| 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 6 3 | 7 6 I | 8 7 4 | 9 8 I | 10 9 5 | 11 9 I | 12 10 6 | 13 10 I | 14 11 | 15 10 I | 16 10 7 | 17 9 I | 18 9 8 | 19 6 I | 20 6 9 | 21 5 I | 22 4 10 | 23 3 I | 24 3 11 | 25 2 I | 26 2 12 | 27 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_55953.3_Instance_1 IL_55953.3,IL_4QK9_001,G29_C103 | G | G | A | C | C | C | G | C | U | A | A | C | ||||||||||||||||||||
| IL_55953.3_Sequence_1 IL_55953.34QK9_G29_C103 | G | G | A | C | C | C | * | G | C | U | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| IL_55953.3_Instance_2 IL_55953.3,IL_4W90_002,G28_C106 | G | G | A | C | C | C | G | C | U | A | A | C | ||||||||||||||||||||
| IL_55953.3_Sequence_2 IL_55953.34W90_G28_C106 | G | G | A | C | C | C | * | G | C | U | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| IL_55953.3_Instance_3 IL_55953.3,IL_6N5P_001,G31_C104 | G | G | A | A | C | C | G | C | U | A | A | C | ||||||||||||||||||||
| IL_55953.3_Sequence_3 IL_55953.36N5P_G31_C104 | G | G | A | A | C | C | * | G | C | U | A | A | C | true | 96 | 0 | 0 | 0.85 | ||||||||||||||
| IL_55953.3_Instance_4 IL_55953.3,IL_4QLM_002,G27_C101 | G | G | A | C | C | C | G | C | U | A | A | C | ||||||||||||||||||||
| IL_55953.3_Sequence_4 IL_55953.34QLM_G27_C101 | G | G | A | C | C | C | * | G | C | U | A | A | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 12 cWW 2 9 s33 2 11 tSH 2 12 s55 3 4 s35 3 9 tHS 3 10 s55 4 5 s35 5 6 s35 5 8 bif 6 7 cWW 7 8 s35 8 9 s35 10 11 s35 11 12 s35 9 3 6BPh 5 4 7BPh 8 7 7BPh 9 8 7BPh 2 10 6BPh 12 11 7BPh 11 2 6BR 3 9 7BRJAR3D SCFG/MRF model for IL_55953.3:
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 [12] // Initial node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.003750350,0.054674460,0.004270648,0.077568035,0.000000000],[0.006587592,0.025743166,0.078225305,0.005118269,0.000000000],[0.004223220,0.601955120,0.000804991,0.010312508,0.000000000],[0.076575313,0.037185886,0.009039378,0.003965758,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair G29 - C103 cWW BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.042857649,0.045370598,0.000514478,0.002424734,0.000000000],[0.043176051,0.045265538,0.000514478,0.000514478,0.000000000],[0.398595795,0.003601343,0.017605820,0.305668340,0.000000000],[0.047840582,0.045021164,0.000514478,0.000514478,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair G30 - A102 tSH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [2] | Left Index [3] | Right Index [10] // Fixed node on right for 4QK9|1|A|A|101 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [9] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.008601579,0.008634808,0.008882643,0.506528766,0.000000000],[0.007856715,0.008124521,0.000095524,0.432636978,0.000000000],[0.000095524,0.000095524,0.000590385,0.004680672,0.000000000],[0.000469902,0.000095524,0.007930261,0.004680672,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [9] // Basepair A31 - U100 tHS FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.250000000,0.583333333,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [4] | Right Index [8] // Fixed node on left for 4QK9|1|A|C|32 InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [5] | Right Index [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.001273899,0.015383631,0.000456515,0.000456515,0.000000000],[0.010536812,0.957957164,0.003195604,0.003195604,0.000000000],[0.000456515,0.001313565,0.001340801,0.000456515,0.000000000],[0.000456515,0.001313565,0.001750266,0.000456515,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair C33 - C99 bif BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009353183,0.016772504,0.010752635,0.194966481,0.000000000],[0.019886467,0.009525946,0.243418233,0.013525436,0.000000000],[0.010873390,0.199167485,0.002049567,0.023014932,0.000000000],[0.197494026,0.013031497,0.026256418,0.009911799,0.000000000],[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 [6] | Right Index [7] // Basepair C34 - G98 cWW HairpinNode | Num Bases [1] | Left Index [7] | Right Index [7] | 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_55953.3:
> IL_55953.3 4QK9 G 29 C 103 GGACCC*GCUAAC > IL_55953.3 4W90 G 28 C 106 GGACCC*GCUAAC > IL_55953.3 6N5P G 31 C 104 GGAACC*GCUAAC > IL_55953.3 4QLM G 27 C 101 GGACCC*GCUAAC