| 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 9 3 | 7 9 I | 8 10 4 | 9 9 I | 10 9 5 | 11 8 I | 12 7 6 | 13 6 I | 14 5 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_20167.2_Instance_1 HL_20167.2,HL_7A0S_048,G1932_C1940 | G | G | U | A | A | G | U | U | C | |||||||||||||
| HL_20167.2_Sequence_1 HL_20167.27A0S_G_1932_C_1940 | G | G | U | A | A | G | U | U | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_20167.2_Instance_2 HL_20167.2,HL_9DFE_047,G1949_C1957 | G | G | U | A | A | G | U | U | C | |||||||||||||
| HL_20167.2_Sequence_2 HL_20167.29DFE_G_1949_C_1957 | G | G | U | A | A | G | U | U | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_20167.2_Instance_3 HL_20167.2,HL_4WF9_046,G1976_C1984 | G | G | U | A | A | G | U | U | C | |||||||||||||
| HL_20167.2_Sequence_3 HL_20167.24WF9_G_1976_C_1984 | G | G | U | A | A | G | U | U | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_20167.2_Instance_4 HL_20167.2,HL_5J7L_182,G1949_C1957 | G | G | U | A | A | G | U | U | C | |||||||||||||
| HL_20167.2_Sequence_4 HL_20167.25J7L_G_1949_C_1957 | G | G | U | A | A | G | U | U | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_20167.2_Instance_5 HL_20167.2,HL_4V9F_051,C1990_G1998 | C | A | U | C | A | G | U | A | G | |||||||||||||
| HL_20167.2_Sequence_5 HL_20167.24V9F_C_1990_G_1998 | C | A | U | C | A | G | U | A | G | true | 77 | 0 | 0 | 3.14 | ||||||||
| HL_20167.2_Instance_6 HL_20167.2,HL_8CRE_048,U2270_G2278 | U | C | U | A | A | U | U | A | G | |||||||||||||
| HL_20167.2_Sequence_6 HL_20167.28CRE_U_2270_G_2278 | U | C | U | A | A | U | U | A | G | true | 78 | 0 | 0 | 2.90 | ||||||||
| HL_20167.2_Instance_7 HL_20167.2,HL_8P9A_161,U2292_G2300 | U | C | U | A | A | U | U | A | G | |||||||||||||
| HL_20167.2_Sequence_7 HL_20167.28P9A_U_2292_G_2300 | U | C | U | A | A | U | U | A | G | true | 78 | 0 | 0 | 2.90 | ||||||||
| HL_20167.2_Instance_8 HL_20167.2,HL_1U9S_003,G181_C189 | G | G | U | A | A | G | A | G | C | |||||||||||||
| HL_20167.2_Sequence_8 HL_20167.21U9S_G181_C189 | G | G | U | A | A | G | A | G | C | true | 69 | 0 | 0 | 4.17 | ||||||||
| HL_20167.2_Instance_9 HL_20167.2,HL_3CUL_003,G69_C77 | G | U | U | C | G | A | A | U | C | |||||||||||||
| HL_20167.2_Sequence_9 HL_20167.23CUL_G69_C77 | G | U | U | C | G | A | A | U | C | true | 45 | 0 | 0 | 7.41 | ||||||||
| HL_20167.2_Instance_10 HL_20167.2,HL_4WF9_039,A1673_U1681 | A | U | G | A | G | A | A | U | U | |||||||||||||
| HL_20167.2_Sequence_10 HL_20167.24WF9_A_1673_U_1681 | A | U | G | A | G | A | A | U | U | true | 52 | 0 | 0 | 6.47 |
1 2 s35 1 8 cWW 2 3 s35 2 6 s33 3 5 tSH 4 5 s35 6 7 s35 7 8 s35 3 6 6BPhJAR3D SCFG/MRF model for HL_20167.2:
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 [8] // Initial node BasepairNode | Deletion Probability [0.0000141488146644] | Pair Probability [[0.009246203,0.017498623,0.010750568,0.165371436,0.000000000],[0.069124087,0.012282993,0.167284515,0.012603653,0.000000000],[0.010749677,0.214738733,0.002158587,0.024722486,0.000000000],[0.163407812,0.012647864,0.097164932,0.010247830,0.000000000],[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 [0.895351728,0.103902560,0.000720855,0.000024857] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [1] | Right Index [8] // Basepair G1932 - C1940 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.208333333,0.458333333,0.208333333,0.000000000] | Position [1] | Left Index [2] | Right Index [7] // Fixed node on left for 7A0S|1|X|G|1933 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 [7] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.041666667,0.041666667,0.541666667,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // Fixed node on right for 7A0S|1|X|U|1938 InitialNode | Left Length Distribution [1.000000000] | 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 [0.150000000,0.050000000,0.050000000,0.750000000,0.000000000] | Left Index [3] | Right Index [6] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.208333333,0.041666667,0.541666667,0.208333333,0.000000000] | Position [2] | Left Index [3] | Right Index [6] // Fixed node on right for 7A0S|1|X|G|1937 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.895351728,0.103902560,0.000720855,0.000024857] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [3] | Right Index [5] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.042036586,0.038396378,0.000466833,0.002296447,0.000000000],[0.042198976,0.039705166,0.000466833,0.000466833,0.000000000],[0.043410166,0.000466833,0.023062641,0.038755802,0.000000000],[0.399510253,0.302047212,0.023445213,0.003267830,0.000000000],[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 U1934 - A1936 tSH HairpinNode | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A1935:A1935 Interaction | Interacting Bases [1,1] | Pair Probability [[0.708333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.208333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1935Sequences of instances from HL_20167.2:
> HL_20167.2 7A0S G 1932 C 1940 GGUAAGUUC > HL_20167.2 9DFE G 1949 C 1957 GGUAAGUUC > HL_20167.2 4WF9 G 1976 C 1984 GGUAAGUUC > HL_20167.2 5J7L G 1949 C 1957 GGUAAGUUC > HL_20167.2 4V9F C 1990 G 1998 CAUCAGUAG > HL_20167.2 8CRE U 2270 G 2278 UCUAAUUAG > HL_20167.2 8P9A U 2292 G 2300 UCUAAUUAG > HL_20167.2 1U9S G 181 C 189 GGUAAGAGC > HL_20167.2 3CUL G 69 C 77 GUUCGAAUC > HL_20167.2 4WF9 A 1673 U 1681 AUGAGAAUU