| 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 9 2 | 5 9 I | 6 10 3 | 7 10 I | 8 10 4 | 9 10 I | 10 10 5 | 11 9 I | 12 9 6 | 13 8 I | 14 7 7 | 15 6 I | 16 5 8 | 17 4 I | 18 3 9 | 19 2 I | 20 2 10 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_78061.2_Instance_1 HL_78061.2_HL_4LFB_029_C1314_G1323 | C | U | G | C | A | A | C | C | C | G | ||||||||||||||||
| HL_78061.2_Sequence_1 HL_78061.2_HL_4LFB_029_C_1314_G_1323 | C | U | G | C | A | A | C | C | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_78061.2_Instance_2 HL_78061.2_HL_5J7L_028_C1314_G1323 | C | U | G | C | A | A | C | U | C | G | ||||||||||||||||
| HL_78061.2_Sequence_2 HL_78061.2_HL_5J7L_028_C_1314_G_1323 | C | U | G | C | A | A | C | U | C | G | true | 97 | 0 | 0 | 0.51 | |||||||||||
| HL_78061.2_Instance_3 HL_78061.2_HL_6CZR_100_C1296_G1305 | C | U | G | C | A | A | C | C | C | G | ||||||||||||||||
| HL_78061.2_Sequence_3 HL_78061.2_HL_6CZR_100_C_1296_G_1305 | C | U | G | C | A | A | C | C | C | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 10 cWW 2 3 s35 2 6 tWH 2 10 s55 3 6 s55 4 5 s35 6 10 s35 7 8 s35 8 9 s33 3 6 6BPhJAR3D SCFG/MRF model for HL_78061.2:
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 [10] // Initial node C1314 - G1323 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[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 [10] // Basepair C1314 - G1323 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [2] | Right Index [9] // 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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.500000000,0.100000000,0.300000000,0.000000000] | Position [2] | Left Index [2] | Right Index [8] // 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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [2] | 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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [6] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.018593320,0.004114731,0.019312206,0.004114731,0.000000000],[0.041379046,0.331568716,0.004114731,0.004114731,0.000000000],[0.004114731,0.009863283,0.031292185,0.018300908,0.000000000],[0.440599350,0.004114731,0.023873178,0.040529420,0.000000000],[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 [6] // Basepair U1315 - A1319 tWH HairpinNode | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [0.999999999999999] // Hairpin node G1316:A1318 Interaction | Interacting Bases [1,1] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.021739130,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.934782609,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.021739130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1316 Interaction | Interacting Bases [2,2] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C1317 Interaction | Interacting Bases [3,3] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[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 A1318Sequences of instances from HL_78061.2:
> HL_78061.2 HL_4LFB_029 C 1314 G 1323 CUGCAACCCG > HL_78061.2 HL_5J7L_028 C 1314 G 1323 CUGCAACUCG > HL_78061.2 HL_6CZR_100 C 1296 G 1305 CUGCAACCCG