| 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 7 3 | 7 7 I | 8 8 | 9 7 I | 10 7 4 | 11 6 I | 12 10 5 | 13 11 I | 14 14 6 | 15 14 I | 16 15 | 17 14 I | 18 14 7 | 19 13 I | 20 17 8 | 21 18 I | 22 19 9 | 23 20 I | 24 21 10 | 25 21 I | 26 22 | 27 21 I | 28 21 11 | 29 2 I | 30 2 12 | 31 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J4_36296.1_Instance_1 J4_36296.1,J4_2CSX_001,G7_C66 | G | U | A | G | C | G | G | C | A | G | G | UC | G | C | C | |||||||||||||||||||||
| J4_36296.1_Sequence_1 J4_36296.12CSX_G7_C66 | G | U | A | G | * | C | G | G | * | C | A | G | G | UC | G | * | C | C | true | 86 | 0 | 0 | 2.46 | |||||||||||||
| J4_36296.1_Instance_2 J4_36296.1,J4_3WFS_001,G7_C66 | G | U | A | G | C | A | C | G | G | U | G | UC | G | C | C | |||||||||||||||||||||
| J4_36296.1_Sequence_2 J4_36296.13WFS_G7_C66 | G | U | A | G | * | C | A | C | * | G | G | U | G | UC | G | * | C | C | true | 100 | 0 | 0 | 0.01 | |||||||||||||
| J4_36296.1_Instance_3 J4_36296.1,J4_4YCO_001,A7_U66 | A | U | A | G | C | A | G | C | G | U | G | UC | C | G | U | |||||||||||||||||||||
| J4_36296.1_Sequence_3 J4_36296.14YCO_A7_U66 | A | U | A | G | * | C | A | G | * | C | G | U | G | UC | C | * | G | U | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| J4_36296.1_Instance_4 J4_36296.1,J4_1QTQ_001,A907_U966 | A | U | C | G | C | A | C | G | C | A | UUC | C | G | U | ||||||||||||||||||||||
| J4_36296.1_Sequence_4 J4_36296.11QTQ_A907_U966 | A | U | C | G | * | C | A | C | * | G | C | A | UUC | C | * | G | U | true | 77 | 0 | 0 | 4.11 | ||||||||||||||
| J4_36296.1_Instance_5 J4_36296.1,J4_1B23_001,U7_A66 | U | U | A | A | U | A | G | U | C | U | A | G | U | A | A | |||||||||||||||||||||
| J4_36296.1_Sequence_5 J4_36296.11B23_U7_A66 | U | U | A | A | * | U | A | G | * | U | C | U | A | G | U | * | A | A | true | 85 | 0 | 0 | 2.71 |
1 10 s35 1 12 cWW 2 8 s33 2 9 s55 3 4 cWW 3 5 s55 4 5 s35 5 6 s35 6 7 cWW 7 8 s35 10 11 cWW 10 12 s55 11 12 s35JAR3D SCFG/MRF model for J4_36296.1:
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 [12] // Initial node BasepairNode | Deletion Probability [0.0000001230289089] | Pair Probability [[0.009144557,0.019838405,0.010084783,0.214730832,0.000000000],[0.017733483,0.009341630,0.192608427,0.011332799,0.000000000],[0.010033209,0.214437463,0.002002136,0.035555344,0.000000000],[0.202636174,0.011658290,0.028412642,0.010449825,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Left Letter Distribution [0.071428571,0.071428571,0.071428571,0.785714286,0.000000000] | 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 G7 - C66 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.642857143,0.214285714,0.071428571,0.071428571,0.000000000] | Position [1] | Left Index [2] | Right Index [11] // Fixed node on left for 2CSX|1|C|U|8 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 [3] | Right Index [11] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [3] | Right Index [11] // Junction node G10 - C65 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 [3] | Right Index [4] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009368009,0.020030415,0.010540131,0.205635456,0.000000000],[0.016690726,0.009279029,0.195504376,0.012336141,0.000000000],[0.010440720,0.238674882,0.002020236,0.031139040,0.000000000],[0.192537250,0.012857479,0.022703477,0.010242632,0.000000000],[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 [3] | Right Index [4] // Basepair G10 - C25 cWW HairpinNode | Num Bases [1] | Left Index [4] | Right Index [4] | 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 [5] | Right Index [11] // Initial node 2CSX|1|C|G|26 - 2CSX|1|C|C|65 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.642857143,0.071428571,0.214285714,0.071428571,0.000000000] | Position [1] | Left Index [5] | Right Index [11] // Fixed node on left for 2CSX|1|C|C|25 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 [6] | Right Index [11] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [6] | Right Index [11] // Junction node G27 - C65 ID J344 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 [6] | Right Index [7] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.010565328,0.072203042,0.011348759,0.171904585,0.000000000],[0.017188563,0.009967747,0.186218041,0.013319109,0.000000000],[0.011289177,0.187214431,0.002254192,0.092076175,0.000000000],[0.162578230,0.013577401,0.022316085,0.015979133,0.000000000],[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 G27 - C43 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 [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [11] // Initial node 2CSX|1|C|A|44 - 2CSX|1|C|C|65 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.214285714,0.357142857,0.357142857,0.071428571,0.000000000] | Position [1] | Left Index [8] | Right Index [11] // Fixed node on left for 2CSX|1|C|C|43 InitialNode | Left Length Distribution [0.204221895,0.787432499,0.007952872,0.000392734] | Left Letter Distribution [0.083333333,0.083333333,0.250000000,0.583333333,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [11] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.357142857,0.071428571,0.500000000,0.071428571,0.000000000] | Position [1] | Left Index [9] | Right Index [11] // Fixed node on left for 2CSX|1|C|A|44 InitialNode | Left Length Distribution [0.001959824,0.201861832,0.591866732,0.201959824,0.002253797,0.000097991] | Left Letter Distribution [0.041666667,0.375000000,0.125000000,0.458333333,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [11] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009243119,0.017930843,0.010492436,0.193613753,0.000000000],[0.018805252,0.009393104,0.217410587,0.012666299,0.000000000],[0.010496202,0.216920274,0.002021022,0.023996287,0.000000000],[0.204712248,0.012536017,0.029873140,0.009889417,0.000000000],[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 G49 - C65 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 J4_36296.1:
> J4_36296.1 2CSX G 7 C 66 GUAG*CGG*CAGGUCG*CC > J4_36296.1 3WFS G 7 C 66 GUAG*CAC*GGUGUCG*CC > J4_36296.1 4YCO A 7 U 66 AUAG*CAG*CGUGUCC*GU > J4_36296.1 1QTQ A 907 U 966 AUCG*CAC*GCAUUCC*GU > J4_36296.1 1B23 U 7 A 66 UUAA*UAG*UCUAGU*AA