| 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 4 I | 8 4 4 | 9 4 I | 10 4 5 | 11 3 I | 12 3 6 | 13 2 I | 14 2 7 | 15 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_94651.1_Instance_1 HL_94651.1_HL_5F5H_001_C8_G15 | C | G | U | U | C | U | A | G | ||||||||||||
| HL_94651.1_Sequence_1 HL_94651.1_HL_5F5H_001_C8_G15 | C | G | U | U | C | U | A | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_94651.1_Instance_2 HL_94651.1_HL_5F5H_002_C8_G15 | C | G | U | U | C | U | A | G | ||||||||||||
| HL_94651.1_Sequence_2 HL_94651.1_HL_5F5H_002_C8_G15 | C | G | U | U | C | U | A | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_94651.1_Instance_3 HL_94651.1_HL_5F5F_003_C7_G14 | C | G | U | U | U | U | A | G | ||||||||||||
| HL_94651.1_Sequence_3 HL_94651.1_HL_5F5F_003_C7_G14 | C | G | U | U | U | U | A | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_94651.1_Instance_4 HL_94651.1_HL_5F5F_001_C7_G14 | C | G | U | U | U | U | A | G | ||||||||||||
| HL_94651.1_Sequence_4 HL_94651.1_HL_5F5F_001_C7_G14 | C | G | U | U | U | U | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 7 cWW 2 3 s35 2 6 tSS 2 7 s55 4 5 s55JAR3D SCFG/MRF model for HL_94651.1:
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 [7] // Initial node C8 - G15 from junction BasepairNode | Deletion Probability [0.0000239574126029] | 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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair C8 - G15 cWW BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.021020535,0.017279673,0.019905677,0.012636670,0.000000000],[0.002538690,0.002538690,0.220876798,0.002538690,0.000000000],[0.292330587,0.002538690,0.246790864,0.148849673,0.000000000],[0.002538690,0.002538690,0.002538690,0.002538690,0.000000000],[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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [6] // Basepair G9 - A14 tSS HairpinNode | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node U10:U13 Interaction | Interacting Bases [1,1] | 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 U10 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 U11 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 U13 Insertion | Location [2] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000]// Insertion in Hairpin after nucleotide 4, position 2Sequences of instances from HL_94651.1:
> HL_94651.1 HL_5F5H_001 C 8 G 15 CGUUCUAG > HL_94651.1 HL_5F5H_002 C 8 G 15 CGUUCUAG > HL_94651.1 HL_5F5F_003 C 7 G 14 CGUUUUAG > HL_94651.1 HL_5F5F_001 C 7 G 14 CGUUUUAG