| 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_42046.2_Instance_1 HL_42046.2,HL_5F5H_001,C8_G15 | C | G | U | U | C | U | A | G | ||||||||||||
| HL_42046.2_Sequence_1 HL_42046.25F5H_C8_G15 | C | G | U | U | C | U | A | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_42046.2_Instance_2 HL_42046.2,HL_5F5H_002,C8_G15 | C | G | U | U | C | U | A | G | ||||||||||||
| HL_42046.2_Sequence_2 HL_42046.25F5H_C8_G15 | C | G | U | U | C | U | A | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_42046.2_Instance_3 HL_42046.2,HL_5F5F_003,C7_G14 | C | G | U | U | U | U | A | G | ||||||||||||
| HL_42046.2_Sequence_3 HL_42046.25F5F_C7_G14 | C | G | U | U | U | U | A | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_42046.2_Instance_4 HL_42046.2,HL_5F5F_001,C7_G14 | C | G | U | U | U | U | A | G | ||||||||||||
| HL_42046.2_Sequence_4 HL_42046.25F5F_C7_G14 | C | G | U | U | U | U | A | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_42046.2_Instance_5 HL_42046.2,HL_9DFE_017,C612_G615 | C | G | U | U | G | A | G | |||||||||||||
| HL_42046.2_Sequence_5 HL_42046.29DFE_C612_G615 | C | G | U | U | G | A | G | true | 87 | 0 | 0 | 1.57 |
1 2 s35 1 7 cWW 2 3 s35 2 6 tSS 2 7 s55 4 5 s55JAR3D SCFG/MRF model for HL_42046.2:
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 [7] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009264105,0.016612765,0.010650229,0.193109658,0.000000000],[0.019697072,0.009435223,0.250623774,0.013396622,0.000000000],[0.010769834,0.197270651,0.002030047,0.022795742,0.000000000],[0.195613131,0.012907388,0.026006356,0.009817401,0.000000000],[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 [7] // Basepair C8 - G15 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.020820339,0.017115104,0.019716099,0.012516321,0.000000000],[0.002514512,0.002514512,0.218773210,0.002514512,0.000000000],[0.299070295,0.002514512,0.244440474,0.147432057,0.000000000],[0.002514512,0.002514512,0.002514512,0.002514512,0.000000000],[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 [2] | Right Index [6] // Basepair G9 - A14 tSS HairpinNode | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node U10:U13 Interaction | Interacting Bases [1,1] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.785714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U10 Interaction | Interacting Bases [2,2] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.785714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U11 Interaction | Interacting Bases [3,3] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.642857143,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U13 Insertion | Location [2] | Length Distribution [0.204221895,0.787432499,0.007952872,0.000392734] | Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000]// Insertion in Hairpin after nucleotide 4, position 2Sequences of instances from HL_42046.2:
> HL_42046.2 5F5H C 8 G 15 CGUUCUAG > HL_42046.2 5F5H C 8 G 15 CGUUCUAG > HL_42046.2 5F5F C 7 G 14 CGUUUUAG > HL_42046.2 5F5F C 7 G 14 CGUUUUAG > HL_42046.2 9DFE C 612 G 615 CGUUGAG