| 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 2 2 | 5 2 I | 6 2 3 | 7 3 I | 8 4 4 | 9 4 I | 10 5 | 11 4 I | 12 4 5 | 13 3 I | 14 2 6 | 15 2 I | 16 2 7 | 17 2 I | 18 2 8 | 19 2 I | 20 2 9 | 21 2 I | 22 2 10 | 23 2 I | 24 2 11 | 25 2 I | 26 2 12 | 27 2 I | 28 2 13 | 29 2 I | 30 2 14 | 31 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_27243.1_Instance_1 IL_27243.1_IL_3D2V_002_G10_C36 | G | G | U | G | C | U | G | A | G | A | A | A | G | U | C | |||||||||||||||||||||
| IL_27243.1_Sequence_1 IL_27243.1_IL_3D2V_002_G10_C36 | G | G | U | G | * | C | U | G | A | G | A | A | A | G | U | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 14 cWW 2 3 s35 2 9 tSS 2 13 cWH 3 11 s33 3 12 cWH 4 5 cWW 4 10 s53 5 6 s35 6 7 s35 6 10 tWH 7 9 s33 7 10 s55 8 9 s35 8 14 cSS 12 13 s53 13 14 s55 11 4 2BPh 7 10 6BPhJAR3D SCFG/MRF model for IL_27243.1:
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 [14] // Initial node G10 - C36 from junction ClusterNode | Deletion Probability [0.000000000000000000000000000001191720873277651700000000000000] | Num Left Bases [3] | Num Right Bases [9] | Left Index [1] | Right Index [14] | Norm Constant [0.124973342635811] // Cluster node G10:U12 and U27:C36 Interaction | Interacting Bases [2,7] | Pair Probability [[0.011418641,0.014331648,0.024329846,0.014025501,0.000000000],[0.002491479,0.002491479,0.002491479,0.002491479,0.000000000],[0.224007246,0.230872701,0.259048862,0.202033724,0.000000000],[0.002491479,0.002491479,0.002491479,0.002491479,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G11 - G30 tSS Interaction | Interacting Bases [3,10] | Pair Probability [[0.003495037,0.003495037,0.017334262,0.012470772,0.000000000],[0.003495037,0.037384026,0.017149526,0.190754110,0.000000000],[0.015332069,0.003495037,0.013986624,0.003495037,0.000000000],[0.359404723,0.003495037,0.280049403,0.035164262,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U12 - A33 cWH Interaction | Interacting Bases [2,11] | Pair Probability [[0.004796933,0.004796933,0.048610550,0.028102840,0.000000000],[0.004796933,0.045138252,0.223369287,0.025351263,0.000000000],[0.037055570,0.004796933,0.489594339,0.004796933,0.000000000],[0.019196620,0.004796933,0.014757791,0.040041888,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G11 - G34 cWH Interaction | Interacting Bases [1,12] | Pair Probability [[0.010296034,0.020975088,0.011921277,0.195390483,0.000000000],[0.017372323,0.008489812,0.210445347,0.013394761,0.000000000],[0.011771213,0.226979836,0.002170788,0.027844024,0.000000000],[0.194262192,0.014060602,0.024018461,0.010607760,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G10 - C36 cWW Interaction | Interacting Bases [4,8] | Pair Probability [[0.026228946,0.005500826,0.026982756,0.005500826,0.000000000],[0.054639536,0.045670107,0.036513624,0.005500826,0.000000000],[0.005500826,0.005500826,0.064376936,0.025659745,0.000000000],[0.559983562,0.005500826,0.067861159,0.059078674,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U27 - A31 tWH Interaction | Interacting Bases [6,12] | Pair Probability [[0.069980681,0.084135701,0.070448286,0.071021101,0.000000000],[0.066251302,0.064644197,0.006795540,0.066652281,0.000000000],[0.067719711,0.066936321,0.060177817,0.067928475,0.000000000],[0.067869819,0.037376987,0.062185642,0.069876138,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A29 - C36 cSS Interaction | Interacting Bases [5,5] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.833333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G28 Interaction | Interacting Bases [9,9] | Pair Probability [[0.833333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A32 Insertion | Location [11] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 13, position 11 in cluster node InitialNode | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010296034,0.020975088,0.011921277,0.195390483,0.000000000],[0.017372323,0.008489812,0.210445347,0.013394761,0.000000000],[0.011771213,0.226979836,0.002170788,0.027844024,0.000000000],[0.194262192,0.014060602,0.024018461,0.010607760,0.000000000],[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 [4] | Right Index [5] // Basepair G13 - C26 cWW 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_27243.1:
> IL_27243.1 IL_3D2V_002 G 10 C 36 GGUG*CUGAGAAAGUC