| 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 3 I | 8 3 4 | 9 2 I | 10 2 5 | 11 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_08100.1_Instance_1 HL_08100.1,HL_5J7L_214,C1727_G1733 | C | C | U | C | G | C | G | |||||||||
| HL_08100.1_Sequence_1 HL_08100.15J7L_C_1727_G_1733 | C | C | U | C | G | C | G | true | 92 | 0 | 0 | 0.85 | ||||
| HL_08100.1_Instance_2 HL_08100.1,HL_8P9A_179,C3193_G3199 | C | C | U | U | G | U | G | |||||||||
| HL_08100.1_Sequence_2 HL_08100.18P9A_C_3193_G_3199 | C | C | U | U | G | U | G | true | 100 | 0 | 0 | 0.00 | ||||
| HL_08100.1_Instance_3 HL_08100.1,HL_5J7L_200,C2795_G2801 | C | U | U | U | A | A | G | |||||||||
| HL_08100.1_Sequence_3 HL_08100.15J7L_C_2795_G_2801 | C | U | U | U | A | A | G | true | 98 | 0 | 0 | 0.25 | ||||
| HL_08100.1_Instance_4 HL_08100.1,HL_5WTI_001,C12_G18 | C | U | U | U | U | G | G | |||||||||
| HL_08100.1_Sequence_4 HL_08100.15WTI_C12_G18 | C | U | U | U | U | G | G | true | 86 | 0 | 0 | 1.36 |
1 2 s35 1 5 cWW 2 3 s33 2 4 cWW 2 5 s55 3 4 s35 4 5 s35JAR3D SCFG/MRF model for HL_08100.1:
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 [5] // Initial node BasepairNode | Deletion Probability [0.0000001215781528] | 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 [0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair C1727 - G1733 cWW BasepairNode | Deletion Probability [0.0000001215781528] | Pair Probability [[0.008278991,0.015445393,0.009305520,0.176141926,0.000000000],[0.018866590,0.008712977,0.243914458,0.011071788,0.000000000],[0.009369025,0.177222069,0.001842957,0.020736025,0.000000000],[0.190518916,0.010548431,0.035693670,0.062331264,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Left Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000] | 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 [4] // Basepair C1728 - G1731 cWW HairpinNode | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node C1730:C1730 Interaction | Interacting Bases [1,1] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.583333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C1730Sequences of instances from HL_08100.1:
> HL_08100.1 5J7L C 1727 G 1733 CCUCGCG > HL_08100.1 8P9A C 3193 G 3199 CCUUGUG > HL_08100.1 5J7L C 2795 G 2801 CUUUAAG > HL_08100.1 5WTI C 12 G 18 CUUUUGG