| 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 7 I | 8 8 4 | 9 9 I | 10 10 5 | 11 10 I | 12 11 6 | 13 11 I | 14 12 | 15 11 I | 16 11 7 | 17 10 I | 18 10 8 | 19 5 I | 20 14 9 | 21 14 I | 22 15 10 | 23 15 I | 24 16 | 25 15 I | 26 15 11 | 27 14 I | 28 14 12 | 29 3 I | 30 3 13 | 31 2 I | 32 2 14 | 33 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J3_15893.1_Instance_1 J3_15893.1,J3_6N5P_002,U48_A91 | U | U | A | A | U | C | G | U | A | G | C | G | C | A | ||||||||||||||||||||||||
| J3_15893.1_Sequence_1 J3_15893.16N5P_U48_A91 | U | U | A | A | U | C | * | G | U | A | G | * | C | G | C | A | true | 95 | 0 | 0 | 1.04 | |||||||||||||||||
| J3_15893.1_Instance_2 J3_15893.1,J3_4QK9_001,U47_A90 | U | G | A | A | U | C | G | U | A | G | C | G | A | A | ||||||||||||||||||||||||
| J3_15893.1_Sequence_2 J3_15893.14QK9_U47_A90 | U | G | A | A | U | C | * | G | U | A | G | * | C | G | A | A | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||
| J3_15893.1_Instance_3 J3_15893.1,J3_6N5P_001,C7_G111 | C | G | A | A | U | C | G | U | A | C | G | G | A | G | ||||||||||||||||||||||||
| J3_15893.1_Sequence_3 J3_15893.16N5P_C7_G111 | C | G | A | A | U | C | * | G | U | A | C | * | G | G | A | G | true | 99 | 0 | 0 | 0.19 | |||||||||||||||||
| J3_15893.1_Instance_4 J3_15893.1,J3_4W90_001,U62_A93 | U | G | A | A | U | C | G | U | A | G | C | G | A | A | ||||||||||||||||||||||||
| J3_15893.1_Sequence_4 J3_15893.14W90_U62_A93 | U | G | A | A | U | C | * | G | U | A | G | * | C | G | A | A | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||
| J3_15893.1_Instance_5 J3_15893.1,J3_4QLM_001,C43_G88 | C | G | A | A | U | C | G | U | A | G | C | G | A | G | ||||||||||||||||||||||||
| J3_15893.1_Sequence_5 J3_15893.14QLM_C43_G88 | C | G | A | A | U | C | * | G | U | A | G | * | C | G | A | G | true | 100 | 0 | 0 | 0.05 |
1 2 s35 1 14 cWW 2 4 s33 2 13 tSH 2 14 s55 3 4 s35 3 10 cSS 4 13 s35 5 6 s35 5 8 cWW 5 9 s55 6 7 cWW 7 8 s35 8 12 s33 9 10 s35 9 12 tHS 10 11 cWW 10 12 s55 11 12 s35 13 14 s35 2 5 6BPh 5 4 7BR 3 12 2BR 9 12 6BRJAR3D SCFG/MRF model for J3_15893.1:
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 [14] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008971369,0.016871195,0.010036256,0.191671055,0.000000000],[0.020727304,0.009504551,0.215061691,0.011796248,0.000000000],[0.010095364,0.192251066,0.002003525,0.022551723,0.000000000],[0.225967248,0.011209843,0.041465653,0.009815909,0.000000000],[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 U48 - A91 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.043291640,0.042675936,0.000511517,0.002413245,0.000000000],[0.043703614,0.044767300,0.000511517,0.000511517,0.000000000],[0.332546965,0.002957490,0.014489467,0.246350631,0.000000000],[0.105103604,0.117896261,0.001134648,0.001134648,0.000000000],[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 [2] | Right Index [13] // Basepair U49 - C90 tSH JunctionNode | Branches [2] | Left Index [3] | Right Index [12] // Junction node A50 - G89 ID J9705 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.400000000,0.200000000,0.200000000,0.200000000,0.000000000] | 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 [8] // Initial node 6N5P|1|A|A|50 - 6N5P|1|A|U|70 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.944444444,0.018518519,0.018518519,0.018518519,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left for 6N5P|1|A|A|50 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 [4] | Right Index [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Position [1] | Left Index [4] | Right Index [8] // Fixed node on left for 6N5P|1|A|A|51 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 [5] | Right Index [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.005065621,0.092909663,0.004522745,0.007899258,0.000000000],[0.005598713,0.006036798,0.006751979,0.004964929,0.000000000],[0.004428281,0.006878218,0.001396178,0.017836433,0.000000000],[0.034502640,0.026885073,0.028615621,0.745707851,0.000000000],[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 [8] // Basepair U52 - U70 cWW BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009264105,0.016612765,0.010650229,0.193109658,0.000000000],[0.019697072,0.009435223,0.250623774,0.013396622,0.000000000],[0.010769834,0.197270651,0.002030047,0.022795742,0.000000000],[0.195613131,0.012907388,0.026006356,0.009817401,0.000000000],[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 [6] | Right Index [7] // Basepair C53 - G69 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 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 [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [9] | Right Index [12] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.109524473,0.110338161,0.179095876,0.122258561,0.000000000],[0.115946415,0.115677931,0.001314768,0.115053422,0.000000000],[0.001314768,0.001314768,0.006427485,0.001314768,0.000000000],[0.006196507,0.001314768,0.111592561,0.001314768,0.000000000],[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 [9] | Right Index [12] // Basepair A71 - G89 tHS BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009417290,0.019076634,0.010743958,0.195076917,0.000000000],[0.017226610,0.009304766,0.207905455,0.013002891,0.000000000],[0.010672216,0.239916288,0.002029679,0.025359511,0.000000000],[0.193575287,0.013296343,0.023433726,0.009962428,0.000000000],[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 [10] | Right Index [11] // Basepair G72 - C88 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 J3_15893.1:
> J3_15893.1 6N5P U 48 A 91 UUAAUC*GUAG*CGCA > J3_15893.1 4QK9 U 47 A 90 UGAAUC*GUAG*CGAA > J3_15893.1 6N5P C 7 G 111 CGAAUC*GUAC*GGAG > J3_15893.1 4W90 U 62 A 93 UGAAUC*GUAG*CGAA > J3_15893.1 4QLM C 43 G 88 CGAAUC*GUAG*CGAG