| 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 5 4 | 9 5 I | 10 5 5 | 11 6 I | 12 7 6 | 13 7 I | 14 8 7 | 15 9 I | 16 10 8 | 17 11 I | 18 14 9 | 19 14 I | 20 15 10 | 21 15 I | 22 16 | 23 15 I | 24 15 11 | 25 14 I | 26 14 12 | 27 13 I | 28 12 13 | 29 7 I | 30 7 14 | 31 6 I | 32 5 15 | 33 4 I | 34 4 16 | 35 3 I | 36 3 17 | 37 2 I | 38 2 18 | 39 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_43547.1_Instance_1 IL_43547.1,IL_6UFG_002,C53_G41 | C | C | A | G | U | A | G | A | A | C | G | A | A | G | A | A | C | G | ||||||||||||||||||||||||||
| IL_43547.1_Sequence_1 IL_43547.16UFG_C53_G41 | C | C | A | G | U | A | G | A | A | C | * | G | A | A | G | A | A | C | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||||||
| IL_43547.1_Instance_2 IL_43547.1,IL_6UFH_002,C54_G41 | C | C | A | G | U | A | G | A | A | C | G | A | A | G | A | A | C | G | ||||||||||||||||||||||||||
| IL_43547.1_Sequence_2 IL_43547.16UFH_C54_G41 | C | C | A | G | U | A | G | A | A | C | * | G | A | A | G | A | A | C | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||||||
| IL_43547.1_Instance_3 IL_43547.1,IL_6UFM_002,U64_G41 | U | C | A | G | U | A | G | A | A | C | G | A | A | G | A | A | C | G | ||||||||||||||||||||||||||
| IL_43547.1_Sequence_3 IL_43547.16UFM_U64_G41 | U | C | A | G | U | A | G | A | A | C | * | G | A | A | G | A | A | C | G | true | 99 | 0 | 0 | 0.23 |
1 2 s35 1 18 cWW 2 3 s33 2 17 tSH 3 5 s55 3 15 s53 3 16 tHH 4 5 cSH 4 14 s33 5 6 s35 5 14 s33 5 15 tWH 6 7 s35 6 14 tHS 6 15 s55 7 8 s35 8 9 s35 9 10 s35 9 12 cWW 10 11 cWW 11 12 s35 12 13 s35 13 14 s35 15 16 s35 16 17 s35 17 18 s35 14 5 6BPh 4 15 6BPh 3 16 6BPh 17 2 6BR 2 3 7BR 6 14 6BRJAR3D SCFG/MRF model for IL_43547.1:
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 [18] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.010008314,0.015906297,0.011951013,0.143543808,0.000000000],[0.113253323,0.015638746,0.171362823,0.014397321,0.000000000],[0.012135476,0.146322383,0.002470993,0.020335440,0.000000000],[0.161392960,0.013617556,0.136517933,0.011145613,0.000000000],[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 [18] // Basepair C53 - G41 cWW BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.030289734,0.068503029,0.000762594,0.003173752,0.000000000],[0.266785855,0.410423431,0.003812972,0.003812972,0.000000000],[0.067095736,0.000762594,0.003348885,0.009493180,0.000000000],[0.064860346,0.065349730,0.000762594,0.000762594,0.000000000],[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 [17] // Basepair C54 - C40 tSH BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.437389671,0.327985029,0.019573927,0.019970073,0.000000000],[0.051310150,0.000583234,0.049721078,0.005541936,0.000000000],[0.002907841,0.049085648,0.001455750,0.000583234,0.000000000],[0.003961363,0.028764599,0.000583234,0.000583234,0.000000000],[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 [16] // Basepair A55 - A39 tHH ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [15] | Norm Constant [0.266231322387786] // Cluster node 6UFG|1|A|G|56:6UFG|1|A|U|57 and 6UFG|1|A|A|38:6UFG|1|A|A|38 Interaction | Interacting Bases [2,3] | 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]] // Cluster Interaction 6UFG|1|A|U|57 - 6UFG|1|A|A|38 tWH Interaction | Interacting Bases [1,2] | Pair Probability [[0.030804004,0.031387867,0.001725802,0.030674930,0.000000000],[0.022997202,0.034657186,0.000382122,0.030739236,0.000000000],[0.188394657,0.002674853,0.229809368,0.296611539,0.000000000],[0.031281957,0.031094167,0.000382122,0.036382988,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6UFG|1|A|G|56 - 6UFG|1|A|U|57 cSH 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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [14] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.043273743,0.043595236,0.392756919,0.048305054,0.000000000],[0.045811089,0.045705009,0.003636307,0.045458262,0.000000000],[0.000519472,0.000519472,0.017776750,0.000519472,0.000000000],[0.002448275,0.000519472,0.308635994,0.000519472,0.000000000],[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 [6] | Right Index [14] // Basepair A58 - G37 tHS FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [1] | Left Index [7] | Right Index [13] // Fixed node on left for 6UFG|1|A|C|40 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 [8] | Right Index [13] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [8] | Right Index [13] // Fixed node on left for 6UFG|1|A|G|41 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 [9] | Right Index [13] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [9] | Right Index [13] // Fixed node on right for 6UFG|1|A|U|57 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 [9] | Right Index [12] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.618999942,0.027411941,0.048841477,0.026826787,0.000000000],[0.018350871,0.010237698,0.026918842,0.026030599,0.000000000],[0.037348807,0.027481470,0.005898737,0.028798923,0.000000000],[0.026068812,0.029318190,0.020065065,0.021401838,0.000000000],[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 [9] | Right Index [12] // Basepair A61 - A35 cWW BasepairNode | Deletion Probability [0.0000249735224443] | 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 [0.999900000,0.000100000] | 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 [10] | Right Index [11] // Basepair C62 - G34 cWW HairpinNode | Num Bases [1] | Left Index [11] | Right Index [11] | 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_43547.1:
> IL_43547.1 6UFG C 53 G 41 CCAGUAGAAC*GAAGAACG > IL_43547.1 6UFH C 54 G 41 CCAGUAGAAC*GAAGAACG > IL_43547.1 6UFM U 64 G 41 UCAGUAGAAC*GAAGAACG