| 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 6 I | 10 9 5 | 11 9 I | 12 10 6 | 13 10 I | 14 11 | 15 10 I | 16 10 7 | 17 9 I | 18 9 8 | 19 8 I | 20 13 9 | 21 13 I | 22 14 | 23 13 I | 24 13 10 | 25 4 I | 26 4 11 | 27 3 I | 28 3 12 | 29 2 I | 30 2 13 | 31 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J3_89368.2_Instance_1 J3_89368.2,J3_5J7L_044,G2223_C2200 | G | G | A | C | A | G | C | U | G | C | U | A | A | C | ||||||||||||||||||||||
| J3_89368.2_Sequence_1 J3_89368.25J7L_G_2223_C_2200 | G | G | A | C | A | G | * | C | U | G | * | C | U | A | A | C | true | 96 | 0 | 0 | 0.83 | |||||||||||||||
| J3_89368.2_Instance_2 J3_89368.2,J3_7A0S_009,G2202_C2183 | G | G | A | C | C | G | U | U | G | C | U | A | A | C | ||||||||||||||||||||||
| J3_89368.2_Sequence_2 J3_89368.27A0S_G_2202_C_2183 | G | G | A | C | C | G | * | U | U | G | * | C | U | A | A | C | true | 100 | 0 | 0 | 0.09 | |||||||||||||||
| J3_89368.2_Instance_3 J3_89368.2,J3_4Y4O_024,G2223_C2200 | G | G | A | C | A | G | U | U | G | C | U | A | A | C | ||||||||||||||||||||||
| J3_89368.2_Sequence_3 J3_89368.24Y4O_G_2223_C_2200 | G | G | A | C | A | G | * | U | U | G | * | C | U | A | A | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 13 cWW 2 11 s33 2 12 tSH 2 13 s55 3 4 perp 3 8 perp 3 9 s35 3 11 tHW 3 12 s55 4 5 s35 5 6 s35 5 8 tHH 6 7 cWW 7 8 s33 8 12 perp 9 10 cWW 9 11 s55 10 11 s35 12 13 s35 8 4 6BPh 13 12 7BPh 12 2 6BR 3 8 2BR 2 11 6BRJAR3D SCFG/MRF model for J3_89368.2:
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 [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 G2223 - C2200 cWW BasepairNode | Deletion Probability [0.0000001200211660] | Pair Probability [[0.054373565,0.057561746,0.000652718,0.003076264,0.000000000],[0.054777521,0.057428457,0.000652718,0.000652718,0.000000000],[0.355485412,0.003263592,0.015954665,0.277001348,0.000000000],[0.060695419,0.057118419,0.000652718,0.000652718,0.000000000],[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 [0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Left Index [2] | Right Index [12] // Basepair G2224 - A2199 tSH BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.031414977,0.069913377,0.006952185,0.724344680,0.000000000],[0.001390437,0.112042646,0.003332969,0.001390437,0.000000000],[0.006525919,0.001390437,0.010574156,0.008067148,0.000000000],[0.001390437,0.001390437,0.006184185,0.013695573,0.000000000],[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 [11] // Basepair A2225 - U2197 tHW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [4] | Right Index [10] // Fixed node on left for 5J7L|1|DA|C|2196 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 [10] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [5] | Right Index [10] // Junction node A2227 - C2196 ID J2542 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 [5] | Right Index [8] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.004372016,0.023802933,0.040905506,0.468355729,0.000000000],[0.003421711,0.000681199,0.003865228,0.430185828,0.000000000],[0.003214366,0.004196854,0.000681199,0.004768391,0.000000000],[0.003036397,0.003063052,0.000681199,0.004768391,0.000000000],[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 [5] | Right Index [8] // Basepair A2227 - U2092 tHH BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.013670424,0.202694703,0.013111240,0.122296464,0.000000000],[0.014703520,0.011594218,0.091070574,0.013895076,0.000000000],[0.012868105,0.106114901,0.002831594,0.242445403,0.000000000],[0.089753694,0.014939126,0.017249809,0.030761150,0.000000000],[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 G2228 - C2091 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 [10] // Initial 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 [9] | Right Index [10] // Basepair G2093 - C2196 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 truncationSequences of instances from J3_89368.2:
> J3_89368.2 5J7L G 2223 C 2200 GGACAG*CUG*CUAAC > J3_89368.2 7A0S G 2202 C 2183 GGACCG*UUG*CUAAC > J3_89368.2 4Y4O G 2223 C 2200 GGACAG*UUG*CUAAC