| 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 4 3 | 7 4 I | 8 5 4 | 9 4 I | 10 4 5 | 11 3 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_43613.3_Instance_1 HL_43613.3_HL_5J7L_178_U1777_A1787 | U | U | U | AUU | A | A | A | A | A | |||||||||||
| HL_43613.3_Sequence_1 HL_43613.3_HL_5J7L_178_U_1777_A_1787 | U | U | U | AUU | A | A | A | A | A | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_43613.3_Instance_2 HL_43613.3_HL_4Y4O_147_U1777_A1787 | U | U | U | ACC | A | A | A | A | A | |||||||||||
| HL_43613.3_Sequence_2 HL_43613.3_HL_4Y4O_147_U_1777_A_1787 | U | U | U | ACC | A | A | A | A | A | true | 95 | 0 | 0 | 0.90 | ||||||
| HL_43613.3_Instance_3 HL_43613.3_HL_4V9F_047_U1833_A1843 | U | C | U | AGU | A | A | C | A | A | |||||||||||
| HL_43613.3_Sequence_3 HL_43613.3_HL_4V9F_047_U_1833_A_1843 | U | C | U | AGU | A | A | C | A | A | true | 92 | 0 | 0 | 1.46 | ||||||
| HL_43613.3_Instance_4 HL_43613.3_HL_5TBW_046_U2135_A2145 | U | C | U | AAU | U | A | A | A | A | |||||||||||
| HL_43613.3_Sequence_4 HL_43613.3_HL_5TBW_046_U_2135_A_2145 | U | C | U | AAU | U | A | A | A | A | true | 88 | 0 | 0 | 2.29 | ||||||
| HL_43613.3_Instance_5 HL_43613.3_HL_4WF9_043_U1804_A1814 | U | U | U | AUC | A | A | A | A | A | |||||||||||
| HL_43613.3_Sequence_5 HL_43613.3_HL_4WF9_043_U_1804_A_1814 | U | U | U | AUC | A | A | A | A | A | true | 98 | 0 | 0 | 0.45 |
1 2 s35 1 7 cWW 2 5 s35 2 6 tWH 2 7 s55 3 4 s53 3 5 tWH 6 7 s35 5 3 6BPh 4 3 7BRJAR3D SCFG/MRF model for HL_43613.3:
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 U1777 - A1787 from junction BasepairNode | Deletion Probability [0.0000001230289089] | Pair Probability [[0.008776211,0.017043482,0.009626941,0.190711986,0.000000000],[0.021414125,0.009550770,0.191353636,0.010729332,0.000000000],[0.009645717,0.188904676,0.001985843,0.022389043,0.000000000],[0.246203326,0.010078147,0.051771850,0.009814914,0.000000000],[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 [0.009799118,0.979911808,0.009799118,0.000489956] | Right Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Left Index [1] | Right Index [7] // Basepair U1777 - A1787 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.020410803,0.003943665,0.035057120,0.003943665,0.000000000],[0.109609892,0.292216935,0.003943665,0.003943665,0.000000000],[0.003943665,0.009440547,0.029747413,0.021082024,0.000000000],[0.344212553,0.003943665,0.020785752,0.093774971,0.000000000],[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 [2] | Right Index [6] // Basepair U1778 - A1785 tWH BasepairNode | Deletion Probability [0.0000000000030757] | Pair Probability [[0.031622574,0.000999732,0.004692174,0.000999732,0.000000000],[0.070375380,0.080559320,0.000999732,0.000999732,0.000000000],[0.006998126,0.002396424,0.007602880,0.004446465,0.000000000],[0.770660471,0.000999732,0.005800327,0.009847197,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.000000000,0.000000000,0.009799118,0.979911808,0.009799118,0.000489956] | Left Letter Distribution [0.382352941,0.205882353,0.088235294,0.323529412,0.000000000] | 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 U1779 - A1784 tWH HairpinNode | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A1783:A1783 Interaction | Interacting Bases [1,1] | Pair Probability [[0.759259259,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.018518519,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.018518519,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.203703704,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1783Sequences of instances from HL_43613.3:
> HL_43613.3 HL_5J7L_178 U 1777 A 1787 UUUAUUAAAAA > HL_43613.3 HL_4Y4O_147 U 1777 A 1787 UUUACCAAAAA > HL_43613.3 HL_4V9F_047 U 1833 A 1843 UCUAGUAACAA > HL_43613.3 HL_5TBW_046 U 2135 A 2145 UCUAAUUAAAA > HL_43613.3 HL_4WF9_043 U 1804 A 1814 UUUAUCAAAAA