| 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_86769.4_Instance_1 HL_86769.4,HL_4P5J_004,A69_U76 | A | G | G | G | U | C | A | U | ||||||||||||
| HL_86769.4_Sequence_1 HL_86769.44P5J_A69_U76 | A | G | G | G | U | C | A | U | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_86769.4_Instance_2 HL_86769.4,HL_6MJ0_010,A89_U96 | A | G | G | G | U | C | A | U | ||||||||||||
| HL_86769.4_Sequence_2 HL_86769.46MJ0_A89_U96 | A | G | G | G | U | C | A | U | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_86769.4_Instance_3 HL_86769.4,HL_1ET4_001,C219_G226 | C | A | C | C | U | C | A | G | ||||||||||||
| HL_86769.4_Sequence_3 HL_86769.41ET4_C219_G226 | C | A | C | C | U | C | A | G | true | 99 | 0 | 0 | 0.16 | |||||||
| HL_86769.4_Instance_4 HL_86769.4,HL_4WF9_001,G67_U74 | G | A | C | G | A | U | A | U | ||||||||||||
| HL_86769.4_Sequence_4 HL_86769.44WF9_G67_U74 | G | A | C | G | A | U | A | U | true | 86 | 0 | 0 | 1.56 | |||||||
| HL_86769.4_Instance_5 HL_86769.4,HL_3AMU_002,G30_C40 | G | G | C | U | CA | U | A | AC | C | |||||||||||
| HL_86769.4_Sequence_5 HL_86769.43AMU_G30_C40 | G | G | C | U | CA | U | A | AC | C | true | 34 | 0 | 0 | 7.18 |
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_86769.4:
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 [7] // Initial node BasepairNode | Deletion Probability [0.0000027871092024] | Pair Probability [[0.010428470,0.073494637,0.010917675,0.192529849,0.000000000],[0.016734410,0.009948887,0.172095461,0.012084042,0.000000000],[0.010850588,0.174070210,0.002235399,0.102994290,0.000000000],[0.161011617,0.012602435,0.021498745,0.016503284,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.790123457,0.009876543,0.197925926,0.001975309,0.000098765] | Right Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair A69 - U76 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.357142857,0.071428571,0.500000000,0.071428571,0.000000000] | Position [1] | Left Index [2] | Right Index [6] // Fixed node on left for 4P5J|1|A|G|70 InitialNode | Left Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [0.0000003483978778] | Pair Probability [[0.071088788,0.070547281,0.068528632,0.071075143,0.000000000],[0.127964412,0.072101920,0.003321526,0.064469291,0.000000000],[0.095188475,0.003265824,0.006914785,0.075458121,0.000000000],[0.070119471,0.067419472,0.066555314,0.065981545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.204221895,0.787432499,0.007952872,0.000392734] | 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 [[0.043308504,0.045113071,0.005934577,0.106583667,0.000000000],[0.035053997,0.100290019,0.001276476,0.125755463,0.000000000],[0.121086490,0.001276476,0.049794915,0.126793157,0.000000000],[0.045010180,0.047624281,0.001276476,0.143822251,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G72 - U73 cSH Insertion | Location [1] | Length Distribution [0.790123457,0.009876543,0.197925926,0.001975309,0.000098765] | Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000]// Insertion in Hairpin after nucleotide 4, position 1Sequences of instances from HL_86769.4:
> HL_86769.4 4P5J A 69 U 76 AGGGUCAU > HL_86769.4 6MJ0 A 89 U 96 AGGGUCAU > HL_86769.4 1ET4 C 219 G 226 CACCUCAG > HL_86769.4 4WF9 G 67 U 74 GACGAUAU > HL_86769.4 3AMU G 30 C 40 GGCUCAUAACC