| 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 5 3 | 7 5 I | 8 6 4 | 9 6 I | 10 6 5 | 11 6 I | 12 6 6 | 13 6 I | 14 6 7 | 15 5 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_32458.2_Instance_1 HL_32458.2_HL_4V7M_040_G51_C61 | G | G | U | U | CG | A | A | U | C | C | ||||||||||||||
| HL_32458.2_Sequence_1 HL_32458.2_HL_4V7M_040_G51_C61 | G | G | U | U | CG | A | A | U | C | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| HL_32458.2_Instance_2 HL_32458.2_HL_4V9I_040_C52_G62 | C | A | A | C | UC | U | A | C | C | G | ||||||||||||||
| HL_32458.2_Sequence_2 HL_32458.2_HL_4V9I_040_C52_G62 | C | A | A | C | UC | U | A | C | C | G | true | 77 | 0 | 0 | 4.25 | |||||||||
| HL_32458.2_Instance_3 HL_32458.2_HL_1P6V_002_G44_C54 | G | G | U | U | CG | A | U | U | C | C | ||||||||||||||
| HL_32458.2_Sequence_3 HL_32458.2_HL_1P6V_002_G44_C54 | G | G | U | U | CG | A | U | U | C | C | true | 97 | 0 | 0 | 0.51 |
1 2 s35 1 9 cWW 2 3 s35 2 9 s55 3 4 s33 3 8 cWW 5 8 s35 6 7 s35 8 9 s35JAR3D SCFG/MRF model for HL_32458.2:
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 [9] // Initial node G51 - C61 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009574124,0.019028436,0.010936653,0.198530575,0.000000000],[0.017980846,0.009507606,0.212727929,0.013322270,0.000000000],[0.010896029,0.224384255,0.002069153,0.025416337,0.000000000],[0.197680266,0.013488440,0.024325847,0.010131233,0.000000000],[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 [9] // Basepair G51 - C61 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.500000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // 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 [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.017453322,0.071471459,0.043739747,0.018972641,0.000000000],[0.014153304,0.011272015,0.022327095,0.297988175,0.000000000],[0.041397404,0.023173368,0.003511559,0.017030336,0.000000000],[0.017821153,0.370573398,0.015591167,0.013523856,0.000000000],[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 [8] // Basepair U53 - C60 cWW HairpinNode | Num Bases [4] | Left Index [4] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node U54:U59 Interaction | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U54 Interaction | Interacting Bases [2,2] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A57 Interaction | Interacting Bases [3,3] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A58 Interaction | Interacting Bases [4,4] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U59 Insertion | Location [1] | Length Distribution [0.000000000,0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.062500000,0.437500000,0.312500000,0.187500000,0.000000000]// Insertion in Hairpin after nucleotide 4, position 1Sequences of instances from HL_32458.2:
> HL_32458.2 HL_4V7M_040 G 51 C 61 GGUUCGAAUCC > HL_32458.2 HL_4V9I_040 C 52 G 62 CAACUCUACCG > HL_32458.2 HL_1P6V_002 G 44 C 54 GGUUCGAUUCC