| 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 5 I | 8 8 4 | 9 8 I | 10 9 5 | 11 9 I | 12 10 | 13 9 I | 14 9 6 | 15 8 I | 16 8 7 | 17 7 I | 18 12 8 | 19 13 I | 20 14 9 | 21 14 I | 22 15 | 23 14 I | 24 14 10 | 25 3 I | 26 3 11 | 27 2 I | 28 2 12 | 29 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J3_44724.2_Instance_1 J3_44724.2,J3_7A0S_005,C745_G713 | C | G | A | A | C | G | A | U | G | C | A | G | ||||||||||||||||||||||
| J3_44724.2_Sequence_1 J3_44724.27A0S_C745_G713 | C | G | A | A | C | * | G | A | U | G | * | C | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| J3_44724.2_Instance_2 J3_44724.2,J3_4WF9_003,C777_G745 | C | G | A | A | C | G | A | U | G | C | A | G | ||||||||||||||||||||||
| J3_44724.2_Sequence_2 J3_44724.24WF9_C777_G745 | C | G | A | A | C | * | G | A | U | G | * | C | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| J3_44724.2_Instance_3 J3_44724.2,J3_5J7L_039,C732_G700 | C | G | A | A | C | G | A | U | G | C | A | G | ||||||||||||||||||||||
| J3_44724.2_Sequence_3 J3_44724.25J7L_C732_G700 | C | G | A | A | C | * | G | A | U | G | * | C | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| J3_44724.2_Instance_4 J3_44724.2,J3_4V9F_003,U823_A791 | U | G | U | U | A | G | C | G | U | G | C | A | A | |||||||||||||||||||||
| J3_44724.2_Sequence_4 J3_44724.24V9F_U823_A791 | U | G | U | U | A | G | * | C | G | U | G | * | C | A | A | true | 63 | 0 | 0 | 6.34 | ||||||||||||||
| J3_44724.2_Instance_5 J3_44724.2,J3_4Y4O_020,C732_G700 | C | G | A | A | C | G | A | U | G | C | A | G | ||||||||||||||||||||||
| J3_44724.2_Sequence_5 J3_44724.24Y4O_C732_G700 | C | G | A | A | C | * | G | A | U | G | * | C | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 12 cWW 2 7 s33 2 11 tSH 2 12 s55 3 4 s35 3 11 s55 4 5 s35 4 7 tHS 5 6 cWW 5 7 s55 6 7 s35 8 9 s55 8 10 s53 9 10 cWW 11 12 s35 7 3 6BPh 5 4 7BPh 3 11 6BPh 11 2 6BR 4 7 6BRJAR3D SCFG/MRF model for J3_44724.2:
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 [12] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009166526,0.016698909,0.010445572,0.192630123,0.000000000],[0.020040483,0.009458332,0.238769746,0.012863164,0.000000000],[0.010545011,0.195597456,0.002021206,0.022714403,0.000000000],[0.205731170,0.012341540,0.031159455,0.009816904,0.000000000],[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 [12] // Basepair C745 - G713 cWW BasepairNode | Deletion Probability [0.0000081095392462] | Pair Probability [[0.109524473,0.115946415,0.001314768,0.006196507,0.000000000],[0.110338161,0.115677931,0.001314768,0.001314768,0.000000000],[0.179095876,0.001314768,0.006427485,0.111592561,0.000000000],[0.122258561,0.115053422,0.001314768,0.001314768,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.792098765,0.205432099,0.002370370,0.000098765] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | 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 [11] // Basepair G746 - A712 tSH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.770270270,0.013513514,0.013513514,0.202702703,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left for 7A0S|1|X|G|713 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 [10] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [4] | Right Index [10] // Junction node A748 - C711 ID J9502 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | 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 [7] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.467600446,0.066871455,0.130967468,0.063635401,0.000000000],[0.058121641,0.032856091,0.001314859,0.062962726,0.000000000],[0.004312069,0.000703366,0.008712280,0.000703366,0.000000000],[0.026153613,0.000703366,0.073678488,0.000703366,0.000000000],[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 [7] // Basepair A748 - A774 tHS BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.004801084,0.009156790,0.005498843,0.099771814,0.000000000],[0.046631412,0.022600450,0.523904012,0.032037174,0.000000000],[0.005512497,0.112080626,0.001043580,0.012360508,0.000000000],[0.100057605,0.006733082,0.012727023,0.005083501,0.000000000],[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 [5] | Right Index [6] // Basepair C749 - G773 cWW HairpinNode | Num Bases [1] | Left Index [6] | Right Index [6] | 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 [8] | Right Index [10] // Initial node 7A0S|1|X|U|775 - 7A0S|1|X|C|711 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.071428571,0.071428571,0.785714286,0.000000000] | Position [1] | Left Index [8] | Right Index [10] // Fixed node on left for 7A0S|1|X|C|749 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 [9] | Right Index [10] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009455586,0.019692602,0.010767390,0.195568732,0.000000000],[0.016608995,0.009272152,0.197225876,0.012904458,0.000000000],[0.010647812,0.250577697,0.002029586,0.026000454,0.000000000],[0.193065826,0.013393582,0.022790568,0.009998684,0.000000000],[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 G776 - C711 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_44724.2:
> J3_44724.2 7A0S C 745 G 713 CGAAC*GAUG*CAG > J3_44724.2 4WF9 C 777 G 745 CGAAC*GAUG*CAG > J3_44724.2 5J7L C 732 G 700 CGAAC*GAUG*CAG > J3_44724.2 4V9F U 823 A 791 UGUUAG*CGUG*CAA > J3_44724.2 4Y4O C 732 G 700 CGAAC*GAUG*CAG