| 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 4 I | 12 4 6 | 13 4 I | 14 4 7 | 15 4 I | 16 4 8 | 17 4 I | 18 4 9 | 19 4 I | 20 4 10 | 21 4 I | 22 4 11 | 23 4 I | 24 4 12 | 25 4 I | 26 4 13 | 27 3 I | 28 3 14 | 29 2 I | 30 2 15 | 31 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_88364.2_Instance_1 HL_88364.2,HL_4JF2_002,U28_A43 | U | A | C | U | U | A | U | U | U | C | C | U | U | U | G | A | ||||||||||||||||||||
| HL_88364.2_Sequence_1 HL_88364.24JF2_U28_A43 | U | A | C | U | U | A | U | U | U | C | C | U | U | U | G | A | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| HL_88364.2_Instance_2 HL_88364.2,HL_5D5L_002,U28_A43 | U | A | C | U | U | A | U | U | U | C | C | U | U | U | G | A | ||||||||||||||||||||
| HL_88364.2_Sequence_2 HL_88364.25D5L_U28_A43 | U | A | C | U | U | A | U | U | U | C | C | U | U | U | G | A | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| HL_88364.2_Instance_3 HL_88364.2,HL_8P9A_236,A829_U843 | A | U | U | U | U | G | U | U | G | G | U | U | U | C | U | |||||||||||||||||||||
| HL_88364.2_Sequence_3 HL_88364.28P9A_A829_U843 | A | U | U | U | U | G | U | U | G | G | U | U | U | C | U | true | 92 | 0 | 0 | 1.52 |
1 2 s35 1 15 cWW 2 3 s35 2 14 cWW 2 15 s55 4 5 s35 7 8 s35 8 9 s35 9 10 s35 10 11 s35 11 12 s35 12 13 s35 13 14 s35 14 15 s35 8 7 7BPhJAR3D SCFG/MRF model for HL_88364.2:
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 [15] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009028682,0.018848565,0.009815285,0.206696649,0.000000000],[0.020335986,0.009653230,0.194139783,0.010711201,0.000000000],[0.009821675,0.193306351,0.002023380,0.032781568,0.000000000],[0.219084491,0.010489590,0.042781149,0.010482415,0.000000000],[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 [15] // Basepair U28 - A43 cWW BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.028091145,0.013760207,0.358682987,0.016478944,0.000000000],[0.013437108,0.009151593,0.017798873,0.039995656,0.000000000],[0.325952502,0.017998760,0.003392655,0.014971928,0.000000000],[0.016446867,0.098199508,0.014651180,0.010990087,0.000000000],[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 [2] | Right Index [14] // Basepair A29 - G42 cWW HairpinNode | Num Bases [11] | Left Index [3] | Right Index [13] | Norm Constant [0.999999999999999] // Hairpin node C30:U41 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 C30 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],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U31 Interaction | Interacting Bases [3,3] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U32 Interaction | Interacting Bases [4,4] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[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 U34 Interaction | Interacting Bases [5,5] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U35 Interaction | Interacting Bases [6,6] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.021739130,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.021739130,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.934782609,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U36 Interaction | Interacting Bases [7,7] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[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 C37 Interaction | Interacting Bases [8,8] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[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 C38 Interaction | Interacting Bases [9,9] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U39 Interaction | Interacting Bases [10,10] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U40 Interaction | Interacting Bases [11,11] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U41 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 5, position 3 Insertion | Location [4] | Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 6, position 4Sequences of instances from HL_88364.2:
> HL_88364.2 4JF2 U 28 A 43 UACUUAUUUCCUUUGA > HL_88364.2 5D5L U 28 A 43 UACUUAUUUCCUUUGA > HL_88364.2 8P9A A 829 U 843 AUUUUGUUGGUUUCU