| 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 | 17 11 I | 18 11 8 | 19 10 I | 20 10 9 | 21 9 I | 22 9 10 | 23 8 I | 24 8 11 | 25 7 I | 26 7 12 | 27 6 I | 28 5 13 | 29 2 I | 30 2 14 | 31 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_04021.2_Instance_1 IL_04021.2,IL_4WF9_001,G24_C561 | G | U | G | G | A | U | G | C | U | G | A | A | A | C | ||||||||||||||||||||||
| IL_04021.2_Sequence_1 IL_04021.24WF9_G24_C561 | G | U | G | G | A | U | G | * | C | U | G | A | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| IL_04021.2_Instance_2 IL_04021.2,IL_5J7L_245,G24_C516 | G | U | G | G | A | U | G | C | U | G | A | A | A | C | ||||||||||||||||||||||
| IL_04021.2_Sequence_2 IL_04021.25J7L_G24_C516 | G | U | G | G | A | U | G | * | C | U | G | A | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| IL_04021.2_Instance_3 IL_04021.2,IL_7A0S_001,G24_C526 | G | U | G | G | A | U | G | C | U | G | A | A | A | C | ||||||||||||||||||||||
| IL_04021.2_Sequence_3 IL_04021.27A0S_G24_C526 | G | U | G | G | A | U | G | * | C | U | G | A | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| IL_04021.2_Instance_4 IL_04021.2,IL_8CRE_016,A13_U410 | A | C | G | G | A | U | C | G | U | G | A | A | A | U | ||||||||||||||||||||||
| IL_04021.2_Sequence_4 IL_04021.28CRE_A13_U410 | A | C | G | G | A | U | C | * | G | U | G | A | A | A | U | true | 93 | 0 | 0 | 1.37 | ||||||||||||||||
| IL_04021.2_Instance_5 IL_04021.2,IL_9DFE_001,G24_C516 | G | U | G | G | A | U | G | C | U | G | A | A | A | C | ||||||||||||||||||||||
| IL_04021.2_Sequence_5 IL_04021.29DFE_G24_C516 | G | U | G | G | A | U | G | * | C | U | G | A | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| IL_04021.2_Instance_6 IL_04021.2,IL_8P9A_244,A13_U410 | A | C | G | G | A | U | C | G | U | G | A | A | A | U | ||||||||||||||||||||||
| IL_04021.2_Sequence_6 IL_04021.28P9A_A13_U410 | A | C | G | G | A | U | C | * | G | U | G | A | A | A | U | true | 93 | 0 | 0 | 1.37 | ||||||||||||||||
| IL_04021.2_Instance_7 IL_04021.2,IL_4V9F_001,G21_U522 | G | U | G | G | A | U | U | A | U | G | A | A | A | U | ||||||||||||||||||||||
| IL_04021.2_Sequence_7 IL_04021.24V9F_G21_U522 | G | U | G | G | A | U | U | * | A | U | G | A | A | A | U | true | 94 | 0 | 0 | 1.18 |
1 2 s35 1 14 cWW 2 3 s35 3 4 s35 3 11 s33 3 12 tSH 4 10 s33 4 11 tSH 5 6 s35 5 10 tHS 5 11 s55 6 7 s35 6 9 cWW 7 8 cWW 7 9 s55 8 9 s35 9 10 s35 11 12 s35 12 13 s35 13 14 s35 9 8 7BPh 3 11 6BPh 4 11 6BPh 14 13 7BPh 12 3 6BR 13 3 6BR 10 4 6BR 4 10 6BR 5 10 6BRJAR3D SCFG/MRF model for IL_04021.2:
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 [14] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003577311,0.043094597,0.003875863,0.226399722,0.000000000],[0.005906150,0.015714136,0.064259229,0.013704592,0.000000000],[0.003836717,0.371598722,0.000767229,0.132961142,0.000000000],[0.063534774,0.022319394,0.007844230,0.020606190,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Basepair G24 - C561 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.277777778,0.055555556,0.611111111,0.000000000] | Position [1] | Left Index [2] | Right Index [13] // Fixed node on left for 4WF9|1|X|U|25 InitialNode | Left Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [3] | Right Index [13] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.959459459,0.013513514,0.013513514,0.013513514,0.000000000] | Position [2] | Left Index [3] | Right Index [13] // Fixed node on right for 4WF9|1|X|A|560 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [12] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.041656033,0.044098525,0.000500053,0.002356751,0.000000000],[0.041965507,0.043996411,0.000500053,0.000500053,0.000000000],[0.415457595,0.003500370,0.017112199,0.297098200,0.000000000],[0.046499257,0.043758888,0.000500053,0.000500053,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [12] // Basepair G26 - A559 tSH BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.041656033,0.044098525,0.000500053,0.002356751,0.000000000],[0.041965507,0.043996411,0.000500053,0.000500053,0.000000000],[0.415457595,0.003500370,0.017112199,0.297098200,0.000000000],[0.046499257,0.043758888,0.000500053,0.000500053,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [11] // Basepair G27 - A558 tSH BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.060217534,0.060664907,0.353130910,0.067218849,0.000000000],[0.063748375,0.063600760,0.002877103,0.063257399,0.000000000],[0.000722871,0.000722871,0.014065245,0.000722871,0.000000000],[0.003406895,0.000722871,0.244197666,0.000722871,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // Basepair A28 - G557 tHS BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.005120658,0.093919101,0.004571883,0.036238217,0.000000000],[0.005659542,0.006102386,0.006825337,0.022776847,0.000000000],[0.004476393,0.006952948,0.001411347,0.081825479,0.000000000],[0.006975500,0.005435434,0.005785304,0.705923623,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair U29 - U556 cWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009129921,0.018089638,0.010373405,0.190542929,0.000000000],[0.017837979,0.009183620,0.213028027,0.012496319,0.000000000],[0.010342519,0.232983258,0.001985647,0.024109674,0.000000000],[0.200290726,0.012542138,0.027328996,0.009735204,0.000000000],[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 G30 - C555 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_04021.2:
> IL_04021.2 4WF9 G 24 C 561 GUGGAUG*CUGAAAC > IL_04021.2 5J7L G 24 C 516 GUGGAUG*CUGAAAC > IL_04021.2 7A0S G 24 C 526 GUGGAUG*CUGAAAC > IL_04021.2 8CRE A 13 U 410 ACGGAUC*GUGAAAU > IL_04021.2 9DFE G 24 C 516 GUGGAUG*CUGAAAC > IL_04021.2 8P9A A 13 U 410 ACGGAUC*GUGAAAU > IL_04021.2 4V9F G 21 U 522 GUGGAUU*AUGAAAU