| 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 3 3 | 7 3 I | 8 3 4 | 9 3 I | 10 3 5 | 11 3 I | 12 3 6 | 13 3 I | 14 3 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_49873.1_Instance_1 HL_49873.1_HL_3ZGZ_001_G12_C23 | G | G | A | A | UCGGU | A | G | A | C | |||||||||||||
| HL_49873.1_Sequence_1 HL_49873.1_HL_3ZGZ_001_G12_C23 | G | G | A | A | UCGGU | A | G | A | C | true | 94 | 0 | 0 | 1.10 | ||||||||
| HL_49873.1_Instance_2 HL_49873.1_HL_2BTE_001_G12_C23 | G | G | A | A | UGGGU | A | G | A | C | |||||||||||||
| HL_49873.1_Sequence_2 HL_49873.1_HL_2BTE_001_G12_C23 | G | G | A | A | UGGGU | A | G | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_49873.1_Instance_3 HL_49873.1_HL_5AH5_005_G12_C23 | G | A | A | A | UCGGU | A | A | A | C | |||||||||||||
| HL_49873.1_Sequence_3 HL_49873.1_HL_5AH5_005_G12_C23 | G | A | A | A | UCGGU | A | A | A | C | true | 84 | 0 | 0 | 2.78 |
1 2 s35 1 8 cWW 2 3 s35 2 6 cWS 2 7 tSH 2 8 s55 3 4 s35 3 5 cWS 5 6 s35 7 8 s35 8 7 7BPh 7 2 6BR 2 6 6BRJAR3D SCFG/MRF model for HL_49873.1:
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 G12 - C23 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.003786762,0.055205280,0.004312111,0.078321123,0.000000000],[0.006651550,0.025993100,0.078984774,0.005167961,0.000000000],[0.004264222,0.598090606,0.000812806,0.010412629,0.000000000],[0.077318762,0.037546914,0.009127139,0.004004261,0.000000000],[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 G12 - C23 cWW HairpinNode | Num Bases [6] | Left Index [2] | Right Index [7] | Norm Constant [0.285362311623589] // Hairpin node G13:A22 Interaction | Interacting Bases [2,4] | Pair Probability [[0.246892522,0.200307206,0.211681907,0.204611433,0.000000000],[0.016004500,0.013053530,0.002177663,0.013247577,0.000000000],[0.021640765,0.002177663,0.027736420,0.010358648,0.000000000],[0.007774354,0.008200965,0.006489923,0.007644924,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction A14 - A20A cWS Interaction | Interacting Bases [1,5] | Pair Probability [[0.104754894,0.110429214,0.092008273,0.210537532,0.000000000],[0.025184133,0.022941046,0.002489079,0.022167953,0.000000000],[0.151236163,0.002489079,0.204982108,0.011956389,0.000000000],[0.010024486,0.010464037,0.008480656,0.009854957,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G13 - G21 cWS Interaction | Interacting Bases [1,6] | Pair Probability [[0.104355937,0.045189764,0.001019127,0.005611930,0.000000000],[0.093142996,0.061480989,0.001019127,0.001019127,0.000000000],[0.285637838,0.002759710,0.015709346,0.197413341,0.000000000],[0.093049013,0.090553501,0.001019127,0.001019127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G13 - A22 tSH Interaction | Interacting Bases [3,3] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A15 Insertion | Location [3] | Length Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.029411765,0.147058824,0.441176471,0.382352941,0.000000000]// Insertion in Hairpin after nucleotide 4, position 3Sequences of instances from HL_49873.1:
> HL_49873.1 HL_3ZGZ_001 G 12 C 23 GGAAUCGGUAGAC > HL_49873.1 HL_2BTE_001 G 12 C 23 GGAAUGGGUAGAC > HL_49873.1 HL_5AH5_005 G 12 C 23 GAAAUCGGUAAAC