| 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 8 4 | 9 8 I | 10 9 5 | 11 9 I | 12 9 6 | 13 9 I | 14 9 7 | 15 9 I | 16 9 8 | 17 9 I | 18 9 9 | 19 8 I | 20 8 10 | 21 7 I | 22 6 11 | 23 3 I | 24 3 12 | 25 2 I | 26 2 13 | 27 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_05304.3_Instance_1 HL_05304.3,HL_8P9A_203,A520_U532 | A | A | U | G | U | A | A | A | U | A | C | C | U | |||||||||||||||||||
| HL_05304.3_Sequence_1 HL_05304.38P9A_A520_U532 | A | A | U | G | U | A | A | A | U | A | C | C | U | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| HL_05304.3_Instance_2 HL_05304.3,HL_8CRE_204,A518_U530 | A | A | U | G | U | A | A | A | U | A | C | C | U | |||||||||||||||||||
| HL_05304.3_Sequence_2 HL_05304.38CRE_A518_U530 | A | A | U | G | U | A | A | A | U | A | C | C | U | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| HL_05304.3_Instance_3 HL_05304.3,HL_4WFL_001,G19_C31 | G | A | G | G | U | A | G | C | G | G | U | G | C | |||||||||||||||||||
| HL_05304.3_Sequence_3 HL_05304.34WFL_G19_C31 | G | A | G | G | U | A | G | C | G | G | U | G | C | true | 88 | 0 | 0 | 2.37 | ||||||||||||||
| HL_05304.3_Instance_4 HL_05304.3,HL_7A0S_072,G1503_C1517 | G | G | U | C | A | G | A | A | A | A | U | C | U | A | C | |||||||||||||||||
| HL_05304.3_Sequence_4 HL_05304.37A0S_G_1503_C_1517 | G | G | U | C | A | G | A | A | A | A | U | C | U | A | C | true | 71 | 0 | 0 | 5.65 | ||||||||||||
| HL_05304.3_Instance_5 HL_05304.3,HL_5E81_248,A51_U63 | A | G | G | U | U | C | G | A | A | U | C | C | U | |||||||||||||||||||
| HL_05304.3_Sequence_5 HL_05304.35E81_A51_U63 | A | G | G | U | U | C | G | A | A | U | C | C | U | true | 82 | 0 | 0 | 3.47 |
1 2 s35 1 13 cWW 2 3 s35 2 12 cWW 2 13 s55 3 4 s35 4 5 s35 4 10 tSH 6 7 s35 7 8 s35 8 9 s35 9 10 s35 10 11 s35 11 12 s35 12 13 s35 5 8 6BPhJAR3D SCFG/MRF model for HL_05304.3:
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 [13] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009192854,0.020706043,0.010085615,0.225768905,0.000000000],[0.016854189,0.009292783,0.192061375,0.011199507,0.000000000],[0.010026535,0.214869253,0.002001534,0.041416213,0.000000000],[0.191480098,0.011785275,0.022529294,0.010730527,0.000000000],[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 [13] // Basepair A520 - U532 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.017504873,0.144178177,0.153873507,0.058382730,0.000000000],[0.013652174,0.010224476,0.056303245,0.024244761,0.000000000],[0.153758886,0.068729203,0.002964323,0.117079132,0.000000000],[0.055338617,0.024792593,0.015570486,0.083402819,0.000000000],[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 [2] | Right Index [12] // Basepair A521 - C531 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.071428571,0.357142857,0.500000000,0.000000000] | Position [1] | Left Index [3] | Right Index [11] // Fixed node on left for 8P9A|1|sR|U|522 InitialNode | Left Length Distribution [0.792098765,0.205432099,0.002370370,0.000098765] | Left Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [11] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.500000000,0.071428571,0.357142857,0.000000000] | Position [2] | Left Index [4] | Right Index [11] // Fixed node on right for 8P9A|1|sR|C|530 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 [4] | Right Index [10] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000081095392462] | Pair Probability [[0.079048681,0.116995098,0.002041505,0.113964655,0.000000000],[0.077425316,0.077655272,0.002041505,0.002041505,0.000000000],[0.107183730,0.002041505,0.135518510,0.078485222,0.000000000],[0.083950413,0.078238356,0.002041505,0.041327220,0.000000000],[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 [0.792098765,0.205432099,0.002370370,0.000098765] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [4] | Right Index [10] // Basepair G523 - A529 tSH HairpinNode | Num Bases [5] | Left Index [5] | Right Index [9] | Norm Constant [1.000000000000000] // Hairpin node U524:U528 Interaction | Interacting Bases [1,1] | Pair Probability [[0.013513514,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.013513514,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.202702703,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.770270270,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U524 Interaction | Interacting Bases [2,2] | Pair Probability [[0.642857143,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A525 Interaction | Interacting Bases [3,3] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.357142857,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A526 Interaction | Interacting Bases [4,4] | Pair Probability [[0.642857143,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A527 Interaction | Interacting Bases [5,5] | Pair Probability [[0.357142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.357142857,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U528Sequences of instances from HL_05304.3:
> HL_05304.3 8P9A A 520 U 532 AAUGUAAAUACCU > HL_05304.3 8CRE A 518 U 530 AAUGUAAAUACCU > HL_05304.3 4WFL G 19 C 31 GAGGUAGCGGUGC > HL_05304.3 7A0S G 1503 C 1517 GGUCAGAAAAUCUAC > HL_05304.3 5E81 A 51 U 63 AGGUUCGAAUCCU