| 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 8 I | 16 9 | 17 8 I | 18 8 8 | 19 7 I | 20 7 9 | 21 6 I | 22 5 10 | 23 4 I | 24 4 11 | 25 3 I | 26 3 12 | 27 2 I | 28 2 13 | 29 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_02349.4_Instance_1 IL_02349.4,IL_4Y1M_006,G8_C101 | G | G | G | A | G | U | A | G | C | G | A | G | A | C | ||||||||||||||||||||
| IL_02349.4_Sequence_1 IL_02349.44Y1M_G8_C101 | G | G | G | A | G | U | A | G | * | C | G | A | G | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| IL_02349.4_Instance_2 IL_02349.4,IL_6N2V_001,G7_C93 | G | G | G | A | G | U | A | G | C | G | A | G | A | C | ||||||||||||||||||||
| IL_02349.4_Sequence_2 IL_02349.46N2V_G7_C93 | G | G | G | A | G | U | A | G | * | C | G | A | G | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| IL_02349.4_Instance_3 IL_02349.4,IL_6CB3_003,G7_C96 | G | G | G | A | G | U | A | G | C | A | A | G | A | C | ||||||||||||||||||||
| IL_02349.4_Sequence_3 IL_02349.46CB3_G7_C96 | G | G | G | A | G | U | A | G | * | C | A | A | G | A | C | true | 99 | 0 | 0 | 0.26 |
1 2 s35 1 13 cWW 2 3 s35 2 12 tSH 2 13 s55 3 5 s35 3 10 s33 3 11 tWH 4 5 cSH 4 9 s33 5 6 s35 5 10 tWH 6 7 s35 6 9 tHS 6 10 s55 7 8 cWW 8 9 s35 10 11 s35 11 12 s35 12 13 s35 4 10 6BPh 2 11 6BPh 13 12 7BPh 12 2 6BR 9 4 6BR 6 9 6BRJAR3D SCFG/MRF model for IL_02349.4:
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 [13] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.003786762,0.055205280,0.004312111,0.078321123,0.000000000],[0.006651550,0.025993100,0.078984774,0.005167961,0.000000000],[0.004264222,0.598090606,0.000812806,0.010412629,0.000000000],[0.077318762,0.037546914,0.009127139,0.004004261,0.000000000],[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 [13] // Basepair G8 - C101 cWW 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 [2] | Right Index [12] // Basepair G9 - A100 tSH BasepairNode | Deletion Probability [0.0000001200211660] | Pair Probability [[0.169517503,0.004611790,0.088526941,0.004611790,0.000000000],[0.041471763,0.028297675,0.004611790,0.004611790,0.000000000],[0.004611790,0.007147729,0.490305195,0.046443821,0.000000000],[0.035072272,0.004611790,0.035889002,0.029657359,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | 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 [11] // Basepair G10 - G99 tWH ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [10] | Norm Constant [0.266231322387786] // Cluster node 4Y1M|1|B|G|12:4Y1M|1|B|U|13 and 4Y1M|1|B|A|98:4Y1M|1|B|A|98 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 4Y1M|1|B|U|13 - 4Y1M|1|B|A|98 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 4Y1M|1|B|G|12 - 4Y1M|1|B|U|13 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 [9] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.203172741,0.067006440,0.263183310,0.068776875,0.000000000],[0.056722026,0.050774581,0.002490158,0.066332526,0.000000000],[0.002007295,0.000749576,0.013367818,0.000749576,0.000000000],[0.011637725,0.000749576,0.191530202,0.000749576,0.000000000],[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 [9] // Basepair A14 - G97 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009639190,0.020074982,0.010976465,0.199366183,0.000000000],[0.016931500,0.009452194,0.201055505,0.013155030,0.000000000],[0.010854565,0.236025807,0.002068996,0.026505317,0.000000000],[0.196814677,0.013653651,0.023233104,0.010192834,0.000000000],[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 [7] | Right Index [8] // Basepair G15 - C96 cWW HairpinNode | Num Bases [1] | Left Index [8] | Right Index [8] | 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_02349.4:
> IL_02349.4 4Y1M G 8 C 101 GGGAGUAG*CGAGAC > IL_02349.4 6N2V G 7 C 93 GGGAGUAG*CGAGAC > IL_02349.4 6CB3 G 7 C 96 GGGAGUAG*CAAGAC