| 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 9 4 | 9 9 I | 10 10 | 11 9 I | 12 9 5 | 13 8 I | 14 12 6 | 15 12 I | 16 13 | 17 12 I | 18 12 7 | 19 2 I | 20 2 8 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J3_82061.2_Instance_1 J3_82061.2,J3_5T5A_001,C13_G48 | C | C | A | G | C | C | G | C | G | |||||||||||||||||
| J3_82061.2_Sequence_1 J3_82061.25T5A_C13_G48 | C | C | A | G | * | C | C | * | G | C | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| J3_82061.2_Instance_2 J3_82061.2,J3_7K16_001,C40_G24 | C | C | C | U | C | G | U | A | G | |||||||||||||||||
| J3_82061.2_Sequence_2 J3_82061.27K16_C40_G24 | C | C | C | U | C | * | G | U | * | A | G | true | 81 | 0 | 0 | 2.18 | ||||||||||
| J3_82061.2_Instance_3 J3_82061.2,J3_5TPY_002,G43_C23 | G | C | A | G | C | C | G | C | C | |||||||||||||||||
| J3_82061.2_Sequence_3 J3_82061.25TPY_G43_C23 | G | C | A | G | * | C | C | * | G | C | C | true | 100 | 0 | 0 | 0.05 |
1 2 s35 1 8 cWW 2 3 s35 2 8 s55 4 5 cWW 4 7 s53 5 6 s35 6 7 cWWJAR3D SCFG/MRF model for J3_82061.2:
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 [8] // Initial node BasepairNode | Deletion Probability [0.0000006691671388] | Pair Probability [[0.009509057,0.017981890,0.010896842,0.197694967,0.000000000],[0.019030193,0.009563019,0.224400354,0.013489511,0.000000000],[0.010937493,0.212742702,0.002069309,0.024327358,0.000000000],[0.198545855,0.013323228,0.025418591,0.010069631,0.000000000],[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 [0.334863624,0.653524170,0.011072104,0.000540103] | Right Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair C13 - G48 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [7] // Fixed node on left for 5T5A|1|A|C|14 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 [3] | Right Index [7] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.300000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [3] | Right Index [7] // Fixed node on left for 5T5A|1|A|A|15 InitialNode | Left Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [4] | Right Index [7] // Junction node G16 - G46 ID J5059 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 [4] | Right Index [5] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009574124,0.019028436,0.010936653,0.198530575,0.000000000],[0.017980846,0.009507606,0.212727929,0.013322270,0.000000000],[0.010896029,0.224384255,0.002069153,0.025416337,0.000000000],[0.197680266,0.013488440,0.024325847,0.010131233,0.000000000],[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 G16 - C34 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 [6] | Right Index [7] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009278201,0.017081703,0.010509311,0.196044617,0.000000000],[0.020663004,0.009657695,0.222404933,0.012750390,0.000000000],[0.010596976,0.198258342,0.002054445,0.023100179,0.000000000],[0.210129795,0.012196624,0.035266599,0.010007185,0.000000000],[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 C35 - G46 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 truncationSequences of instances from J3_82061.2:
> J3_82061.2 5T5A C 13 G 48 CCAG*CC*GCG > J3_82061.2 7K16 C 40 G 24 CCCUC*GU*AG > J3_82061.2 5TPY G 43 C 23 GCAG*CC*GCC