| 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 4 I | 6 5 | 7 4 I | 8 4 3 | 9 3 I | 10 2 4 | 11 2 I | 12 2 5 | 13 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_87065.1_Instance_1 IL_87065.1_IL_4A1B_094_G2391_C2972 | G | A | A | U | A | C | C | |||||||||||
| IL_87065.1_Sequence_1 IL_87065.1_IL_4A1B_094_G_2391_C_2972 | G | A | A | * | U | A | C | C | true | 100 | 0 | 0 | 0.00 | |||||
| IL_87065.1_Instance_2 IL_87065.1_IL_3U5H_097_G2396_C2984 | G | A | A | U | A | C | C | |||||||||||
| IL_87065.1_Sequence_2 IL_87065.1_IL_3U5H_097_G_2396_C_2984 | G | A | A | * | U | A | C | C | true | 100 | 0 | 0 | 0.00 | |||||
| IL_87065.1_Instance_3 IL_87065.1_IL_2QBG_079_A2054_U2615 | A | C | G | C | U | A | U | |||||||||||
| IL_87065.1_Sequence_3 IL_87065.1_IL_2QBG_079_A_2054_U_2615 | A | C | G | * | C | U | A | U | true | 68 | 0 | 0 | 3.04 |
1 5 cWW 2 3 cWW 4 5 cSH 5 4 7BRJAR3D SCFG/MRF model for IL_87065.1:
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 [5] // Initial node G2391 - C2972 from junction ClusterNode | Deletion Probability [0.0000000034550030] | Num Left Bases [1] | Num Right Bases [2] | Left Index [1] | Right Index [5] | Norm Constant [0.305651423960523] // Cluster node G2391:G2391 and A2970:C2972 Interaction | Interacting Bases [1,3] | Pair Probability [[0.004733746,0.037240585,0.005339211,0.240859165,0.000000000],[0.008690836,0.014981024,0.097250365,0.012347507,0.000000000],[0.005288794,0.395468482,0.001029139,0.030717388,0.000000000],[0.094380619,0.024015626,0.011358393,0.016299118,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2391 - C2972 cWW Interaction | Interacting Bases [2,3] | Pair Probability [[0.101253721,0.135894093,0.006054057,0.060998411,0.000000000],[0.104207646,0.097420758,0.001164766,0.100868758,0.000000000],[0.005756469,0.006285621,0.013783047,0.100415395,0.000000000],[0.058267301,0.110073967,0.001164766,0.096391223,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A2970 - C2972 cSH Insertion | Location [2] | Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 4, position 2 in cluster node InitialNode | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.500000000,0.300000000,0.100000000,0.100000000,0.000000000] | Right Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [2] | Right Index [3] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009472747,0.022988174,0.010372983,0.225098889,0.000000000],[0.018936855,0.008916940,0.195696316,0.011163054,0.000000000],[0.010312898,0.208310389,0.002127705,0.027444663,0.000000000],[0.199992661,0.011428674,0.023422512,0.014314540,0.000000000],[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 [2] | Right Index [3] // Basepair A2393 - U2969 cWW HairpinNode | Num Bases [1] | Left Index [3] | Right Index [3] | 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_87065.1:
> IL_87065.1 IL_4A1B_094 G 2391 C 2972 GAA*UACC > IL_87065.1 IL_3U5H_097 G 2396 C 2984 GAA*UACC > IL_87065.1 IL_2QBG_079 A 2054 U 2615 ACG*CUAU