| 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 7 2 | 5 7 I | 6 8 3 | 7 8 I | 8 8 4 | 9 8 I | 10 8 5 | 11 8 I | 12 8 6 | 13 8 I | 14 8 7 | 15 8 I | 16 8 8 | 17 8 I | 18 8 9 | 19 7 I | 20 7 10 | 21 6 I | 22 5 11 | 23 4 I | 24 3 12 | 25 2 I | 26 2 13 | 27 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_20751.2_Instance_1 HL_20751.2,HL_3D0U_001,C38_G51 | C | A | G | G | G | G | A | G | G | A | A | U | C | G | ||||||||||||||||||
| HL_20751.2_Sequence_1 HL_20751.23D0U_C38_G51 | C | A | G | G | G | G | A | G | G | A | A | U | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| HL_20751.2_Instance_2 HL_20751.2,HL_3DIL_001,C41_G54 | C | A | G | G | G | G | A | G | G | A | A | U | C | G | ||||||||||||||||||
| HL_20751.2_Sequence_2 HL_20751.23DIL_C41_G54 | C | A | G | G | G | G | A | G | G | A | A | U | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| HL_20751.2_Instance_3 HL_20751.2,HL_3SUX_005,G37_U49 | G | A | C | G | G | G | G | A | G | U | U | G | U | |||||||||||||||||||
| HL_20751.2_Sequence_3 HL_20751.23SUX_G37_U49 | G | A | C | G | G | G | G | A | G | U | U | G | U | true | 76 | 0 | 0 | 4.62 |
1 13 cWW 2 10 tHW 3 4 perp 4 5 s35 5 6 s35 6 7 s35 7 8 s35 8 9 s35 9 10 s35 10 11 s35 11 13 perp 12 13 s55JAR3D SCFG/MRF model for HL_20751.2:
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 [13] // Initial node BasepairNode | Deletion Probability [0.0000006691671388] | Pair Probability [[0.011524674,0.109291750,0.011964229,0.159160108,0.000000000],[0.017916203,0.010634031,0.169407889,0.013859534,0.000000000],[0.011944263,0.147787249,0.002450608,0.132297401,0.000000000],[0.145015364,0.013965966,0.022426943,0.020353790,0.000000000],[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 [0.334863624,0.653524170,0.011072104,0.000540103] | Right Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Left Index [1] | Right Index [13] // Basepair C38 - G51 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.300000000,0.500000000,0.000000000] | Position [2] | Left Index [2] | Right Index [12] // Fixed node on right for 3D0U|1|A|U|49 InitialNode | Left Length Distribution [1.000000000] | 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 [11] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.100000000,0.300000000,0.000000000] | Position [2] | Left Index [2] | Right Index [11] // Fixed node on right for 3D0U|1|A|A|48 InitialNode | Left Length Distribution [1.000000000] | 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 [10] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.360433204,0.029188915,0.003410157,0.071350370,0.000000000],[0.003410157,0.014471503,0.008447424,0.003410157,0.000000000],[0.300837146,0.003410157,0.125348589,0.016344882,0.000000000],[0.003410157,0.003410157,0.036501254,0.016615771,0.000000000],[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 [10] // Basepair A39 - A47 tHW HairpinNode | Num Bases [7] | Left Index [3] | Right Index [9] | Norm Constant [0.999999999999999] // Hairpin node G40:G46 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],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[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 G40 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],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[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 G41 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],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[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 G42 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],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[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 G43 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 A44 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 G45 Interaction | Interacting Bases [7,7] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[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 G46Sequences of instances from HL_20751.2:
> HL_20751.2 3D0U C 38 G 51 CAGGGGAGGAAUCG > HL_20751.2 3DIL C 41 G 54 CAGGGGAGGAAUCG > HL_20751.2 3SUX G 37 U 49 GACGGGGAGUUGU