| 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 13 6 | 13 13 I | 14 14 7 | 15 15 I | 16 16 8 | 17 16 I | 18 17 | 19 16 I | 20 16 9 | 21 13 I | 22 13 10 | 23 12 I | 24 19 11 | 25 19 I | 26 20 | 27 19 I | 28 19 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_11934.2_Instance_1 J3_11934.2,J3_1G1X_004,C717_G673 | C | G | C | C | G | A | U | G | G | C | A | G | U | G | ||||||||||||||||||||||
| J3_11934.2_Sequence_1 J3_11934.21G1X_C717_G673 | C | G | C | C | G | A | U | G | G | * | C | A | G | * | U | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| J3_11934.2_Instance_2 J3_11934.2,J3_6CZR_017,C701_G657 | C | G | C | C | G | A | U | G | G | C | A | G | U | G | ||||||||||||||||||||||
| J3_11934.2_Sequence_2 J3_11934.26CZR_C701_G657 | C | G | C | C | G | A | U | G | G | * | C | A | G | * | U | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| J3_11934.2_Instance_3 J3_11934.2,J3_5J7L_003,U717_A673 | U | A | C | C | G | G | U | G | G | C | G | G | U | A | ||||||||||||||||||||||
| J3_11934.2_Sequence_3 J3_11934.25J7L_U717_A673 | U | A | C | C | G | G | U | G | G | * | C | G | G | * | U | A | true | 95 | 0 | 0 | 1.04 | |||||||||||||||
| J3_11934.2_Instance_4 J3_11934.2,J3_1G1X_002,C717_G673 | C | G | C | C | G | A | U | G | G | C | A | G | U | G | ||||||||||||||||||||||
| J3_11934.2_Sequence_4 J3_11934.21G1X_C717_G673 | C | G | C | C | G | A | U | G | G | * | C | A | G | * | U | G | true | 100 | 0 | 0 | 0.00 |
1 11 s35 1 13 cWW 2 3 s35 3 4 s35 4 5 s33 5 6 s53 5 10 s53 6 7 s55 6 10 tWW 7 8 s35 8 9 cWW 11 12 cWW 11 13 s55 4 2 6BPh 4 3 7BPhJAR3D SCFG/MRF model for J3_11934.2:
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 [0.0000239574126029] | Pair Probability [[0.009230036,0.016881218,0.010494353,0.194361300,0.000000000],[0.020319858,0.009555111,0.230862069,0.012852202,0.000000000],[0.010589659,0.197055880,0.002038410,0.022912280,0.000000000],[0.207859340,0.012317386,0.032759727,0.009911172,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [13] // Basepair C717 - G673 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.250000000,0.083333333,0.583333333,0.083333333,0.000000000] | Position [1] | Left Index [2] | Right Index [12] // Fixed node on left for 1G1X|1|I|G|673 InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [3] | Right Index [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [3] | Right Index [12] // Fixed node on left for 1G1X|1|J|C|717 InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.002525253,0.992424242,0.002525253,0.002525253,0.000000000] | Position [1] | Left Index [4] | Right Index [12] // Fixed node on left for 1G1X|1|J|G|718 InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.083333333,0.750000000,0.083333333,0.000000000] | Position [1] | Left Index [5] | Right Index [12] // Fixed node on left for 1G1X|1|J|C|719 InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [6] | Right Index [12] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [6] | Right Index [12] // Junction node A722 - U672 ID J9648 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [10] // Initial node BasepairNode | Deletion Probability [0.0000001215781528] | Pair Probability [[0.401255674,0.027522755,0.003794261,0.018143346,0.000000000],[0.032304027,0.013953029,0.011536164,0.013951289,0.000000000],[0.003794261,0.011321351,0.367498044,0.020737530,0.000000000],[0.018419390,0.013983695,0.023974231,0.017810950,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Left Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [10] // Basepair A722 - A733 tWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.083333333,0.750000000,0.083333333,0.000000000] | Position [1] | Left Index [7] | Right Index [9] // Fixed node on left for 1G1X|1|J|G|721 InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [8] | Right Index [9] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009546506,0.019881954,0.010870922,0.197449200,0.000000000],[0.016768697,0.009361308,0.199122279,0.013028540,0.000000000],[0.010750195,0.243371713,0.002049102,0.026250458,0.000000000],[0.194922229,0.013522366,0.023009709,0.010094826,0.000000000],[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 [8] | Right Index [9] // Basepair G725 - C732 cWW HairpinNode | Num Bases [1] | Left Index [9] | Right Index [9] | 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 [11] | Right Index [12] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.015535214,0.291177596,0.014042294,0.082956205,0.000000000],[0.013458861,0.012543449,0.035731204,0.014127935,0.000000000],[0.013741462,0.040763683,0.003181999,0.356661451,0.000000000],[0.035874902,0.015432038,0.014121064,0.040650641,0.000000000],[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 [11] | Right Index [12] // Basepair G734 - U672 cWW HairpinNode | Num Bases [1] | Left Index [12] | Right Index [12] | 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_11934.2:
> J3_11934.2 1G1X C 717 G 673 CGCCGAUGG*CAG*UG > J3_11934.2 6CZR C 701 G 657 CGCCGAUGG*CAG*UG > J3_11934.2 5J7L U 717 A 673 UACCGGUGG*CGG*UA > J3_11934.2 1G1X C 717 G 673 CGCCGAUGG*CAG*UG