| 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 9 5 | 11 9 I | 12 10 6 | 13 10 I | 14 11 7 | 15 11 I | 16 12 8 | 17 12 I | 18 13 | 19 12 I | 20 12 9 | 21 11 I | 22 11 10 | 23 10 I | 24 10 11 | 25 9 I | 26 9 12 | 27 8 I | 28 8 13 | 29 7 I | 30 7 14 | 31 6 I | 32 5 15 | 33 2 I | 34 2 16 | 35 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_84694.2_Instance_1 IL_84694.2,IL_8CRE_005,C30_G52 | C | U | G | A | A | C | U | U | A | U | C | A | A | U | A | A | G | |||||||||||||||||||||||
| IL_84694.2_Sequence_1 IL_84694.28CRE_C30_G52 | C | U | G | A | A | C | U | U | * | A | U | C | A | A | U | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||
| IL_84694.2_Instance_2 IL_84694.2,IL_8P9A_234,C31_G53 | C | U | G | A | A | C | U | U | A | U | C | A | A | U | A | A | G | |||||||||||||||||||||||
| IL_84694.2_Sequence_2 IL_84694.28P9A_C31_G53 | C | U | G | A | A | C | U | U | * | A | U | C | A | A | U | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||
| IL_84694.2_Instance_3 IL_84694.2,IL_4WF9_008,G190_C212 | G | A | G | A | A | C | U | G | C | U | U | A | G | U | A | C | C | |||||||||||||||||||||||
| IL_84694.2_Sequence_3 IL_84694.24WF9_G190_C212 | G | A | G | A | A | C | U | G | * | C | U | U | A | G | U | A | C | C | true | 92 | 0 | 0 | 1.76 |
1 2 s35 1 16 cWW 2 3 s35 2 16 s55 3 13 s33 3 14 tSH 4 5 s35 4 12 s35 4 13 tHW 4 14 s55 5 6 s35 5 12 tHH 6 7 s35 6 11 tHS 7 8 s35 7 10 cWW 7 11 s55 8 9 cWW 8 10 s55 9 10 s35 10 11 s35 11 12 s33 12 13 s55 13 14 s35 14 15 s35 15 16 s35 12 5 6BPh 7 6 7BPh 3 13 6BPh 14 3 6BRJAR3D SCFG/MRF model for IL_84694.2:
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 [16] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009509057,0.017981890,0.010896842,0.197694967,0.000000000],[0.019030193,0.009563019,0.224400354,0.013489511,0.000000000],[0.010937493,0.212742702,0.002069309,0.024327358,0.000000000],[0.198545855,0.013323228,0.025418591,0.010069631,0.000000000],[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 [16] // Basepair C30 - G52 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.100000000,0.500000000,0.000000000] | Position [1] | Left Index [2] | Right Index [15] // Fixed node on left for 8CRE|1|1|U|31 InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [15] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.300000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [3] | Right Index [15] // Fixed node on right for 8CRE|1|1|A|50 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 [3] | Right Index [14] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.043273743,0.045811089,0.000519472,0.002448275,0.000000000],[0.043595236,0.045705009,0.000519472,0.000519472,0.000000000],[0.392756919,0.003636307,0.017776750,0.308635994,0.000000000],[0.048305054,0.045458262,0.000519472,0.000519472,0.000000000],[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 [3] | Right Index [14] // Basepair G32 - A50 tSH BasepairNode | Deletion Probability [0.0000001200211660] | Pair Probability [[0.018593320,0.041379046,0.004114731,0.440599350,0.000000000],[0.004114731,0.331568716,0.009863283,0.004114731,0.000000000],[0.019312206,0.004114731,0.031292185,0.023873178,0.000000000],[0.004114731,0.004114731,0.018300908,0.040529420,0.000000000],[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 [0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | Left Index [4] | Right Index [13] // Basepair A33 - U49 tHW BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.423555925,0.045267352,0.002701525,0.002756200,0.000000000],[0.347000771,0.000563471,0.048036311,0.005354151,0.000000000],[0.019665174,0.047422412,0.001406423,0.000563471,0.000000000],[0.026789942,0.027789929,0.000563471,0.000563471,0.000000000],[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 [5] | Right Index [12] // Basepair A34 - A47 tHH BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.087494077,0.121692735,0.139732981,0.138877570,0.000000000],[0.130741883,0.171560190,0.001590790,0.152966086,0.000000000],[0.001590790,0.001590790,0.007372771,0.001590790,0.000000000],[0.006899277,0.001590790,0.033117691,0.001590790,0.000000000],[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 [6] | Right Index [11] // Basepair C35 - C46 tHS BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.003879780,0.071159900,0.003463989,0.006050075,0.000000000],[0.004288078,0.004623609,0.005171369,0.003802660,0.000000000],[0.003391639,0.005268056,0.001069338,0.013660999,0.000000000],[0.036996003,0.028827946,0.030683553,0.777663006,0.000000000],[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 [7] | Right Index [10] // Basepair U36 - U45 cWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009177479,0.018274610,0.010201403,0.196065482,0.000000000],[0.020197122,0.009641546,0.197064662,0.011676789,0.000000000],[0.010173530,0.207057088,0.002039267,0.024050960,0.000000000],[0.219982557,0.011400443,0.042929120,0.010067941,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [8] | Right Index [9] // Basepair U37 - A44 cWW HairpinNode | Num Bases [1] | Left Index [9] | Right Index [9] | Norm Constant [1.000000000000000] // Hairpin node type * Interaction | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncationSequences of instances from IL_84694.2:
> IL_84694.2 8CRE C 30 G 52 CUGAACUU*AUCAAUAAG > IL_84694.2 8P9A C 31 G 53 CUGAACUU*AUCAAUAAG > IL_84694.2 4WF9 G 190 C 212 GAGAACUG*CUUAGUACC