| 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 7 2 | 5 7 I | 6 8 3 | 7 7 I | 8 7 4 | 9 6 I | 10 5 5 | 11 4 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_90642.4_Instance_1 HL_90642.4_HL_4Y4O_153_G2027_C2036 | G | U | G | AAG | A | U | G | C | ||||||||||||
| HL_90642.4_Sequence_1 HL_90642.4_HL_4Y4O_153_G_2027_C_2036 | G | U | G | AAG | A | U | G | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_90642.4_Instance_2 HL_90642.4_HL_7A0S_049_G2010_C2019 | G | U | A | AAG | A | U | G | C | ||||||||||||
| HL_90642.4_Sequence_2 HL_90642.4_HL_7A0S_049_G_2010_C_2019 | G | U | A | AAG | A | U | G | C | true | 92 | 0 | 0 | 1.34 | |||||||
| HL_90642.4_Instance_3 HL_90642.4_HL_4WF9_047_G2054_C2063 | G | U | G | AAG | A | U | G | C | ||||||||||||
| HL_90642.4_Sequence_3 HL_90642.4_HL_4WF9_047_G_2054_C_2063 | G | U | G | AAG | A | U | G | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_90642.4_Instance_4 HL_90642.4_HL_4V9F_052_G2068_C2077 | G | U | G | CGG | A | G | U | C | ||||||||||||
| HL_90642.4_Sequence_4 HL_90642.4_HL_4V9F_052_G_2068_C_2077 | G | U | G | CGG | A | G | U | C | true | 82 | 0 | 0 | 3.09 | |||||||
| HL_90642.4_Instance_5 HL_90642.4_HL_5TBW_051_G2369_C2378 | G | G | G | AAC | G | G | G | C | ||||||||||||
| HL_90642.4_Sequence_5 HL_90642.4_HL_5TBW_051_G_2369_C_2378 | G | G | G | AAC | G | G | G | C | true | 87 | 0 | 0 | 2.21 |
1 2 s35 1 7 cWW 2 3 s35 2 4 tWH 3 4 s55 4 7 s35 5 6 s35 3 4 6BPh 7 6 7BPhJAR3D SCFG/MRF model for HL_90642.4:
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 [7] // Initial node G2027 - C2036 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003714633,0.054153751,0.004229975,0.076829292,0.000000000],[0.006524853,0.025497993,0.077480302,0.005069524,0.000000000],[0.004182999,0.605746023,0.000797324,0.010214294,0.000000000],[0.075846024,0.036831735,0.008953288,0.003927989,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair G2027 - C2036 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.071428571,0.642857143,0.214285714,0.000000000] | Position [2] | Left Index [2] | Right Index [6] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [5] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.071428571,0.357142857,0.500000000,0.000000000] | Position [2] | Left Index [2] | Right Index [5] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [4] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000000000030757] | Pair Probability [[0.047849049,0.004133874,0.032523626,0.004133874,0.000000000],[0.040609064,0.265754232,0.004133874,0.004133874,0.000000000],[0.004133874,0.009142645,0.124559648,0.023473691,0.000000000],[0.367884526,0.004133874,0.025775841,0.037624437,0.000000000],[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 [0.000000000,0.000000000,0.009799118,0.979911808,0.009799118,0.000489956] | Right Letter Distribution [0.500000000,0.147058824,0.323529412,0.029411765,0.000000000] | Left Index [2] | Right Index [4] // Basepair U2028 - A2033 tWH HairpinNode | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node G2029:G2029 Interaction | Interacting Bases [1,1] | Pair Probability [[0.202702703,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.013513514,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.770270270,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.013513514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2029Sequences of instances from HL_90642.4:
> HL_90642.4 HL_4Y4O_153 G 2027 C 2036 GUGAAGAUGC > HL_90642.4 HL_7A0S_049 G 2010 C 2019 GUAAAGAUGC > HL_90642.4 HL_4WF9_047 G 2054 C 2063 GUGAAGAUGC > HL_90642.4 HL_4V9F_052 G 2068 C 2077 GUGCGGAGUC > HL_90642.4 HL_5TBW_051 G 2369 C 2378 GGGAACGGGC