| 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 4 I | 6 7 3 | 7 7 I | 8 8 4 | 9 8 I | 10 8 5 | 11 7 I | 12 7 6 | 13 6 I | 14 5 7 | 15 2 I | 16 2 8 | 17 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_20743.2_Instance_1 HL_20743.2_HL_5KPY_001_G31_C39 | G | G | A | U | A | U | G | G | C | |||||||||||||
| HL_20743.2_Sequence_1 HL_20743.2_HL_5KPY_001_G31_C39 | G | G | A | U | A | U | G | G | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_20743.2_Instance_2 HL_20743.2_HL_1Y27_001_G31_C39 | G | G | A | U | A | U | G | G | C | |||||||||||||
| HL_20743.2_Sequence_2 HL_20743.2_HL_1Y27_001_G31_C39 | G | G | A | U | A | U | G | G | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_20743.2_Instance_3 HL_20743.2_HL_6P2H_001_A31_U39 | A | A | A | U | A | U | G | G | U | |||||||||||||
| HL_20743.2_Sequence_3 HL_20743.2_HL_6P2H_001_A31_U39 | A | A | A | U | A | U | G | G | U | true | 97 | 0 | 0 | 0.40 | ||||||||
| HL_20743.2_Instance_4 HL_20743.2_HL_3RKF_007_G31_C39 | G | G | A | U | A | U | A | G | C | |||||||||||||
| HL_20743.2_Sequence_4 HL_20743.2_HL_3RKF_007_G31_C39 | G | G | A | U | A | U | A | G | C | true | 98 | 0 | 0 | 0.32 | ||||||||
| HL_20743.2_Instance_5 HL_20743.2_HL_4FEN_001_G31_C39 | G | G | A | U | A | U | G | G | C | |||||||||||||
| HL_20743.2_Sequence_5 HL_20743.2_HL_4FEN_001_G31_C39 | G | G | A | U | A | U | G | G | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_20743.2_Instance_6 HL_20743.2_HL_3SKL_004_C38_G46 | C | A | U | A | A | U | G | G | G | |||||||||||||
| HL_20743.2_Sequence_6 HL_20743.2_HL_3SKL_004_C38_G46 | C | A | U | A | A | U | G | G | G | true | 92 | 0 | 0 | 1.22 | ||||||||
| HL_20743.2_Instance_7 HL_20743.2_HL_3SKI_001_C39_G47 | C | A | U | A | A | U | G | G | G | |||||||||||||
| HL_20743.2_Sequence_7 HL_20743.2_HL_3SKI_001_C39_G47 | C | A | U | A | A | U | G | G | G | true | 92 | 0 | 0 | 1.22 |
1 2 s35 1 8 cWW 2 3 s35 2 8 s55 3 4 s35 3 6 cSS 5 6 s55 6 7 s35JAR3D SCFG/MRF model for HL_20743.2:
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 [8] // Initial node G31 - C39 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009163774,0.018697796,0.010373988,0.200950124,0.000000000],[0.017221651,0.009149382,0.212644579,0.012402890,0.000000000],[0.010337841,0.233285914,0.001985225,0.028217760,0.000000000],[0.189800820,0.012631146,0.023205154,0.009931957,0.000000000],[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 [8] // Basepair G31 - C39 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.388888889,0.055555556,0.500000000,0.055555556,0.000000000] | Position [1] | Left Index [2] | Right Index [7] // Fixed node on left InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [7] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.055555556,0.833333333,0.055555556,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | 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 [6] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000001232089072] | Pair Probability [[0.085442255,0.077767185,0.117184383,0.075950894,0.000000000],[0.070630775,0.076690491,0.003189304,0.070257479,0.000000000],[0.072441527,0.003122949,0.006832457,0.071535525,0.000000000],[0.067174129,0.018021842,0.107403135,0.076355670,0.000000000],[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 [0.007039775,0.985568462,0.007039775,0.000351989] | Right Letter Distribution [0.055555556,0.055555556,0.055555556,0.833333333,0.000000000] | Left Index [3] | Right Index [6] // Basepair A33 - G37 cSS HairpinNode | Num Bases [2] | Left Index [4] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node U34:A35 Interaction | Interacting Bases [1,1] | Pair Probability [[0.277777778,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.611111111,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U34 Interaction | Interacting Bases [2,2] | Pair Probability [[0.833333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A35Sequences of instances from HL_20743.2:
> HL_20743.2 HL_5KPY_001 G 31 C 39 GGAUAUGGC > HL_20743.2 HL_1Y27_001 G 31 C 39 GGAUAUGGC > HL_20743.2 HL_6P2H_001 A 31 U 39 AAAUAUGGU > HL_20743.2 HL_3RKF_007 G 31 C 39 GGAUAUAGC > HL_20743.2 HL_4FEN_001 G 31 C 39 GGAUAUGGC > HL_20743.2 HL_3SKL_004 C 38 G 46 CAUAAUGGG > HL_20743.2 HL_3SKI_001 C 39 G 47 CAUAAUGGG