| 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 3 I | 8 3 4 | 9 2 I | 10 2 5 | 11 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_81327.2_Instance_1 HL_81327.2_HL_4V90_032_C13_G22 | C | A | G | CCGGU | A | G | ||||||||||
| HL_81327.2_Sequence_1 HL_81327.2_HL_4V90_032_C13_G22 | C | A | G | CCGGU | A | G | true | 81 | 0 | 0 | 3.00 | |||||
| HL_81327.2_Instance_2 HL_81327.2_HL_6JXM_001_C13_G21 | C | A | G | UGGU | A | G | ||||||||||
| HL_81327.2_Sequence_2 HL_81327.2_HL_6JXM_001_C13_G21 | C | A | G | UGGU | A | G | true | 100 | 0 | 0 | 0.00 | |||||
| HL_81327.2_Instance_3 HL_81327.2_HL_4V9K_033_C13_G22 | C | A | G | UUGGUU | A | G | ||||||||||
| HL_81327.2_Sequence_3 HL_81327.2_HL_4V9K_033_C13_G22 | C | A | G | UUGGUU | A | G | true | 89 | 0 | 0 | 1.64 |
1 5 cWW 2 3 s35 2 4 cWS 2 5 s55JAR3D SCFG/MRF model for HL_81327.2:
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 [5] // Initial node C13 - G22 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[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 [5] // Basepair C13 - G22 cWW BasepairNode | Deletion Probability [0.0000000000000001] | Pair Probability [[0.282754783,0.190768767,0.201601816,0.194868032,0.000000000],[0.015242381,0.012431933,0.002073965,0.012616740,0.000000000],[0.020610252,0.002073965,0.026415638,0.009865379,0.000000000],[0.007404147,0.007810443,0.006180879,0.007280880,0.000000000],[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 [0.000000000,0.000000000,0.000000000,0.005372012,0.327692721,0.333064733,0.327961322,0.005640612,0.000268601] | Right Letter Distribution [0.029411765,0.147058824,0.382352941,0.441176471,0.000000000] | Left Index [2] | Right Index [4] // Basepair A14 - A21 cWS HairpinNode | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node G15:G15 Interaction | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[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 G15Sequences of instances from HL_81327.2:
> HL_81327.2 HL_4V90_032 C 13 G 22 CAGCCGGUAG > HL_81327.2 HL_6JXM_001 C 13 G 21 CAGUGGUAG > HL_81327.2 HL_4V9K_033 C 13 G 22 CAGUUGGUUAG