| 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 11 3 | 7 11 I | 8 12 4 | 9 11 I | 10 11 5 | 11 10 I | 12 9 6 | 13 8 I | 14 7 7 | 15 6 I | 16 5 8 | 17 2 I | 18 2 9 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_75091.3_Instance_1 HL_75091.3_HL_5X2G_002_G54_C64 | G | U | U | U | G | C | G | G | G | A | C | |||||||||||||
| HL_75091.3_Sequence_1 HL_75091.3_HL_5X2G_002_G54_C64 | G | U | U | U | G | C | G | G | G | A | C | true | 85 | 0 | 0 | 2.20 | ||||||||
| HL_75091.3_Instance_2 HL_75091.3_HL_5J7L_134_U59_G68 | U | G | C | U | A | A | U | C | U | G | ||||||||||||||
| HL_75091.3_Sequence_2 HL_75091.3_HL_5J7L_134_U59_G68 | U | G | C | U | A | A | U | C | U | G | true | 89 | 0 | 0 | 1.57 | |||||||||
| HL_75091.3_Instance_3 HL_75091.3_HL_2JLT_001_G5_C14 | G | G | U | C | C | C | A | G | A | C | ||||||||||||||
| HL_75091.3_Sequence_3 HL_75091.3_HL_2JLT_001_G5_C14 | G | G | U | C | C | C | A | G | A | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 9 cWW 3 5 cSH 4 5 s35 5 6 s35 6 7 s35 7 8 s35 8 9 s35JAR3D SCFG/MRF model for HL_75091.3:
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 [9] // Initial node G54 - C64 from junction BasepairNode | Deletion Probability [0.0000038011627649] | Pair Probability [[0.010138447,0.017999390,0.012030637,0.145215023,0.000000000],[0.111154629,0.015527922,0.148017973,0.014062841,0.000000000],[0.012052549,0.169605488,0.002470680,0.022513399,0.000000000],[0.159661783,0.013947978,0.134332446,0.011268815,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [1] | Right Index [9] // Basepair G54 - C64 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.500000000,0.300000000,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // Fixed node on left InitialNode | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.100000000,0.300000000,0.100000000,0.500000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.300000000,0.300000000,0.000000000] | Position [2] | Left Index [3] | Right Index [8] // 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 [0.993970181,0.005999820,0.000029999] | 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 [0.100000000,0.300000000,0.500000000,0.100000000,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // 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 [0.993970181,0.005999820,0.000029999] | 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 FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.300000000,0.300000000,0.000000000] | 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 [0.993970181,0.005999820,0.000029999] | 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 [0.0000234451146992] | Pair Probability [[0.095660449,0.095928050,0.006544771,0.050788838,0.000000000],[0.095415297,0.149051757,0.001058658,0.010350084,0.000000000],[0.011122316,0.001058658,0.092735258,0.086415640,0.000000000],[0.108354382,0.107776738,0.001058658,0.086680449,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // Basepair U57 - C59 cSH HairpinNode | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G58:G58 Interaction | Interacting Bases [1,1] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G58Sequences of instances from HL_75091.3:
> HL_75091.3 HL_5X2G_002 G 54 C 64 GUUUGCGGGAC > HL_75091.3 HL_5J7L_134 U 59 G 68 UGCUAAUCUG > HL_75091.3 HL_2JLT_001 G 5 C 14 GGUCCCAGAC