| 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 6 3 | 7 6 I | 8 7 4 | 9 6 I | 10 6 5 | 11 5 I | 12 4 6 | 13 3 I | 14 3 7 | 15 2 I | 16 2 8 | 17 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_53760.2_Instance_1 HL_53760.2_HL_4Y4O_151_G1949_C1957 | G | G | U | A | A | G | U | U | C | |||||||||||||
| HL_53760.2_Sequence_1 HL_53760.2_HL_4Y4O_151_G_1949_C_1957 | G | G | U | A | A | G | U | U | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_53760.2_Instance_2 HL_53760.2_HL_5J7L_182_G1949_C1957 | G | G | U | A | A | G | U | U | C | |||||||||||||
| HL_53760.2_Sequence_2 HL_53760.2_HL_5J7L_182_G_1949_C_1957 | G | G | U | A | A | G | U | U | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_53760.2_Instance_3 HL_53760.2_HL_4WF9_046_G1976_C1984 | G | G | U | A | A | G | U | U | C | |||||||||||||
| HL_53760.2_Sequence_3 HL_53760.2_HL_4WF9_046_G_1976_C_1984 | G | G | U | A | A | G | U | U | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_53760.2_Instance_4 HL_53760.2_HL_7A0S_048_G1932_C1940 | G | G | U | A | A | G | U | U | C | |||||||||||||
| HL_53760.2_Sequence_4 HL_53760.2_HL_7A0S_048_G_1932_C_1940 | G | G | U | A | A | G | U | U | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_53760.2_Instance_5 HL_53760.2_HL_4V9F_051_C1990_G1998 | C | A | U | C | A | G | U | A | G | |||||||||||||
| HL_53760.2_Sequence_5 HL_53760.2_HL_4V9F_051_C_1990_G_1998 | C | A | U | C | A | G | U | A | G | true | 77 | 0 | 0 | 3.25 | ||||||||
| HL_53760.2_Instance_6 HL_53760.2_HL_5TBW_050_U2292_G2300 | U | C | U | A | A | U | U | A | G | |||||||||||||
| HL_53760.2_Sequence_6 HL_53760.2_HL_5TBW_050_U_2292_G_2300 | U | C | U | A | A | U | U | A | G | true | 76 | 0 | 0 | 3.42 | ||||||||
| HL_53760.2_Instance_7 HL_53760.2_HL_4R4V_003_G689_C697 | G | U | U | G | A | C | U | A | C | |||||||||||||
| HL_53760.2_Sequence_7 HL_53760.2_HL_4R4V_003_G689_C697 | G | U | U | G | A | C | U | A | C | true | 78 | 0 | 0 | 3.09 | ||||||||
| HL_53760.2_Instance_8 HL_53760.2_HL_4R4V_007_G689_C697 | G | U | U | G | A | C | U | A | C | |||||||||||||
| HL_53760.2_Sequence_8 HL_53760.2_HL_4R4V_007_G689_C697 | G | U | U | G | A | C | U | A | C | true | 78 | 0 | 0 | 3.09 | ||||||||
| HL_53760.2_Instance_9 HL_53760.2_HL_4V9F_049_C1916_G1923 | C | G | U | A | C | A | A | G | ||||||||||||||
| HL_53760.2_Sequence_9 HL_53760.2_HL_4V9F_049_C_1916_G_1923 | C | G | U | A | C | A | A | G | true | 62 | 0 | 0 | 5.32 | |||||||||
| HL_53760.2_Instance_10 HL_53760.2_HL_4V9F_038_G1557_C1564 | G | C | A | U | U | C | G | C | ||||||||||||||
| HL_53760.2_Sequence_10 HL_53760.2_HL_4V9F_038_G_1557_C_1564 | G | C | A | U | U | C | G | C | true | 42 | 0 | 0 | 8.23 |
1 2 s35 1 8 cWW 2 3 s35 2 6 s33 2 7 bif 3 5 tSH 4 5 s35 5 6 s35 6 7 s35 7 8 s35 3 6 6BPhJAR3D SCFG/MRF model for HL_53760.2:
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 [8] // Initial node G1949 - C1957 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009129477,0.017626462,0.010551722,0.170998231,0.000000000],[0.042911716,0.010588550,0.192647392,0.012666863,0.000000000],[0.010523640,0.240352930,0.002050257,0.023085440,0.000000000],[0.174339825,0.012774643,0.059941008,0.009811843,0.000000000],[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 [8] // Basepair G1949 - C1957 cWW BasepairNode | Deletion Probability [0.0000003525527566] | Pair Probability [[0.062029806,0.212148009,0.003700315,0.003700315,0.000000000],[0.142492471,0.023420514,0.029320149,0.003700315,0.000000000],[0.029320149,0.003700315,0.123744185,0.296682531,0.000000000],[0.054939984,0.003700315,0.003700315,0.003700315,0.000000000],[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 [0.202130295,0.793658657,0.004012881,0.000198167] | Right Letter Distribution [0.050000000,0.050000000,0.050000000,0.850000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair G1950 - U1956 bif FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.291666667,0.458333333,0.125000000,0.000000000] | Position [2] | Left Index [3] | 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 [3] | Right Index [5] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.040394532,0.036896519,0.000448597,0.025502196,0.000000000],[0.040550578,0.038154183,0.000448597,0.000448597,0.000000000],[0.041714457,0.000448597,0.002772552,0.037241903,0.000000000],[0.415154383,0.313543947,0.003140180,0.003140180,0.000000000],[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 [3] | Right Index [5] // Basepair U1951 - A1953 tSH HairpinNode | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A1952:A1952 Interaction | Interacting Bases [1,1] | Pair Probability [[0.541666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.208333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1952Sequences of instances from HL_53760.2:
> HL_53760.2 HL_4Y4O_151 G 1949 C 1957 GGUAAGUUC > HL_53760.2 HL_5J7L_182 G 1949 C 1957 GGUAAGUUC > HL_53760.2 HL_4WF9_046 G 1976 C 1984 GGUAAGUUC > HL_53760.2 HL_7A0S_048 G 1932 C 1940 GGUAAGUUC > HL_53760.2 HL_4V9F_051 C 1990 G 1998 CAUCAGUAG > HL_53760.2 HL_5TBW_050 U 2292 G 2300 UCUAAUUAG > HL_53760.2 HL_4R4V_003 G 689 C 697 GUUGACUAC > HL_53760.2 HL_4R4V_007 G 689 C 697 GUUGACUAC > HL_53760.2 HL_4V9F_049 C 1916 G 1923 CGUACAAG > HL_53760.2 HL_4V9F_038 G 1557 C 1564 GCAUUCGC