| 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 12 3 | 7 12 I | 8 13 4 | 9 12 I | 10 12 5 | 11 11 I | 12 10 6 | 13 9 I | 14 8 7 | 15 7 I | 16 6 8 | 17 5 I | 18 4 9 | 19 3 I | 20 3 10 | 21 2 I | 22 2 11 | 23 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_72714.2_Instance_1 HL_72714.2_HL_6QN3_004_U32_A43 | U | A | G | G | G | A | A | C | G | G | G | A | ||||||||||||||||
| HL_72714.2_Sequence_1 HL_72714.2_HL_6QN3_004_U32_A43 | U | A | G | G | G | A | A | C | G | G | G | A | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_72714.2_Instance_2 HL_72714.2_HL_6QN3_002_U32_A43 | U | A | G | G | G | A | A | C | G | G | G | A | ||||||||||||||||
| HL_72714.2_Sequence_2 HL_72714.2_HL_6QN3_002_U32_A43 | U | A | G | G | G | A | A | C | G | G | G | A | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_72714.2_Instance_3 HL_72714.2_HL_7A0S_002_C85_G95 | C | U | G | G | A | G | A | U | A | C | G | |||||||||||||||||
| HL_72714.2_Sequence_3 HL_72714.2_HL_7A0S_002_C85_G95 | C | U | G | G | A | G | A | U | A | C | G | true | 85 | 0 | 0 | 2.82 |
1 2 s35 1 11 cWW 2 10 cWW 2 11 s55 3 4 s53 3 5 cWH 4 5 s35 5 6 s35 6 7 s35 7 8 s35 8 9 s35 9 10 s35 10 11 s35JAR3D SCFG/MRF model for HL_72714.2:
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 [11] // Initial node U32 - A43 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009112412,0.017228063,0.010161591,0.195229874,0.000000000],[0.021246469,0.009696958,0.208737087,0.011844029,0.000000000],[0.010214994,0.195415535,0.002039424,0.022961981,0.000000000],[0.220848146,0.011235231,0.044021864,0.010006340,0.000000000],[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 [11] // Basepair U32 - A43 cWW BasepairNode | Deletion Probability [0.0000006691671388] | Pair Probability [[0.025772464,0.015067867,0.272212245,0.018175685,0.000000000],[0.014359632,0.010351320,0.020273694,0.132292821,0.000000000],[0.242655843,0.020709811,0.003603904,0.016440967,0.000000000],[0.017750210,0.162194390,0.015712734,0.012426411,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Left Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | 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 [10] // Basepair A33 - G42 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.500000000,0.100000000,0.000000000] | Position [2] | Left Index [3] | 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 [3] | Right Index [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.500000000,0.300000000,0.000000000] | Position [2] | Left Index [3] | Right Index [8] // 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 [3] | Right Index [7] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.500000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // 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 [3] | Right Index [6] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | Position [2] | Left Index [3] | Right Index [6] // 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 [3] | Right Index [5] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.002677805,0.002677805,0.231769374,0.221900815,0.000000000],[0.002677805,0.018366056,0.002677805,0.010138700,0.000000000],[0.343138843,0.002677805,0.111342811,0.002677805,0.000000000],[0.009865549,0.002677805,0.009147676,0.025585536,0.000000000],[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 [3] | Right Index [5] // Basepair G35 - A37 cWH HairpinNode | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G36:G36 Interaction | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[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 G36Sequences of instances from HL_72714.2:
> HL_72714.2 HL_6QN3_004 U 32 A 43 UAGGGAACGGGA > HL_72714.2 HL_6QN3_002 U 32 A 43 UAGGGAACGGGA > HL_72714.2 HL_7A0S_002 C 85 G 95 CUGGAGAUACG