| 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 4 I | 12 4 6 | 13 4 I | 14 4 7 | 15 3 I | 16 3 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_31286.3_Instance_1 HL_31286.3_HL_5TPY_011_U28_G38 | U | U | U | G | G | G | G | A | A | A | G | |||||||||||||
| HL_31286.3_Sequence_1 HL_31286.3_HL_5TPY_011_U28_G38 | U | U | U | G | G | G | G | A | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_31286.3_Instance_2 HL_31286.3_HL_5TPY_008_U28_G38 | U | U | U | G | G | G | G | A | A | A | G | |||||||||||||
| HL_31286.3_Sequence_2 HL_31286.3_HL_5TPY_008_U28_G38 | U | U | U | G | G | G | G | A | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_31286.3_Instance_3 HL_31286.3_HL_5TPY_002_U28_G38 | U | U | U | G | G | G | G | A | A | A | G | |||||||||||||
| HL_31286.3_Sequence_3 HL_31286.3_HL_5TPY_002_U28_G38 | U | U | U | G | G | G | G | A | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_31286.3_Instance_4 HL_31286.3_HL_5TPY_005_U28_G38 | U | U | U | G | G | G | G | A | A | A | G | |||||||||||||
| HL_31286.3_Sequence_4 HL_31286.3_HL_5TPY_005_U28_G38 | U | U | U | G | G | G | G | A | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_31286.3_Instance_5 HL_31286.3_HL_6VMY_005_U333_A342 | U | C | U | G | C | G | A | G | G | A | ||||||||||||||
| HL_31286.3_Sequence_5 HL_31286.3_HL_6VMY_005_U333_A342 | U | C | U | G | C | G | A | G | G | A | true | 69 | 0 | 0 | 6.16 | |||||||||
| HL_31286.3_Instance_6 HL_31286.3_HL_4V83_139_A6160_U6169 | A | U | U | A | A | G | U | G | G | U | ||||||||||||||
| HL_31286.3_Sequence_6 HL_31286.3_HL_4V83_139_A_6160_U_6169 | A | U | U | A | A | G | U | G | G | U | true | 71 | 0 | 0 | 5.68 | |||||||||
| HL_31286.3_Instance_7 HL_31286.3_HL_3MJA_001_A6184_U6193 | A | U | U | A | G | G | U | A | G | U | ||||||||||||||
| HL_31286.3_Sequence_7 HL_31286.3_HL_3MJA_001_A_6184_U_6193 | A | U | U | A | G | G | U | A | G | U | true | 82 | 0 | 0 | 3.60 |
1 2 s35 1 9 cWW 2 7 s33 2 8 tWH 2 9 s55 3 4 s35 4 5 s35 5 6 s35 6 7 s35 7 8 s35 8 9 s35JAR3D SCFG/MRF model for HL_31286.3:
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 [9] // Initial node U28 - G38 from junction BasepairNode | Deletion Probability [0.0000011637255024] | Pair Probability [[0.009884709,0.016001571,0.011827262,0.121324816,0.000000000],[0.172573773,0.019173708,0.102780333,0.013059692,0.000000000],[0.011994903,0.100274326,0.002635269,0.025624353,0.000000000],[0.137525817,0.012412607,0.231003262,0.011903598,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.427699602,0.567912443,0.004186211,0.000201745] | Right Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Left Index [1] | Right Index [9] // Basepair U28 - G38 cWW BasepairNode | Deletion Probability [0.0000001232089072] | Pair Probability [[0.016649528,0.003684567,0.017293259,0.003684567,0.000000000],[0.037053177,0.296905697,0.034764767,0.003684567,0.000000000],[0.003684567,0.008832151,0.028020822,0.016387686,0.000000000],[0.405839888,0.003684567,0.083537816,0.036292374,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.007039775,0.985568462,0.007039775,0.000351989] | Left Letter Distribution [0.055555556,0.055555556,0.055555556,0.833333333,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair U29 - A36 tWH HairpinNode | Num Bases [5] | Left Index [3] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node G31:A35 Interaction | Interacting Bases [1,1] | Pair Probability [[0.277777778,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.611111111,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G31 Interaction | Interacting Bases [2,2] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.611111111,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G32 Interaction | Interacting Bases [3,3] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.833333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G33 Interaction | Interacting Bases [4,4] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.277777778,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G34 Interaction | Interacting Bases [5,5] | Pair Probability [[0.611111111,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.277777778,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A35Sequences of instances from HL_31286.3:
> HL_31286.3 HL_5TPY_011 U 28 G 38 UUUGGGGAAAG > HL_31286.3 HL_5TPY_008 U 28 G 38 UUUGGGGAAAG > HL_31286.3 HL_5TPY_002 U 28 G 38 UUUGGGGAAAG > HL_31286.3 HL_5TPY_005 U 28 G 38 UUUGGGGAAAG > HL_31286.3 HL_6VMY_005 U 333 A 342 UCUGCGAGGA > HL_31286.3 HL_4V83_139 A 6160 U 6169 AUUAAGUGGU > HL_31286.3 HL_3MJA_001 A 6184 U 6193 AUUAGGUAGU