after Cluster ClusterNode | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [5] | Right Index [8] | Norm Constant [1.000000000000000] // Cluster node G1022:G1024 and C1140:C1140 Interaction | Interacting Bases [3,4] | Pair Probability [[0.004887557,0.009956935,0.005659065,0.092752426,0.000000000],[0.008246692,0.004030138,0.099899013,0.006358532,0.000000000],[0.027939145,0.553701311,0.005152398,0.066088192,0.000000000],[0.092216823,0.006674609,0.011401633,0.005035534,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1024 - C1140 cWW Interaction | Interacting Bases [1,2] | Pair Probability [[0.106243868,0.109450239,0.005969057,0.004938655,0.000000000],[0.102770254,0.119376597,0.001269566,0.120308197,0.000000000],[0.010380152,0.005676417,0.011603300,0.165418103,0.000000000],[0.009141931,0.106461489,0.001269566,0.119722610,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1022 - U1023 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 [8] | Right Index [7] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [8] | Right Index [8] | 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_38807.3:
> IL_38807.3 IL_3V2F_039 C 1018 G 1144 CUAAGUG*CUUAAG > IL_38807.3 IL_1S72_041 U 1115 A 1248 UUAAGUG*CUCAAA > IL_38807.3 IL_4IOA_035 C 1029 G 1155 CUCAGUG*CUCAAG > IL_38807.3 IL_2QBG_039 U 1018 A 1144 UUAAGUG*CUAAA