| 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 8 3 | 7 8 I | 8 9 4 | 9 9 I | 10 10 | 11 9 I | 12 9 5 | 13 8 I | 14 8 6 | 15 7 I | 16 12 7 | 17 12 I | 18 13 | 19 12 I | 20 12 8 | 21 5 I | 22 4 9 | 23 3 I | 24 3 10 | 25 2 I | 26 2 11 | 27 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J3_52655.1_Instance_1 J3_52655.1,J3_4V88_036,U1168_A1577 | U | G | G | A | U | A | C | G | G | A | A | |||||||||||||||||||||
| J3_52655.1_Sequence_1 J3_52655.14V88_U_1168_A_1577 | U | G | G | A | * | U | A | C | * | G | G | A | A | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| J3_52655.1_Instance_2 J3_52655.1,J3_4LFB_003,U943_A1340 | U | G | G | A | U | A | C | G | G | A | A | |||||||||||||||||||||
| J3_52655.1_Sequence_2 J3_52655.14LFB_U943_A_1340 | U | G | G | A | * | U | A | C | * | G | G | A | A | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| J3_52655.1_Instance_3 J3_52655.1,J3_5J7L_005,U943_A1340 | U | G | G | A | U | A | C | G | G | A | A | |||||||||||||||||||||
| J3_52655.1_Sequence_3 J3_52655.15J7L_U943_A_1340 | U | G | G | A | * | U | A | C | * | G | G | A | A | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 11 cWW 2 8 perp 2 9 s33 2 10 tSH 2 11 s55 3 4 s35 3 6 cWW 3 8 s53 4 5 cWW 4 6 s55 5 6 s35 6 7 s35 7 8 cWW 9 10 s35 10 11 s35 2 9 6BPh 10 2 6BRJAR3D SCFG/MRF model for J3_52655.1:
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 [11] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.008946623,0.017374423,0.009813872,0.194415132,0.000000000],[0.021829934,0.009736222,0.195069241,0.010937668,0.000000000],[0.009833013,0.192572728,0.002024403,0.022823782,0.000000000],[0.231566497,0.010273839,0.052777129,0.010005495,0.000000000],[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 [11] // Basepair U1168 - A1577 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 [10] // Basepair G1169 - A1576 tSH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [2] | Left Index [3] | Right Index [9] // Fixed node on right for 4V88|1|A6|G|1575 InitialNode | Left Length Distribution [1.000000000] | 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 [8] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [3] | Right Index [8] // Junction node G1170 - G1574 ID J4897 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 [3] | Right Index [6] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.022714400,0.014208547,0.344665804,0.017391100,0.000000000],[0.014550196,0.010056568,0.019032089,0.044684804,0.000000000],[0.387869342,0.018820727,0.003587431,0.015492321,0.000000000],[0.017425019,0.042291852,0.015831483,0.011378317,0.000000000],[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 [6] // Basepair G1170 - A1469 cWW BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009192800,0.021796849,0.009818110,0.231259682,0.000000000],[0.017348091,0.009487247,0.192280868,0.010258268,0.000000000],[0.009798999,0.194773596,0.002021335,0.052697140,0.000000000],[0.194120479,0.010921091,0.022789191,0.011436255,0.000000000],[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 [4] | Right Index [5] // Basepair A1171 - U1468 cWW HairpinNode | Num Bases [1] | Left Index [5] | Right Index [5] | 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 [7] | Right Index [8] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[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 C1470 - G1574 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 J3_52655.1:
> J3_52655.1 4V88 U 1168 A 1577 UGGA*UAC*GGAA > J3_52655.1 4LFB U 943 A 1340 UGGA*UAC*GGAA > J3_52655.1 5J7L U 943 A 1340 UGGA*UAC*GGAA