| 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 3 I | 16 3 8 | 17 2 I | 18 2 9 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_68572.1_Instance_1 HL_68572.1,HL_4V9I_038,C11_G24 | C | G | G | A | G | CGGCU | G | A | A | G | ||||||||||||||
| HL_68572.1_Sequence_1 HL_68572.14V9I_C11_G24 | C | G | G | A | G | CGGCU | G | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||
| HL_68572.1_Instance_2 HL_68572.1,HL_7KJT_001,U11_G24 | U | C | A | G | U | CUGGC | A | G | A | G | ||||||||||||||
| HL_68572.1_Sequence_2 HL_68572.17KJT_U11_G24 | U | C | A | G | U | CUGGC | A | G | A | G | true | 99 | 0 | 0 | 0.23 | |||||||||
| HL_68572.1_Instance_3 HL_68572.1,HL_4GCW_001,C11_G24 | C | U | C | A | G | CAGGU | A | G | A | G | ||||||||||||||
| HL_68572.1_Sequence_3 HL_68572.14GCW_C11_G24 | C | U | C | A | G | CAGGU | A | G | A | G | true | 98 | 0 | 0 | 0.28 |
1 9 cWW 2 3 s35 2 9 s55 4 5 s35 4 7 s55 7 8 s35 8 9 s35JAR3D SCFG/MRF model for HL_68572.1:
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 [9] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.010008314,0.015906297,0.011951013,0.143543808,0.000000000],[0.113253323,0.015638746,0.171362823,0.014397321,0.000000000],[0.012135476,0.146322383,0.002470993,0.020335440,0.000000000],[0.161392960,0.013617556,0.136517933,0.011145613,0.000000000],[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 [9] // Basepair C11 - G24 cWW HairpinNode | Num Bases [7] | Left Index [2] | Right Index [8] | Norm Constant [0.999999999999999] // Hairpin node G12:A23 Interaction | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[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 G12 Interaction | Interacting Bases [2,2] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[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 G13 Interaction | Interacting Bases [3,3] | 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 A14 Interaction | Interacting Bases [4,4] | 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 G15 Interaction | Interacting Bases [5,5] | 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 G21 Interaction | Interacting Bases [6,6] | 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 A22 Interaction | Interacting Bases [7,7] | 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 A23 Insertion | Location [4] | Length Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.088235294,0.323529412,0.382352941,0.205882353,0.000000000]// Insertion in Hairpin after nucleotide 5, position 4Sequences of instances from HL_68572.1:
> HL_68572.1 4V9I C 11 G 24 CGGAGCGGCUGAAG > HL_68572.1 7KJT U 11 G 24 UCAGUCUGGCAGAG > HL_68572.1 4GCW C 11 G 24 CUCAGCAGGUAGAG