| 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 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_68493.4_Instance_1 HL_68493.4_HL_5DH6_002_C27_G34 | C | U | G | G | G | A | U | G | ||||||||||||
| HL_68493.4_Sequence_1 HL_68493.4_HL_5DH6_002_C27_G34 | C | U | G | G | G | A | U | G | true | 92 | 0 | 0 | 0.89 | |||||||
| HL_68493.4_Instance_2 HL_68493.4_HL_5J7L_142_C305_G312 | C | U | G | G | A | A | A | G | ||||||||||||
| HL_68493.4_Sequence_2 HL_68493.4_HL_5J7L_142_C305_G312 | C | U | G | G | A | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_68493.4_Instance_3 HL_68493.4_HL_4V9F_010_U312_A319 | U | U | G | G | A | A | U | A | ||||||||||||
| HL_68493.4_Sequence_3 HL_68493.4_HL_4V9F_010_U312_A319 | U | U | G | G | A | A | U | A | true | 99 | 0 | 0 | 0.17 | |||||||
| HL_68493.4_Instance_4 HL_68493.4_HL_7A0S_010_C316_G323 | C | U | G | G | A | A | A | G | ||||||||||||
| HL_68493.4_Sequence_4 HL_68493.4_HL_7A0S_010_C316_G323 | C | U | G | G | A | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_68493.4_Instance_5 HL_68493.4_HL_5TBW_005_U194_A201 | U | U | G | G | A | A | C | A | ||||||||||||
| HL_68493.4_Sequence_5 HL_68493.4_HL_5TBW_005_U194_A201 | U | U | G | G | A | A | C | A | true | 89 | 0 | 0 | 1.27 | |||||||
| HL_68493.4_Instance_6 HL_68493.4_HL_4Y4O_112_U305_G312 | U | U | G | G | G | A | A | G | ||||||||||||
| HL_68493.4_Sequence_6 HL_68493.4_HL_4Y4O_112_U305_G312 | U | U | G | G | G | A | A | G | true | 81 | 0 | 0 | 2.18 | |||||||
| HL_68493.4_Instance_7 HL_68493.4_HL_2A64_002_C69_G76 | C | U | G | A | G | A | U | G | ||||||||||||
| HL_68493.4_Sequence_7 HL_68493.4_HL_2A64_002_C69_G76 | C | U | G | A | G | A | U | G | true | 85 | 0 | 0 | 1.77 | |||||||
| HL_68493.4_Instance_8 HL_68493.4_HL_4V88_191_G243_C250 | G | A | U | G | A | U | U | C | ||||||||||||
| HL_68493.4_Sequence_8 HL_68493.4_HL_4V88_191_G243_C250 | G | A | U | G | A | U | U | C | true | 70 | 0 | 0 | 3.47 | |||||||
| HL_68493.4_Instance_9 HL_68493.4_HL_2GDI_002_G66_C73 | G | A | U | A | A | U | G | C | ||||||||||||
| HL_68493.4_Sequence_9 HL_68493.4_HL_2GDI_002_G66_C73 | G | A | U | A | A | U | G | C | true | 53 | 0 | 0 | 5.45 | |||||||
| HL_68493.4_Instance_10 HL_68493.4_HL_4WF9_010_C348_G355 | C | U | G | G | A | A | A | G | ||||||||||||
| HL_68493.4_Sequence_10 HL_68493.4_HL_4WF9_010_C348_G355 | C | U | G | G | A | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_68493.4_Instance_11 HL_68493.4_HL_4V9F_039_C1594_G1600 | C | G | U | A | A | U | G | |||||||||||||
| HL_68493.4_Sequence_11 HL_68493.4_HL_4V9F_039_C_1594_G_1600 | C | G | U | A | A | U | G | true | 52 | 0 | 0 | 5.63 |
1 2 s35 1 7 cWW 2 3 s35 2 6 tWH 2 7 s55 3 6 s55 4 5 s35 6 7 s35 3 6 6BPhJAR3D SCFG/MRF model for HL_68493.4:
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 C27 - G34 from junction BasepairNode | Deletion Probability [0.0000001988889326] | Pair Probability [[0.008855177,0.016058137,0.010195552,0.169189225,0.000000000],[0.041976169,0.010440606,0.229168546,0.012316502,0.000000000],[0.010266039,0.190301874,0.002014248,0.021310121,0.000000000],[0.193508978,0.011923006,0.062870450,0.009605372,0.000000000],[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 [0.094202453,0.901476521,0.004116238,0.000204788] | Right Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair C27 - G34 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.016629649,0.003680168,0.017272612,0.043406641,0.000000000],[0.037008937,0.296551202,0.003680168,0.003680168,0.000000000],[0.003680168,0.008821605,0.027987366,0.036231356,0.000000000],[0.440088858,0.003680168,0.021351893,0.036249042,0.000000000],[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 [6] // Basepair U28 - A32 tWH HairpinNode | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node G29:G31 Interaction | Interacting Bases [1,1] | Pair Probability [[0.006329114,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.006329114,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.715189873,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.272151899,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G29 Interaction | Interacting Bases [2,2] | Pair Probability [[0.269230769,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.653846154,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G30 Interaction | Interacting Bases [3,3] | Pair Probability [[0.653846154,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.269230769,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G31Sequences of instances from HL_68493.4:
> HL_68493.4 HL_5DH6_002 C 27 G 34 CUGGGAUG > HL_68493.4 HL_5J7L_142 C 305 G 312 CUGGAAAG > HL_68493.4 HL_4V9F_010 U 312 A 319 UUGGAAUA > HL_68493.4 HL_7A0S_010 C 316 G 323 CUGGAAAG > HL_68493.4 HL_5TBW_005 U 194 A 201 UUGGAACA > HL_68493.4 HL_4Y4O_112 U 305 G 312 UUGGGAAG > HL_68493.4 HL_2A64_002 C 69 G 76 CUGAGAUG > HL_68493.4 HL_4V88_191 G 243 C 250 GAUGAUUC > HL_68493.4 HL_2GDI_002 G 66 C 73 GAUAAUGC > HL_68493.4 HL_4WF9_010 C 348 G 355 CUGGAAAG > HL_68493.4 HL_4V9F_039 C 1594 G 1600 CGUAAUG