| 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 | 7 4 I | 8 3 3 | 9 3 I | 10 3 4 | 11 3 I | 12 3 5 | 13 3 I | 14 3 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_40845.1_Instance_1 IL_40845.1_IL_1FJG_037_G933_C1384 | G | C | A | U | U | C | C | C | ||||||||||||||
| IL_40845.1_Sequence_1 IL_40845.1_IL_1FJG_037_G933_C_1384 | G | C | A | * | U | U | C | C | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 7 cWW 2 3 cWW 2 6 cSW 3 5 cSH 4 5 s35 5 6 s35 6 7 s35 4 3 7BRJAR3D SCFG/MRF model for IL_40845.1:
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 [7] // Initial node G933 - C1384 from junction BasepairNode | Deletion Probability [0.0000001156129129] | 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 [0.045351474,0.907029478,0.045351474,0.002267574] | Left Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair G933 - C1384 cWW ClusterNode | Deletion Probability [0.0000000000031250] | Num Left Bases [1] | Num Right Bases [4] | Left Index [2] | Right Index [6] | Norm Constant [0.063589505299535] // Cluster node A935:A935 and U1380:C1383 Interaction | Interacting Bases [1,2] | Pair Probability [[0.009342473,0.024677534,0.009906945,0.226837217,0.000000000],[0.020281602,0.009395363,0.194134563,0.010378776,0.000000000],[0.009890064,0.195262113,0.002169362,0.028060170,0.000000000],[0.208798271,0.010452176,0.023820256,0.016593115,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A935 - U1380 cWW Interaction | Interacting Bases [1,5] | Pair Probability [[0.013193013,0.224582598,0.016169100,0.013905434,0.000000000],[0.024242786,0.199371626,0.010467927,0.016672555,0.000000000],[0.012572530,0.195105390,0.020324651,0.009999227,0.000000000],[0.019171853,0.204671249,0.009205732,0.010344329,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A935 - C1383 cSW Interaction | Interacting Bases [2,4] | Pair Probability [[0.108922010,0.119014665,0.006154086,0.005319225,0.000000000],[0.108926731,0.101556193,0.001259374,0.106947749,0.000000000],[0.005937266,0.007835953,0.012756289,0.105606824,0.000000000],[0.071179172,0.135838357,0.001259374,0.101486732,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1380 - C1382 cSH Interaction | Interacting Bases [3,3] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.785714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion U1381 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 [3] | Right Index [2] // New Initial node after Cluster 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_40845.1:
> IL_40845.1 IL_1FJG_037 G 933 C 1384 GCA*UUCCC