| 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 5 4 | 9 5 I | 10 5 5 | 11 5 I | 12 5 6 | 13 4 I | 14 4 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_73266.3_Instance_1 HL_73266.3_HL_4FEN_003_A59_U67 | A | C | C | G | U | A | A | A | U | |||||||||||||||
| HL_73266.3_Sequence_1 HL_73266.3_HL_4FEN_003_A59_U67 | A | C | C | G | U | A | A | A | U | true | 99 | 0 | 0 | 0.16 | ||||||||||
| HL_73266.3_Instance_2 HL_73266.3_HL_1Y27_003_A59_U67 | A | C | C | G | U | A | A | A | U | |||||||||||||||
| HL_73266.3_Sequence_2 HL_73266.3_HL_1Y27_003_A59_U67 | A | C | C | G | U | A | A | A | U | true | 99 | 0 | 0 | 0.16 | ||||||||||
| HL_73266.3_Instance_3 HL_73266.3_HL_4LX6_003_G59_C67 | G | C | C | U | U | A | A | A | C | |||||||||||||||
| HL_73266.3_Sequence_3 HL_73266.3_HL_4LX6_003_G59_C67 | G | C | C | U | U | A | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_73266.3_Instance_4 HL_73266.3_HL_5SWD_006_G59_C67 | G | C | C | U | U | A | A | A | C | |||||||||||||||
| HL_73266.3_Sequence_4 HL_73266.3_HL_5SWD_006_G59_C67 | G | C | C | U | U | A | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_73266.3_Instance_5 HL_73266.3_HL_3LA5_003_G59_C67 | G | C | C | U | U | A | A | A | C | |||||||||||||||
| HL_73266.3_Sequence_5 HL_73266.3_HL_3LA5_003_G59_C67 | G | C | C | U | U | A | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_73266.3_Instance_6 HL_73266.3_HL_5KPY_002_A59_U67 | A | C | C | G | U | A | A | A | U | |||||||||||||||
| HL_73266.3_Sequence_6 HL_73266.3_HL_5KPY_002_A59_U67 | A | C | C | G | U | A | A | A | U | true | 99 | 0 | 0 | 0.16 | ||||||||||
| HL_73266.3_Instance_7 HL_73266.3_HL_3RKF_009_A59_U67 | A | C | U | G | U | A | A | A | U | |||||||||||||||
| HL_73266.3_Sequence_7 HL_73266.3_HL_3RKF_009_A59_U67 | A | C | U | G | U | A | A | A | U | true | 98 | 0 | 0 | 0.24 | ||||||||||
| HL_73266.3_Instance_8 HL_73266.3_HL_4XNR_003_G59_C67 | G | C | C | U | U | A | A | A | C | |||||||||||||||
| HL_73266.3_Sequence_8 HL_73266.3_HL_4XNR_003_G59_C67 | G | C | C | U | U | A | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_73266.3_Instance_9 HL_73266.3_HL_1Y26_003_G59_C67 | G | C | C | U | U | A | A | A | C | |||||||||||||||
| HL_73266.3_Sequence_9 HL_73266.3_HL_1Y26_003_G59_C67 | G | C | C | U | U | A | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_73266.3_Instance_10 HL_73266.3_HL_2ZNI_002_A31_U39 | A | C | U | C | U | A | A | A | U | |||||||||||||||
| HL_73266.3_Sequence_10 HL_73266.3_HL_2ZNI_002_A31_U39 | A | C | U | C | U | A | A | A | U | true | 96 | 0 | 0 | 0.54 | ||||||||||
| HL_73266.3_Instance_11 HL_73266.3_HL_3RG5_010_G31_C39 | G | C | U | U | C | A | A | A | C | |||||||||||||||
| HL_73266.3_Sequence_11 HL_73266.3_HL_3RG5_010_G31_C39 | G | C | U | U | C | A | A | A | C | true | 98 | 0 | 0 | 0.27 | ||||||||||
| HL_73266.3_Instance_12 HL_73266.3_HL_3RG5_006_G31_C39 | G | C | U | U | C | A | A | A | C | |||||||||||||||
| HL_73266.3_Sequence_12 HL_73266.3_HL_3RG5_006_G31_C39 | G | C | U | U | C | A | A | A | C | true | 98 | 0 | 0 | 0.27 |
1 2 s35 1 9 cWW 2 3 s35 2 8 cWW 3 7 cSW 4 5 cSH 5 6 s55 6 7 s35 7 8 s35 8 9 s35 6 4 2BPhJAR3D SCFG/MRF model for HL_73266.3:
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 [9] // Initial node A59 - U67 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008693563,0.019121607,0.009650564,0.229048924,0.000000000],[0.015730564,0.008706074,0.181536954,0.010987935,0.000000000],[0.009577847,0.248127239,0.001884474,0.034411727,0.000000000],[0.179966837,0.011509408,0.021196057,0.009850227,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair A59 - U67 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.010080286,0.013199009,0.012833387,0.027809212,0.000000000],[0.439209153,0.036996213,0.031439147,0.014330603,0.000000000],[0.013141970,0.026516183,0.003240225,0.013705140,0.000000000],[0.034940627,0.013059696,0.296505749,0.012993400,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair C60 - A66 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.173725874,0.016835553,0.016595177,0.006850719,0.000000000],[0.258053928,0.014812852,0.001884678,0.007301182,0.000000000],[0.173299871,0.001884678,0.057094116,0.005818232,0.000000000],[0.236187312,0.014491142,0.008431629,0.006733057,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [7] // Basepair C61 - A65 cSW HairpinNode | Num Bases [3] | Left Index [4] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node G62:A64 Interaction | Interacting Bases [1,2] | Pair Probability [[0.068584304,0.069343764,0.003849349,0.069093448,0.000000000],[0.060530190,0.077944113,0.000850733,0.088124335,0.000000000],[0.065142913,0.000850733,0.072248020,0.118559606,0.000000000],[0.069829572,0.106326511,0.000850733,0.127871676,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G62 - U63 cSH Interaction | Interacting Bases [3,3] | Pair Probability [[0.982558140,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.005813953,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.005813953,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.005813953,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A64Sequences of instances from HL_73266.3:
> HL_73266.3 HL_4FEN_003 A 59 U 67 ACCGUAAAU > HL_73266.3 HL_1Y27_003 A 59 U 67 ACCGUAAAU > HL_73266.3 HL_4LX6_003 G 59 C 67 GCCUUAAAC > HL_73266.3 HL_5SWD_006 G 59 C 67 GCCUUAAAC > HL_73266.3 HL_3LA5_003 G 59 C 67 GCCUUAAAC > HL_73266.3 HL_5KPY_002 A 59 U 67 ACCGUAAAU > HL_73266.3 HL_3RKF_009 A 59 U 67 ACUGUAAAU > HL_73266.3 HL_4XNR_003 G 59 C 67 GCCUUAAAC > HL_73266.3 HL_1Y26_003 G 59 C 67 GCCUUAAAC > HL_73266.3 HL_2ZNI_002 A 31 U 39 ACUCUAAAU > HL_73266.3 HL_3RG5_010 G 31 C 39 GCUUCAAAC > HL_73266.3 HL_3RG5_006 G 31 C 39 GCUUCAAAC