| 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 11 5 | 11 11 I | 12 12 6 | 13 12 I | 14 12 7 | 15 11 I | 16 11 8 | 17 10 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_17086.2_Instance_1 HL_17086.2_HL_4V88_199_A520_U532 | A | A | U | G | U | A | A | A | U | A | C | C | U | |||||||||||||||||||
| HL_17086.2_Sequence_1 HL_17086.2_HL_4V88_199_A520_U532 | A | A | U | G | U | A | A | A | U | A | C | C | U | true | 95 | 0 | 0 | 1.03 | ||||||||||||||
| HL_17086.2_Instance_2 HL_17086.2_HL_4WFL_001_G19_C31 | G | A | G | G | U | A | G | C | G | G | U | G | C | |||||||||||||||||||
| HL_17086.2_Sequence_2 HL_17086.2_HL_4WFL_001_G19_C31 | G | A | G | G | U | A | G | C | G | G | U | G | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| HL_17086.2_Instance_3 HL_17086.2_HL_6GSL_221_C30_G42 | C | G | G | C | U | A | C | G | A | A | C | C | G | |||||||||||||||||||
| HL_17086.2_Sequence_3 HL_17086.2_HL_6GSL_221_C30_G42 | C | G | G | C | U | A | C | G | A | A | C | C | G | true | 89 | 0 | 0 | 2.11 |
1 2 s35 1 13 cWW 2 3 s35 2 12 cWW 3 4 s35 3 12 s55 4 5 s35 4 10 tSH 5 8 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_17086.2:
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 [13] // Initial node A520 - U532 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009425327,0.019602391,0.010550535,0.209161741,0.000000000],[0.018119710,0.009519290,0.209803050,0.012356683,0.000000000],[0.010544174,0.210633518,0.002053265,0.034146945,0.000000000],[0.196782200,0.012577586,0.024177876,0.010545706,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [0.0000234451146992] | Pair Probability [[0.017607393,0.119394744,0.136092483,0.082809975,0.000000000],[0.014346098,0.010186641,0.081282465,0.022340555,0.000000000],[0.121590058,0.094500843,0.002858877,0.103916014,0.000000000],[0.079787439,0.023683905,0.017024915,0.072577594,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [0.100000000,0.100000000,0.500000000,0.300000000,0.000000000] | Position [1] | Left Index [3] | Right Index [11] // Fixed node on left InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [11] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.500000000,0.100000000,0.300000000,0.000000000] | Position [2] | Left Index [4] | Right Index [11] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [0.0000234451146992] | Pair Probability [[0.069626847,0.064428939,0.002533033,0.174024460,0.000000000],[0.122650945,0.064475214,0.002533033,0.002533033,0.000000000],[0.082795499,0.002533033,0.202308523,0.067747645,0.000000000],[0.071059593,0.065684135,0.002533033,0.002533033,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [10] // Basepair G523 - A529 tSH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.300000000,0.300000000,0.000000000] | Position [2] | Left Index [5] | Right Index [9] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.044562893,0.036337907,0.000495420,0.002391071,0.000000000],[0.045035112,0.042298318,0.000495420,0.000495420,0.000000000],[0.044687019,0.000495420,0.002812122,0.030262453,0.000000000],[0.343146052,0.343608673,0.059408762,0.003467939,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair U524 - A527 tSH HairpinNode | Num Bases [2] | Left Index [6] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node A525:A526 Interaction | Interacting Bases [1,1] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A525 Interaction | Interacting Bases [2,2] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A526Sequences of instances from HL_17086.2:
> HL_17086.2 HL_4V88_199 A 520 U 532 AAUGUAAAUACCU > HL_17086.2 HL_4WFL_001 G 19 C 31 GAGGUAGCGGUGC > HL_17086.2 HL_6GSL_221 C 30 G 42 CGGCUACGAACCG