| 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 2 I | 14 2 7 | 15 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_80105.3_Instance_1 HL_80105.3_HL_6CF2_001_A13_U20 | A | C | U | U | C | G | G | U | ||||||||||||
| HL_80105.3_Sequence_1 HL_80105.3_HL_6CF2_001_A13_U20 | A | C | U | U | C | G | G | U | true | 96 | 0 | 0 | 0.57 | |||||||
| HL_80105.3_Instance_2 HL_80105.3_HL_5TBW_015_G686_C694 | G | U | G | U | A | A | A | A | C | |||||||||||
| HL_80105.3_Sequence_2 HL_80105.3_HL_5TBW_015_G686_C694 | G | U | G | U | A | A | A | A | C | true | 81 | 0 | 0 | 2.38 | ||||||
| HL_80105.3_Instance_3 HL_80105.3_HL_5H9F_001_G50_C57 | G | C | G | C | C | A | G | C | ||||||||||||
| HL_80105.3_Sequence_3 HL_80105.3_HL_5H9F_001_G50_C57 | G | C | G | C | C | A | G | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 7 cWW 2 3 s35 3 4 s35 5 6 s35 6 7 s35JAR3D SCFG/MRF model for HL_80105.3:
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 [7] // Initial node A13 - U20 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009490394,0.020648938,0.010590347,0.209997349,0.000000000],[0.017070363,0.009463878,0.198130626,0.012189443,0.000000000],[0.010502710,0.222275070,0.002053109,0.035235925,0.000000000],[0.195916611,0.012742798,0.023085133,0.010607307,0.000000000],[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 [7] // Basepair A13 - U20 cWW HairpinNode | Num Bases [5] | Left Index [2] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node C14:G19 Interaction | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C14 Interaction | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U15 Interaction | Interacting Bases [3,3] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C17 Interaction | Interacting Bases [4,4] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[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 G18 Interaction | Interacting Bases [5,5] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[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 G19 Insertion | Location [2] | Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.100000000,0.300000000,0.100000000,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2 Insertion | Location [3] | Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 4, position 3Sequences of instances from HL_80105.3:
> HL_80105.3 HL_6CF2_001 A 13 U 20 ACUUCGGU > HL_80105.3 HL_5TBW_015 G 686 C 694 GUGUAAAAC > HL_80105.3 HL_5H9F_001 G 50 C 57 GCGCCAGC