| 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 15 2 | 5 15 I | 6 16 | 7 15 I | 8 15 3 | 9 14 I | 10 18 4 | 11 19 I | 12 20 5 | 13 21 I | 14 22 6 | 15 23 I | 16 26 7 | 17 26 I | 18 27 | 19 26 I | 20 26 8 | 21 25 I | 22 29 9 | 23 29 I | 24 30 | 25 29 I | 26 29 10 | 27 12 I | 28 11 11 | 29 10 I | 30 9 12 | 31 8 I | 32 7 13 | 33 6 I | 34 5 14 | 35 4 I | 36 3 15 | 37 2 I | 38 2 16 | 39 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J4_10313.2_Instance_1 J4_10313.2,J4_4Y4O_018,U1313_A1603 | U | C | G | G | U | U | A | G | C | U | A | C | C | C | G | U | A | |||||||||||||||||||||||||||
| J4_10313.2_Sequence_1 J4_10313.24Y4O_U_1313_A_1603 | U | C | * | G | G | U | U | A | G | * | C | U | * | A | C | C | C | G | U | A | true | 100 | 0 | 0 | 0.05 | |||||||||||||||||||
| J4_10313.2_Instance_2 J4_10313.2,J4_4WF9_006,U1350_A1647 | U | C | G | G | U | U | A | G | C | C | G | C | C | C | G | U | A | |||||||||||||||||||||||||||
| J4_10313.2_Sequence_2 J4_10313.24WF9_U_1350_A_1647 | U | C | * | G | G | U | U | A | G | * | C | C | * | G | C | C | C | G | U | A | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||||
| J4_10313.2_Instance_3 J4_10313.2,J4_4V9F_005,U1419_A1678 | U | C | G | G | U | U | A | G | C | C | G | U | C | C | G | U | A | |||||||||||||||||||||||||||
| J4_10313.2_Sequence_3 J4_10313.24V9F_U_1419_A_1678 | U | C | * | G | G | U | U | A | G | * | C | C | * | G | U | C | C | G | U | A | true | 96 | 0 | 0 | 0.85 | |||||||||||||||||||
| J4_10313.2_Instance_4 J4_10313.2,J4_7A0S_006,U1326_A1619 | U | C | G | G | A | A | A | G | C | C | G | C | C | C | G | U | A | |||||||||||||||||||||||||||
| J4_10313.2_Sequence_4 J4_10313.27A0S_U_1326_A_1619 | U | C | * | G | G | A | A | A | G | * | C | C | * | G | C | C | C | G | U | A | true | 90 | 0 | 0 | 1.95 | |||||||||||||||||||
| J4_10313.2_Instance_5 J4_10313.2,J4_5J7L_023,U1313_A1603 | U | C | G | G | U | G | A | G | C | U | A | A | U | C | G | U | A | |||||||||||||||||||||||||||
| J4_10313.2_Sequence_5 J4_10313.25J7L_U_1313_A_1603 | U | C | * | G | G | U | G | A | G | * | C | U | * | A | A | U | C | G | U | A | true | 86 | 0 | 0 | 2.84 |
1 16 cWW 2 3 cWW 2 4 s55 2 16 perp 3 4 s35 4 16 perp 5 16 s55 6 15 tHW 7 8 cWW 7 9 s55 7 10 s53 8 9 s35 9 10 cWW 11 12 s35 12 13 s35 13 14 s35 14 15 s35 2 1 7BPh 4 16 2BRJAR3D SCFG/MRF model for J4_10313.2:
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 [16] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008776211,0.017043482,0.009626941,0.190711986,0.000000000],[0.021414125,0.009550770,0.191353636,0.010729332,0.000000000],[0.009645717,0.188904676,0.001985843,0.022389043,0.000000000],[0.246203326,0.010078147,0.051771850,0.009814914,0.000000000],[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 [16] // Basepair U1313 - A1603 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.071428571,0.071428571,0.785714286,0.000000000] | Position [2] | Left Index [2] | Right Index [15] // Fixed node on right for 4Y4O|1|2A|G|1601 InitialNode | Left Length Distribution [1.000000000] | 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 [2] | Right Index [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.071428571,0.785714286,0.071428571,0.000000000] | Position [2] | Left Index [2] | Right Index [14] // Fixed node on right for 4Y4O|1|2A|C|1600 InitialNode | Left Length Distribution [1.000000000] | 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 [2] | Right Index [13] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.785714286,0.071428571,0.071428571,0.000000000] | Position [2] | Left Index [2] | Right Index [13] // Fixed node on right for 4Y4O|1|2A|C|1599 InitialNode | Left Length Distribution [1.000000000] | 