| 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 3 3 | 7 3 I | 8 3 4 | 9 3 I | 10 3 5 | 11 3 I | 12 3 6 | 13 3 I | 14 3 7 | 15 3 I | 16 3 8 | 17 3 I | 18 3 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_31581.6_Instance_1 HL_31581.6,HL_4PR6_002,C147_G158 | C | A | U | U | G | C | A | C | U | C | C | G | ||||||||||||||||
| HL_31581.6_Sequence_1 HL_31581.64PR6_C147_G158 | C | A | U | U | G | C | A | C | U | C | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_31581.6_Instance_2 HL_31581.6,HL_4PRF_002,C147_G158 | C | A | U | U | G | C | A | C | U | C | C | G | ||||||||||||||||
| HL_31581.6_Sequence_2 HL_31581.64PRF_C147_G158 | C | A | U | U | G | C | A | C | U | C | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_31581.6_Instance_3 HL_31581.6,HL_6F4G_001,U8_G20 | U | A | U | U | G | C | A | G | U | A | C | C | G | |||||||||||||||
| HL_31581.6_Sequence_3 HL_31581.66F4G_U8_G20 | U | A | U | U | G | C | A | G | U | A | C | C | G | true | 90 | 0 | 0 | 2.10 |
1 2 s35 1 11 cWW 2 3 s35 2 11 s55 4 5 s55 6 7 s35 8 9 cSH 9 10 s35JAR3D SCFG/MRF model for HL_31581.6:
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 [11] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.010008314,0.015906297,0.011951013,0.143543808,0.000000000],[0.113253323,0.015638746,0.171362823,0.014397321,0.000000000],[0.012135476,0.146322383,0.002470993,0.020335440,0.000000000],[0.161392960,0.013617556,0.136517933,0.011145613,0.000000000],[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 C147 - G158 cWW HairpinNode | Num Bases [9] | Left Index [2] | Right Index [10] | Norm Constant [0.999999999999999] // Hairpin node A148:C157 Interaction | Interacting Bases [7,8] | Pair Probability [[0.085529458,0.091659460,0.007968609,0.087290064,0.000000000],[0.087501437,0.089524399,0.001017938,0.011494833,0.000000000],[0.012860867,0.001017938,0.092855544,0.082832031,0.000000000],[0.087353527,0.177152093,0.001017938,0.082923865,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U155 - C156 cSH 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 A148 Interaction | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U149 Interaction | Interacting Bases [3,3] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U150 Interaction | Interacting Bases [4,4] | 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 G151 Interaction | Interacting Bases [5,5] | 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 A153 Interaction | Interacting Bases [6,6] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[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 C154 Interaction | Interacting Bases [9,9] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C157 Insertion | Location [4] | Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000]// Insertion in Hairpin after nucleotide 5, position 4 Insertion | Location [7] | Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 8, position 7Sequences of instances from HL_31581.6:
> HL_31581.6 4PR6 C 147 G 158 CAUUGCACUCCG > HL_31581.6 4PRF C 147 G 158 CAUUGCACUCCG > HL_31581.6 6F4G U 8 G 20 UAUUGCAGUACCG