| 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 3 | 7 5 I | 8 6 4 | 9 6 I | 10 7 | 11 6 I | 12 6 5 | 13 5 I | 14 5 6 | 15 4 I | 16 3 7 | 17 3 I | 18 3 8 | 19 2 I | 20 2 9 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_22732.1_Instance_1 IL_22732.1_IL_1FJG_061_C1466_G1435 | C | G | A | G | C | G | A | A | G | |||||||||||||||||
| IL_22732.1_Sequence_1 IL_22732.1_IL_1FJG_061_C_1466_G_1435 | C | G | A | G | * | C | G | A | A | G | true | 89 | 0 | 0 | 1.20 | |||||||||||
| IL_22732.1_Instance_2 IL_22732.1_IL_2QBG_061_C1526_G1546 | C | G | A | G | U | G | A | A | G | |||||||||||||||||
| IL_22732.1_Sequence_2 IL_22732.1_IL_2QBG_061_C_1526_G_1546 | C | G | A | G | * | U | G | A | A | G | true | 84 | 0 | 0 | 1.74 | |||||||||||
| IL_22732.1_Instance_3 IL_22732.1_IL_2QBG_075_U1864_G1878 | U | U | A | G | C | G | A | A | G | |||||||||||||||||
| IL_22732.1_Sequence_3 IL_22732.1_IL_2QBG_075_U_1864_G_1878 | U | U | A | G | * | C | G | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_22732.1_Instance_4 IL_22732.1_IL_2ZY6_001_A7_U29 | A | U | A | G | C | G | A | G | U | |||||||||||||||||
| IL_22732.1_Sequence_4 IL_22732.1_IL_2ZY6_001_A7_U29 | A | U | A | G | * | C | G | A | G | U | true | 93 | 0 | 0 | 0.72 |
1 2 s35 1 9 cWW 2 6 s33 2 7 tWH 2 8 tSH 3 4 s35 3 6 tHS 3 7 s55 4 5 cWW 4 6 s55 5 6 s35 7 8 s35 8 9 s35 6 3 6BPhJAR3D SCFG/MRF model for IL_22732.1:
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 [9] // Initial node C1466 - G1435 from junction BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.010379139,0.018054448,0.011936187,0.166132001,0.000000000],[0.092831895,0.010420694,0.182890129,0.013631115,0.000000000],[0.012091289,0.159186893,0.002446059,0.022275606,0.000000000],[0.156779526,0.012908548,0.115428336,0.012608136,0.000000000],[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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair C1466 - G1435 cWW ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [2] | Right Index [8] | Norm Constant [0.287323481329397] // Cluster node G1467:G1467 and A1433:A1434 Interaction | Interacting Bases [1,2] | Pair Probability [[0.023156674,0.004856498,0.023822189,0.004856498,0.000000000],[0.048239451,0.040320637,0.032236679,0.004856498,0.000000000],[0.111499855,0.004856498,0.056836281,0.022654145,0.000000000],[0.504880592,0.004856498,0.059912387,0.052158619,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1467 - A1433 tWH Interaction | Interacting Bases [1,3] | Pair Probability [[0.099771965,0.116296998,0.001202125,0.005724366,0.000000000],[0.100659637,0.105505979,0.001202125,0.001202125,0.000000000],[0.139443264,0.001202125,0.005824043,0.099992658,0.000000000],[0.161770273,0.104476389,0.054523803,0.001202125,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1467 - A1434 tSH 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 [3] | Right Index [6] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.059593935,0.060124143,0.342732568,0.064776498,0.000000000],[0.069464361,0.063018870,0.003042710,0.062403894,0.000000000],[0.000718031,0.000718031,0.014741292,0.000718031,0.000000000],[0.003419172,0.000718031,0.253092402,0.000718031,0.000000000],[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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair A1468 - G1432 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.011545053,0.091357941,0.012500960,0.153268922,0.000000000],[0.016202600,0.009015557,0.162650528,0.013540081,0.000000000],[0.012307163,0.197820616,0.002427935,0.114576839,0.000000000],[0.150792068,0.014433261,0.021211816,0.016348660,0.000000000],[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 G1469 - C1431 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_22732.1:
> IL_22732.1 IL_1FJG_061 C 1466 G 1435 CGAG*CGAAG > IL_22732.1 IL_2QBG_061 C 1526 G 1546 CGAG*UGAAG > IL_22732.1 IL_2QBG_075 U 1864 G 1878 UUAG*CGAAG > IL_22732.1 IL_2ZY6_001 A 7 U 29 AUAG*CGAGU