| 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 5 3 | 7 6 I | 8 7 4 | 9 8 I | 10 9 5 | 11 10 I | 12 11 6 | 13 12 I | 14 15 7 | 15 15 I | 16 16 | 17 15 I | 18 15 8 | 19 14 I | 20 20 9 | 21 20 I | 22 21 | 23 20 I | 24 20 10 | 25 19 I | 26 23 11 | 27 24 I | 28 25 12 | 29 26 I | 30 27 13 | 31 27 I | 32 28 | 33 27 I | 34 27 14 | 35 2 I | 36 2 15 | 37 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J4_35578.2_Instance_1 J4_35578.2,J4_4LFB_001,G115_C312 | G | A | G | U | A | A | C | G | U | C | G | U | A | G | C | C | ||||||||||||||||||||||||||
| J4_35578.2_Sequence_1 J4_35578.24LFB_G115_C312 | G | A | G | U | A | A | C | G | * | U | C | * | G | U | A | G | * | C | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||||
| J4_35578.2_Instance_2 J4_35578.2,J4_5J7L_001,G115_C312 | G | A | G | U | A | A | U | G | U | G | C | U | A | G | C | C | ||||||||||||||||||||||||||
| J4_35578.2_Sequence_2 J4_35578.25J7L_G115_C312 | G | A | G | U | A | A | U | G | * | U | G | * | C | U | A | G | * | C | C | true | 97 | 0 | 0 | 0.56 | ||||||||||||||||||
| J4_35578.2_Instance_3 J4_35578.2,J4_6CZR_027,G109_C308 | G | A | G | U | A | A | C | G | U | C | G | U | A | G | C | C | ||||||||||||||||||||||||||
| J4_35578.2_Sequence_3 J4_35578.26CZR_G109_C308 | G | A | G | U | A | A | C | G | * | U | C | * | G | U | A | G | * | C | C | true | 100 | 0 | 0 | 0.00 |
1 13 s35 1 15 cWW 2 3 s35 3 4 s35 4 12 s33 5 6 perp 5 9 s35 5 11 tHW 5 12 s55 6 7 s35 7 8 cWW 7 13 rib 9 10 cWW 10 11 s35 11 12 s35 13 14 cWW 13 15 s55 14 15 s35 12 5 6BPh 4 13 6BRJAR3D SCFG/MRF model for J4_35578.2:
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 [15] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | 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 [0.993970181,0.005999820,0.000029999] | 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 [15] // Basepair G115 - C312 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [14] // Fixed node on left for 4LFB|1|A|A|116 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 [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [1] | Left Index [3] | Right Index [14] // Fixed node on left for 4LFB|1|A|G|117 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 [4] | Right Index [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.029411765,0.029411765,0.029411765,0.911764706,0.000000000] | Position [1] | Left Index [4] | Right Index [14] // Fixed node on left for 4LFB|1|A|U|118 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 [5] | Right Index [14] // 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 [5] | Right Index [14] // Fixed node on left for 4LFB|1|A|A|119 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 [6] | Right Index [14] // 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 [6] | Right Index [14] // Fixed node on left for 4LFB|1|A|A|120 InitialNode | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.100000000,0.500000000,0.100000000,0.300000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [14] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [7] | Right Index [14] // Junction node G122 - C311 ID J6948 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | 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 [8] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.015686042,0.294004563,0.014178627,0.083761605,0.000000000],[0.013589530,0.012665230,0.036078109,0.014265099,0.000000000],[0.013874874,0.041159447,0.003212892,0.350415446,0.000000000],[0.036223202,0.015581863,0.014258162,0.041045308,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // Basepair G122 - U239 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 truncation InitialNode | Left Length Distribution [1.000000000] | 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 [14] // Initial node 4LFB|1|A|C|240 - 4LFB|1|A|C|311 from node JunctionNode | Branches [2] | Left Index [9] | Right Index [14] // Junction node C240 - C311 ID J3170 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | 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 [10] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | 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 [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [10] // Basepair C240 - G286 cWW HairpinNode | Num Bases [1] | Left Index [10] | Right Index [10] | 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 truncation InitialNode | Left Length Distribution [1.000000000] | 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 [11] | Right Index [14] // Initial node 4LFB|1|A|U|287 - 4LFB|1|A|C|311 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000] | Position [1] | Left Index [11] | Right Index [14] // Fixed node on left for 4LFB|1|A|G|286 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 [12] | Right Index [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.934782609,0.021739130,0.021739130,0.021739130,0.000000000] | Position [1] | Left Index [12] | Right Index [14] // Fixed node on left for 4LFB|1|A|U|287 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 [13] | Right Index [14] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | 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 [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [13] | Right Index [14] // Basepair G289 - C311 cWW HairpinNode | Num Bases [1] | Left Index [14] | Right Index [14] | 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 J4_35578.2:
> J4_35578.2 4LFB G 115 C 312 GAGUAACG*UC*GUAG*CC > J4_35578.2 5J7L G 115 C 312 GAGUAAUG*UG*CUAG*CC > J4_35578.2 6CZR G 109 C 308 GAGUAACG*UC*GUAG*CC