| 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 2 I | 16 2 8 | 17 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_31581.4_Instance_1 HL_31581.4_HL_4PRF_002_C147_G158 | C | A | U | U | G | C | A | C | UCC | G | ||||||||||||
| HL_31581.4_Sequence_1 HL_31581.4_HL_4PRF_002_C147_G158 | C | A | U | U | G | C | A | C | UCC | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_31581.4_Instance_2 HL_31581.4_HL_4PR6_002_C147_G158 | C | A | U | U | G | C | A | C | UCC | G | ||||||||||||
| HL_31581.4_Sequence_2 HL_31581.4_HL_4PR6_002_C147_G158 | C | A | U | U | G | C | A | C | UCC | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_31581.4_Instance_3 HL_31581.4_HL_1M5K_002_C35_G46 | C | A | U | U | G | C | A | C | UCC | G | ||||||||||||
| HL_31581.4_Sequence_3 HL_31581.4_HL_1M5K_002_C35_G46 | C | A | U | U | G | C | A | C | UCC | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_31581.4_Instance_4 HL_31581.4_HL_6LAX_001_C15_G26 | C | A | U | U | G | C | A | C | UCC | G | ||||||||||||
| HL_31581.4_Sequence_4 HL_31581.4_HL_6LAX_001_C15_G26 | C | A | U | U | G | C | A | C | UCC | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 8 cWW 2 3 s35 2 8 s55 4 5 s55 6 7 s35JAR3D SCFG/MRF model for HL_31581.4:
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 [8] // Initial node C147 - G158 from junction BasepairNode | Deletion Probability [0.0000000000030395] | Pair Probability [[0.009353183,0.016772504,0.010752635,0.194966481,0.000000000],[0.019886467,0.009525946,0.243418233,0.013525436,0.000000000],[0.010873390,0.199167485,0.002049567,0.023014932,0.000000000],[0.197494026,0.013031497,0.026256418,0.009911799,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.000000000,0.000000000,0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.035714286,0.607142857,0.035714286,0.321428571,0.000000000] | Left Index [1] | Right Index [8] // Basepair C147 - G158 cWW HairpinNode | Num Bases [6] | Left Index [2] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node A148:C154 Interaction | Interacting Bases [1,1] | Pair Probability [[0.750000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A148 Interaction | Interacting Bases [2,2] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.750000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U149 Interaction | Interacting Bases [3,3] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.750000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U150 Interaction | Interacting Bases [4,4] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.750000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G151 Interaction | Interacting Bases [5,5] | Pair Probability [[0.750000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A153 Interaction | Interacting Bases [6,6] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.750000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C154 Insertion | Location [4] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000]// Insertion in Hairpin after nucleotide 5, position 4Sequences of instances from HL_31581.4:
> HL_31581.4 HL_4PRF_002 C 147 G 158 CAUUGCACUCCG > HL_31581.4 HL_4PR6_002 C 147 G 158 CAUUGCACUCCG > HL_31581.4 HL_1M5K_002 C 35 G 46 CAUUGCACUCCG > HL_31581.4 HL_6LAX_001 C 15 G 26 CAUUGCACUCCG