| 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_28075.1_Instance_1 HL_28075.1,HL_6N5P_001,A14_U22 | A | U | G | U | C | G | U | U | U | |||||||||||
| HL_28075.1_Sequence_1 HL_28075.16N5P_A14_U22 | A | U | G | U | C | G | U | U | U | true | 84 | 0 | 0 | 1.60 | ||||||
| HL_28075.1_Instance_2 HL_28075.1,HL_8CRE_033,G1562_C1569 | G | A | U | U | U | U | U | C | ||||||||||||
| HL_28075.1_Sequence_2 HL_28075.18CRE_G_1562_C_1569 | G | A | U | U | U | U | U | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_28075.1_Instance_3 HL_28075.1,HL_7A0S_021,C651_G658 | C | C | G | A | A | U | A | G | ||||||||||||
| HL_28075.1_Sequence_3 HL_28075.17A0S_C651_G658 | C | C | G | A | A | U | A | G | true | 80 | 0 | 0 | 1.97 | |||||||
| HL_28075.1_Instance_4 HL_28075.1,HL_8CRE_067,C3160_G3167 | C | U | U | U | U | U | A | G | ||||||||||||
| HL_28075.1_Sequence_4 HL_28075.18CRE_C_3160_G_3167 | C | U | U | U | U | U | A | G | true | 98 | 0 | 0 | 0.20 |
1 2 s35 1 7 cWW 2 3 s35 2 6 cWW 2 7 s55 3 4 s35 6 7 s35JAR3D SCFG/MRF model for HL_28075.1:
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 [7] // Initial node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009339320,0.018753556,0.010524974,0.206508395,0.000000000],[0.018430728,0.009452306,0.219097689,0.012559761,0.000000000],[0.010550438,0.208651864,0.002037534,0.031117690,0.000000000],[0.195541054,0.012600360,0.024523152,0.010311179,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair A14 - U22 cWW BasepairNode | Deletion Probability [0.0000016375373120] | Pair Probability [[0.011272907,0.099700808,0.011991994,0.120104211,0.000000000],[0.135571195,0.021896395,0.079847453,0.013301943,0.000000000],[0.012015262,0.077445750,0.003127910,0.029282384,0.000000000],[0.093188319,0.013041408,0.126316578,0.151895482,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Right Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Left Index [2] | Right Index [6] // Basepair U15 - U21 cWW HairpinNode | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node G16:G19 Interaction | Interacting Bases [1,1] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.416666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G16 Interaction | Interacting Bases [2,2] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.583333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U17 Interaction | Interacting Bases [3,3] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.583333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G19 Insertion | Location [1] | Length Distribution [0.741082411,0.255227552,0.003536285,0.000153752] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 3, position 1 Insertion | Location [2] | Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000]// Insertion in Hairpin after nucleotide 4, position 2Sequences of instances from HL_28075.1:
> HL_28075.1 6N5P A 14 U 22 AUGUCGUUU > HL_28075.1 8CRE G 1562 C 1569 GAUUUUUC > HL_28075.1 7A0S C 651 G 658 CCGAAUAG > HL_28075.1 8CRE C 3160 G 3167 CUUUUUAG