| 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 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_56052.2_Instance_1 J3_56052.2,J3_5J7L_002,C586_G755 | C | G | G | C | U | U | G | C | G | |||||||||||||||||
| J3_56052.2_Sequence_1 J3_56052.25J7L_C586_G755 | C | G | G | * | C | U | U | G | * | C | G | true | 93 | 0 | 0 | 0.85 | ||||||||||
| J3_56052.2_Instance_2 J3_56052.2,J3_6CZR_016,C570_G739 | C | G | G | C | U | A | G | C | G | |||||||||||||||||
| J3_56052.2_Sequence_2 J3_56052.26CZR_C570_G739 | C | G | G | * | C | U | A | G | * | C | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| J3_56052.2_Instance_3 J3_56052.2,J3_1G1X_001,C586_G755 | C | G | G | C | U | A | G | C | G | |||||||||||||||||
| J3_56052.2_Sequence_3 J3_56052.21G1X_C586_G755 | C | G | G | * | C | U | A | G | * | C | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| J3_56052.2_Instance_4 J3_56052.2,J3_1KUQ_001,C4_G54 | C | G | G | C | U | A | G | C | G | |||||||||||||||||
| J3_56052.2_Sequence_4 J3_56052.21KUQ_C4_G54 | C | G | G | * | C | U | A | G | * | C | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 8 cWW 2 8 s55 3 4 cWW 3 5 s55 4 5 s35 6 7 cWW 2 7 6BPh 6 8 2BRJAR3D SCFG/MRF model for J3_56052.2:
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 [0.0000239574126029] | Pair Probability [[0.009353183,0.016772504,0.010752635,0.194966481,0.000000000],[0.019886467,0.009525946,0.243418233,0.013525436,0.000000000],[0.010873390,0.199167485,0.002049567,0.023014932,0.000000000],[0.197494026,0.013031497,0.026256418,0.009911799,0.000000000],[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 [8] // Basepair C586 - G755 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.016666667,0.016666667,0.950000000,0.016666667,0.000000000] | Position [1] | Left Index [2] | Right Index [7] // Fixed node on left for 5J7L|1|AA|G|587 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 [7] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [3] | Right Index [7] // Junction node G588 - C754 ID J7093 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 [3] | Right Index [4] // Initial 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 [3] | Right Index [4] // Basepair G588 - C651 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 [7] // Initial node 5J7L|1|AA|U|652 - 5J7L|1|AA|C|754 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000] | Position [1] | Left Index [5] | Right Index [7] // Fixed node on left for 5J7L|1|AA|U|652 InitialNode | Left Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Left Letter Distribution [0.583333333,0.083333333,0.083333333,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.004738018,0.009867595,0.005395338,0.097995839,0.000000000],[0.008322457,0.004646102,0.098826203,0.006466183,0.000000000],[0.026677098,0.546955482,0.005084939,0.065141709,0.000000000],[0.096741680,0.006711274,0.011419928,0.005010154,0.000000000],[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 G654 - C754 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_56052.2:
> J3_56052.2 5J7L C 586 G 755 CGG*CUUG*CG > J3_56052.2 6CZR C 570 G 739 CGG*CUAG*CG > J3_56052.2 1G1X C 586 G 755 CGG*CUAG*CG > J3_56052.2 1KUQ C 4 G 54 CGG*CUAG*CG