| 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_78197.1_Instance_1 HL_78197.1,HL_6UFG_003,G69_C76 | G | G | U | U | G | G | C | C | ||||||||||||||
| HL_78197.1_Sequence_1 HL_78197.16UFG_G69_C76 | G | G | U | U | G | G | C | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| HL_78197.1_Instance_2 HL_78197.1,HL_6UFM_006,G80_C87 | G | G | U | G | A | G | C | C | ||||||||||||||
| HL_78197.1_Sequence_2 HL_78197.16UFM_G80_C87 | G | G | U | G | A | G | C | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| HL_78197.1_Instance_3 HL_78197.1,HL_6UFG_001,G13_C20 | G | C | G | A | U | C | A | C | ||||||||||||||
| HL_78197.1_Sequence_3 HL_78197.16UFG_G13_C20 | G | C | G | A | U | C | A | C | true | 79 | 0 | 0 | 2.21 | |||||||||
| HL_78197.1_Instance_4 HL_78197.1,HL_5ZQ8_002,C744_G753 | C | G | U | UG | A | A | A | A | G | |||||||||||||
| HL_78197.1_Sequence_4 HL_78197.15ZQ8_C744_G753 | C | G | U | UG | A | A | A | A | G | true | 67 | 0 | 0 | 3.44 | ||||||||
| HL_78197.1_Instance_5 HL_78197.1,HL_9BZC_002,U54_A61 | U | U | A | U | C | U | U | A | ||||||||||||||
| HL_78197.1_Sequence_5 HL_78197.19BZC_U54_A61 | U | U | A | U | C | U | U | A | true | 73 | 0 | 0 | 2.82 |
1 2 s33 1 8 cWW 2 3 s53 4 5 s35 5 6 s35 6 7 s35 7 8 s35JAR3D SCFG/MRF model for HL_78197.1:
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 [0.0000244705618206] | Pair Probability [[0.009281415,0.018546810,0.010515868,0.194105568,0.000000000],[0.018187636,0.009360490,0.206731007,0.012567866,0.000000000],[0.010471797,0.227581684,0.002020930,0.024637229,0.000000000],[0.204202787,0.012633256,0.029229982,0.009925674,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair G69 - C76 cWW HairpinNode | Num Bases [6] | Left Index [2] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node G70:C75 Interaction | Interacting Bases [1,1] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.214285714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G70 Interaction | Interacting Bases [2,2] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U71 Interaction | Interacting Bases [3,3] | Pair Probability [[0.357142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.357142857,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U72 Interaction | Interacting Bases [4,4] | Pair Probability [[0.357142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.214285714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G73 Interaction | Interacting Bases [5,5] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.357142857,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.214285714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G74 Interaction | Interacting Bases [6,6] | Pair Probability [[0.357142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.357142857,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.214285714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C75 Insertion | Location [2] | Length Distribution [0.790123457,0.009876543,0.197925926,0.001975309,0.000098765] | Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2Sequences of instances from HL_78197.1:
> HL_78197.1 6UFG G 69 C 76 GGUUGGCC > HL_78197.1 6UFM G 80 C 87 GGUGAGCC > HL_78197.1 6UFG G 13 C 20 GCGAUCAC > HL_78197.1 5ZQ8 C 744 G 753 CGUUGAAAAG > HL_78197.1 9BZC U 54 A 61 UUAUCUUA