| 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 3 I | 6 4 3 | 7 5 I | 8 6 4 | 9 7 I | 10 8 5 | 11 8 I | 12 9 | 13 8 I | 14 8 6 | 15 3 I | 16 3 7 | 17 2 I | 18 2 8 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_49061.1_Instance_1 IL_49061.1,IL_4LFB_064,C1440_G1461 | C | G | G | G | A | G | C | A | G | |||||||||||||||
| IL_49061.1_Sequence_1 IL_49061.14LFB_C_1440_G_1461 | C | G | G | G | A | G | * | C | A | G | true | 85 | 0 | 0 | 1.43 | |||||||||
| IL_49061.1_Instance_2 IL_49061.1,IL_5UNE_002,C33_G12 | C | G | G | A | A | A | U | G | G | |||||||||||||||
| IL_49061.1_Sequence_2 IL_49061.15UNE_C33_G12 | C | G | G | A | A | A | * | U | G | G | true | 84 | 0 | 0 | 1.56 | |||||||||
| IL_49061.1_Instance_3 IL_49061.1,IL_1XJR_001,C9_G41 | C | C | G | A | G | C | A | G | ||||||||||||||||
| IL_49061.1_Sequence_3 IL_49061.11XJR_C9_G41 | C | C | G | A | G | * | C | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_49061.1_Instance_4 IL_49061.1,IL_4GXY_009,G122_C107 | G | G | A | A | G | C | A | C | ||||||||||||||||
| IL_49061.1_Sequence_4 IL_49061.14GXY_G122_C107 | G | G | A | A | G | * | C | A | C | true | 96 | 0 | 0 | 0.41 | ||||||||||
| IL_49061.1_Instance_5 IL_49061.1,IL_4WF9_012,G409_C306 | G | G | A | U | C | G | A | C | ||||||||||||||||
| IL_49061.1_Sequence_5 IL_49061.14WF9_G409_C306 | G | G | A | U | C | * | G | A | C | true | 88 | 0 | 0 | 1.10 | ||||||||||
| IL_49061.1_Instance_6 IL_49061.1,IL_8P9A_440,U1430_G1278 | U | C | U | G | U | G | A | U | G | G | ||||||||||||||
| IL_49061.1_Sequence_6 IL_49061.18P9A_U_1430_G_1278 | U | C | U | G | U | G | A | * | U | G | G | true | 25 | 0 | 0 | 7.09 |
1 2 s35 1 8 cWW 2 6 s33 2 7 tSH 2 8 s55 3 4 s35 5 6 cWW 5 7 s55 6 7 s35 7 8 s35JAR3D SCFG/MRF model for IL_49061.1:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [8] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009514109,0.016973007,0.011119951,0.166196516,0.000000000],[0.063759997,0.012217332,0.200761073,0.013467537,0.000000000],[0.011189835,0.189541432,0.002205826,0.022228458,0.000000000],[0.174455388,0.013169422,0.082862780,0.010337335,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair C1440 - G1461 cWW BasepairNode | Deletion Probability [0.0000097596267952] | Pair Probability [[0.075930122,0.074643662,0.001960966,0.109468622,0.000000000],[0.112392528,0.074591685,0.039982692,0.001960966,0.000000000],[0.141548695,0.001960966,0.130458031,0.075388892,0.000000000],[0.080638476,0.075151766,0.001960966,0.001960966,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.826344012,0.171868555,0.001718686,0.000068747] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair G1441 - A1460 tSH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.312500000,0.062500000,0.562500000,0.062500000,0.000000000] | Position [1] | Left Index [3] | Right Index [6] // Fixed node on left for 4LFB|1|A|G|1442 InitialNode | Left Length Distribution [0.661815186,0.335026775,0.003020733,0.000137306] | Left Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [6] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.562500000,0.062500000,0.062500000,0.312500000,0.000000000] | Position [1] | Left Index [4] | Right Index [6] // Fixed node on left for 4LFB|1|A|G|1443 InitialNode | Left Length Distribution [0.826344012,0.171868555,0.001718686,0.000068747] | Left Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009190185,0.019556070,0.010271277,0.213082011,0.000000000],[0.017097064,0.009222955,0.202911173,0.011925712,0.000000000],[0.010225608,0.224479173,0.001995078,0.033709602,0.000000000],[0.190792347,0.012301885,0.022962688,0.010277172,0.000000000],[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 [5] | Right Index [6] // Basepair G1447 - C1459 cWW HairpinNode | Num Bases [1] | Left Index [6] | Right Index [6] | 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_49061.1:
> IL_49061.1 4LFB C 1440 G 1461 CGGGAG*CAG > IL_49061.1 5UNE C 33 G 12 CGGAAA*UGG > IL_49061.1 1XJR C 9 G 41 CCGAG*CAG > IL_49061.1 4GXY G 122 C 107 GGAAG*CAC > IL_49061.1 4WF9 G 409 C 306 GGAUC*GAC > IL_49061.1 8P9A U 1430 G 1278 UCUGUGA*UGG