| 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 7 3 | 7 7 I | 8 8 4 | 9 8 I | 10 8 5 | 11 7 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_42733.3_Instance_1 HL_42733.3_HL_4V9F_043_C1705_G1713 | C | G | G | C | G | A | A | A | G | |||||||||||||
| HL_42733.3_Sequence_1 HL_42733.3_HL_4V9F_043_C_1705_G_1713 | C | G | G | C | G | A | A | A | G | true | 92 | 0 | 0 | 0.86 | ||||||||
| HL_42733.3_Instance_2 HL_42733.3_HL_5J7L_012_G462_C470 | G | U | U | A | A | U | A | C | C | |||||||||||||
| HL_42733.3_Sequence_2 HL_42733.3_HL_5J7L_012_G462_C470 | G | U | U | A | A | U | A | C | C | true | 96 | 0 | 0 | 0.50 | ||||||||
| HL_42733.3_Instance_3 HL_42733.3_HL_1QTQ_002_A931_U939 | A | U | U | C | U | G | A | U | U | |||||||||||||
| HL_42733.3_Sequence_3 HL_42733.3_HL_1QTQ_002_A931_U939 | A | U | U | C | U | G | A | U | U | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 8 cWW 2 3 s35 3 6 tSH 4 5 s35 5 6 s35 6 7 s35 7 8 s35JAR3D SCFG/MRF model for HL_42733.3:
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 [8] // Initial node C1705 - G1713 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009425327,0.019602391,0.010550535,0.209161741,0.000000000],[0.018119710,0.009519290,0.209803050,0.012356683,0.000000000],[0.010544174,0.210633518,0.002053265,0.034146945,0.000000000],[0.196782200,0.012577586,0.024177876,0.010545706,0.000000000],[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 [1] | Right Index [8] // Basepair C1705 - G1713 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.300000000,0.500000000,0.000000000] | Position [1] | Left Index [2] | Right Index [7] // Fixed node on left InitialNode | 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 [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 [0.300000000,0.300000000,0.100000000,0.300000000,0.000000000] | 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 BasepairNode | Deletion Probability [0.0000001200211660] | Pair Probability [[0.109940024,0.108141163,0.001268721,0.006109495,0.000000000],[0.110554335,0.109778424,0.001268721,0.001268721,0.000000000],[0.132160344,0.001268721,0.007016842,0.106513064,0.000000000],[0.188046810,0.114127171,0.001268721,0.001268721,0.000000000],[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 [0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.300000000,0.100000000,0.300000000,0.300000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair G1707 - A1711 tSH HairpinNode | Num Bases [2] | Left Index [4] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node C1708:G1709 Interaction | Interacting Bases [1,1] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[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 C1708 Interaction | Interacting Bases [2,2] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1709Sequences of instances from HL_42733.3:
> HL_42733.3 HL_4V9F_043 C 1705 G 1713 CGGCGAAAG > HL_42733.3 HL_5J7L_012 G 462 C 470 GUUAAUACC > HL_42733.3 HL_1QTQ_002 A 931 U 939 AUUCUGAUU