| 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 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_16398.2_Instance_1 HL_16398.2,HL_8SYK_003,G57_C69 | G | A | A | G | A | AUACG | A | C | C | |||||||||||||
| HL_16398.2_Sequence_1 HL_16398.28SYK_G57_C69 | G | A | A | G | A | AUACG | A | C | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_16398.2_Instance_2 HL_16398.2,HL_3EGZ_001,G12_C24 | G | A | A | G | A | AUACG | A | C | C | |||||||||||||
| HL_16398.2_Sequence_2 HL_16398.23EGZ_G12_C24 | G | A | A | G | A | AUACG | A | C | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_16398.2_Instance_3 HL_16398.2,HL_1EC6_001,G4_C17 | G | A | C | C | U | A | GAUCA | C | C | C | ||||||||||||
| HL_16398.2_Sequence_3 HL_16398.21EC6_G4_C17 | G | A | C | C | U | A | GAUCA | C | C | C | true | 83 | 0 | 0 | 2.89 |
1 2 s35 1 8 cWW 2 3 s35 2 7 cWW 3 4 s35 4 5 s35 6 7 s35 7 8 s35JAR3D SCFG/MRF model for HL_16398.2:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [8] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009639190,0.020074982,0.010976465,0.199366183,0.000000000],[0.016931500,0.009452194,0.201055505,0.013155030,0.000000000],[0.010854565,0.236025807,0.002068996,0.026505317,0.000000000],[0.196814677,0.013653651,0.023233104,0.010192834,0.000000000],[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 G57 - C69 cWW BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.013687287,0.323661033,0.011945983,0.031760850,0.000000000],[0.011997832,0.011498556,0.024103074,0.011871196,0.000000000],[0.011665483,0.028578023,0.002945348,0.269522201,0.000000000],[0.025278430,0.013026444,0.012457902,0.196000356,0.000000000],[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 [7] // Basepair A58 - C68 cWW HairpinNode | Num Bases [4] | Left Index [3] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node A59:A67 Interaction | Interacting Bases [1,1] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A59 Interaction | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[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 G60 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 A61 Interaction | Interacting Bases [4,4] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A67 Insertion | Location [2] | Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 4, position 2 Insertion | Location [3] | Length Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.382352941,0.205882353,0.205882353,0.205882353,0.000000000]// Insertion in Hairpin after nucleotide 5, position 3Sequences of instances from HL_16398.2:
> HL_16398.2 8SYK G 57 C 69 GAAGAAUACGACC > HL_16398.2 3EGZ G 12 C 24 GAAGAAUACGACC > HL_16398.2 1EC6 G 4 C 17 GACCUAGAUCACCC