| 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 2 I | 14 2 6 | 15 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_88119.1_Instance_1 IL_88119.1_IL_3U5F_073_A1345_U1380 | A | AU | A | U | U | C | U | |||||||||||||
| IL_88119.1_Sequence_1 IL_88119.1_IL_3U5F_073_A_1345_U_1380 | A | AU | A | * | U | U | C | U | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 3 s33 1 6 cWW 2 3 cWW 3 5 cSH 4 5 s35 6 5 7BPh 4 3 7BRJAR3D SCFG/MRF model for IL_88119.1:
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 [6] // Initial node A1345 - U1380 from junction BasepairNode | Deletion Probability [0.0000000005780646] | Pair Probability [[0.003527954,0.009318861,0.003741113,0.583345208,0.000000000],[0.007658846,0.003547927,0.073310118,0.027435017,0.000000000],[0.003734738,0.073735909,0.000819206,0.074173606,0.000000000],[0.078847505,0.003947006,0.008995131,0.043861856,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.000000000,0.045351474,0.907029478,0.045351474,0.002267574] | Left Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | 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 [6] // Basepair A1345 - U1380 cWW ClusterNode | Deletion Probability [0.0000000006250000] | Num Left Bases [1] | Num Right Bases [3] | Left Index [2] | Right Index [5] | Norm Constant [0.253574581524345] // Cluster node A1348:A1348 and U1377:C1379 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 A1348 - U1377 cWW 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 U1377 - C1379 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 U1378 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_88119.1:
> IL_88119.1 IL_3U5F_073 A 1345 U 1380 AAUA*UUCU