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 [2] | Right Index [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.642857143,0.071428571,0.214285714,0.000000000] | Position [2] | Left Index [2] | Right Index [12] // Fixed node on right for 4Y4O|1|2A|C|1598 InitialNode | Left Length Distribution [1.000000000] | 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 [2] | Right Index [11] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.214285714,0.500000000,0.071428571,0.214285714,0.000000000] | Position [2] | Left Index [2] | Right Index [11] // Fixed node on right for 4Y4O|1|2A|A|1597 InitialNode | Left Length Distribution [1.000000000] | 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 [2] | Right Index [10] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [2] | Right Index [10] // Junction node C1314 - A1597 ID J9575 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | 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 [3] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.003637459,0.006522837,0.004181706,0.075822585,0.000000000],[0.054137016,0.025932524,0.605573545,0.036820353,0.000000000],[0.004228668,0.077456358,0.000797078,0.008950521,0.000000000],[0.076805549,0.005067957,0.010211137,0.003854705,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [3] // Basepair C1314 - G1338 cWW 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 truncation InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [10] // Initial node 4Y4O|1|2A|G|1339 - 4Y4O|1|2A|A|1597 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.018518519,0.018518519,0.944444444,0.018518519,0.000000000] | Position [1] | Left Index [4] | Right Index [10] // Fixed node on left for 4Y4O|1|2A|G|1339 InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.214285714,0.071428571,0.071428571,0.642857143,0.000000000] | Position [1] | Left Index [5] | Right Index [10] // Fixed node on left for 4Y4O|1|2A|U|1340 InitialNode | Left Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Left Letter Distribution [0.214285714,0.071428571,0.214285714,0.500000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Position [1] | Left Index [6] | Right Index [10] // Fixed node on left for 4Y4O|1|2A|U|1341 InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [7] | Right Index [10] // Junction node G1343 - A1597 ID J9648 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009455586,0.019692602,0.010767390,0.195568732,0.000000000],[0.016608995,0.009272152,0.197225876,0.012904458,0.000000000],[0.010647812,0.250577697,0.002029586,0.026000454,0.000000000],[0.193065826,0.013393582,0.022790568,0.009998684,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // Basepair G1343 - C1404 cWW HairpinNode | Num Bases [1] | Left Index [8] | Right Index [8] | 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 truncation InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [9] | Right Index [10] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009068947,0.016785052,0.010240914,0.192150589,0.000000000],[0.020383894,0.009481442,0.226915719,0.012329706,0.000000000],[0.010320187,0.193924261,0.002012365,0.022633063,0.000000000],[0.215849209,0.011775691,0.036312554,0.009816407,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [10] // Basepair U1405 - A1597 cWW HairpinNode | Num Bases [1] | Left Index [10] | Right Index [10] | 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 J4_10313.2:
> J4_10313.2 4Y4O U 1313 A 1603 UC*GGUUAG*CU*ACCCGUA > J4_10313.2 4WF9 U 1350 A 1647 UC*GGUUAG*CC*GCCCGUA > J4_10313.2 4V9F U 1419 A 1678 UC*GGUUAG*CC*GUCCGUA > J4_10313.2 7A0S U 1326 A 1619 UC*GGAAAG*CC*GCCCGUA > J4_10313.2 5J7L U 1313 A 1603 UC*GGUGAG*CU*AAUCGUA