| 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 4 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_43610.4_Instance_1 HL_43610.4_HL_4ANG_005_G7_C15 | G | G | A | G | A | C | C | |||||||||||||
| HL_43610.4_Sequence_1 HL_43610.4_HL_4ANG_005_G7_C15 | G | G | A | G | A | C | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_43610.4_Instance_2 HL_43610.4_HL_4ANG_001_G7_C15 | G | G | A | G | A | C | C | |||||||||||||
| HL_43610.4_Sequence_2 HL_43610.4_HL_4ANG_001_G7_C15 | G | G | A | G | A | C | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_43610.4_Instance_3 HL_43610.4_HL_4V7M_038_C12_G22 | C | A | A | G | CGGU | A | A | G | ||||||||||||
| HL_43610.4_Sequence_3 HL_43610.4_HL_4V7M_038_C12_G22 | C | A | A | G | CGGU | A | A | G | true | 52 | 0 | 0 | 7.39 |
1 2 s35 1 7 cWW 2 3 s35 2 6 cWW 3 4 s33 3 6 s55 6 7 s35 4 4 2BPh 6 5 7BRJAR3D SCFG/MRF model for HL_43610.4:
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 G7 - C15 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 [7] // Basepair G7 - C15 cWW BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.060462342,0.047083524,0.005148803,0.093518014,0.000000000],[0.007942171,0.022169016,0.094310436,0.006170717,0.000000000],[0.005091623,0.504676282,0.000970518,0.012433024,0.000000000],[0.092321163,0.032023042,0.010898106,0.004781220,0.000000000],[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 [2] | Right Index [6] // Basepair G8 - C14 cWW HairpinNode | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [0.999999999999999] // Hairpin node A9:A13 Interaction | Interacting Bases [1,1] | 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 A9 Interaction | Interacting Bases [2,2] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.021739130,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.934782609,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.021739130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G10 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 A13 Insertion | Location [2] | Length Distribution [0.651642683,0.010860711,0.000543036,0.005430356,0.325821341,0.005430356,0.000271518] | Letter Distribution [0.083333333,0.250000000,0.416666667,0.250000000,0.000000000]// Insertion in Hairpin after nucleotide 4, position 2Sequences of instances from HL_43610.4:
> HL_43610.4 HL_4ANG_005 G 7 C 15 GGAGACC > HL_43610.4 HL_4ANG_001 G 7 C 15 GGAGACC > HL_43610.4 HL_4V7M_038 C 12 G 22 CAAGCGGUAAG