| 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 4 I | 6 5 3 | 7 5 I | 8 6 4 | 9 6 I | 10 6 5 | 11 5 I | 12 5 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_86769.2_Instance_1 HL_86769.2_HL_4P5J_004_A69_U76 | A | G | G | G | U | C | A | U | ||||||||||||
| HL_86769.2_Sequence_1 HL_86769.2_HL_4P5J_004_A69_U76 | A | G | G | G | U | C | A | U | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_86769.2_Instance_2 HL_86769.2_HL_6MJ0_010_A89_U96 | A | G | G | G | U | C | A | U | ||||||||||||
| HL_86769.2_Sequence_2 HL_86769.2_HL_6MJ0_010_A89_U96 | A | G | G | G | U | C | A | U | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_86769.2_Instance_3 HL_86769.2_HL_1ET4_001_C219_G226 | C | A | C | C | U | C | A | G | ||||||||||||
| HL_86769.2_Sequence_3 HL_86769.2_HL_1ET4_001_C219_G226 | C | A | C | C | U | C | A | G | true | 99 | 0 | 0 | 0.14 | |||||||
| HL_86769.2_Instance_4 HL_86769.2_HL_4WF9_001_G67_U74 | G | A | C | G | A | U | A | U | ||||||||||||
| HL_86769.2_Sequence_4 HL_86769.2_HL_4WF9_001_G67_U74 | G | A | C | G | A | U | A | U | true | 88 | 0 | 0 | 1.34 |
1 2 s35 1 7 cWW 2 3 s35 2 7 s55 3 4 s35 3 6 cSS 4 5 cSH 5 6 s55JAR3D SCFG/MRF model for HL_86769.2:
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 [7] // Initial node A69 - U76 from junction BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.010774303,0.087781157,0.011060585,0.188806380,0.000000000],[0.016926973,0.010215360,0.165003366,0.011993158,0.000000000],[0.011006102,0.156433179,0.002308841,0.121014314,0.000000000],[0.154469200,0.012523924,0.021379402,0.018303756,0.000000000],[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 A69 - U76 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.083333333,0.416666667,0.083333333,0.000000000] | Position [1] | Left Index [2] | Right Index [6] // Fixed node on left InitialNode | 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 [1.000000000] | 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 BasepairNode | Deletion Probability [0.0000001215781528] | Pair Probability [[0.073566642,0.073006261,0.070917251,0.073552522,0.000000000],[0.098049710,0.074615088,0.003437300,0.066716418,0.000000000],[0.098025574,0.003379657,0.007155805,0.078088272,0.000000000],[0.072563539,0.069769429,0.068875151,0.068281382,0.000000000],[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 [0.083333333,0.583333333,0.083333333,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair G71 - A75 cSS HairpinNode | Num Bases [2] | Left Index [4] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node G72:U73 Interaction | Interacting Bases [1,2] | Pair Probability [[0.044818056,0.046685522,0.006141431,0.110298723,0.000000000],[0.036275831,0.103785704,0.001320968,0.129898382,0.000000000],[0.125066668,0.001320968,0.051530555,0.130731861,0.000000000],[0.046579044,0.049284262,0.001320968,0.114941055,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G72 - U73 cSHSequences of instances from HL_86769.2:
> HL_86769.2 HL_4P5J_004 A 69 U 76 AGGGUCAU > HL_86769.2 HL_6MJ0_010 A 89 U 96 AGGGUCAU > HL_86769.2 HL_1ET4_001 C 219 G 226 CACCUCAG > HL_86769.2 HL_4WF9_001 G 67 U 74 GACGAUAU