| 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 4 I | 8 5 4 | 9 5 I | 10 5 5 | 11 6 I | 12 7 6 | 13 7 I | 14 8 7 | 15 9 I | 16 10 8 | 17 10 I | 18 11 | 19 10 I | 20 10 9 | 21 7 I | 22 7 10 | 23 6 I | 24 5 11 | 25 4 I | 26 4 12 | 27 3 I | 28 3 13 | 29 2 I | 30 2 14 | 31 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_95652.3_Instance_1 IL_95652.3_IL_1FJG_034_G887_C910 | G | G | A | G | U | A | C | G | U | G | A | A | A | C | ||||||||||||||||||||||
| IL_95652.3_Sequence_1 IL_95652.3_IL_1FJG_034_G887_C910 | G | G | A | G | U | A | C | G | * | U | G | A | A | A | C | |||||||||||||||||||||
| IL_95652.3_Instance_2 IL_95652.3_IL_2AW7_041_G887_C910 | G | G | A | G | U | A | C | G | U | A | A | A | A | C | ||||||||||||||||||||||
| IL_95652.3_Sequence_2 IL_95652.3_IL_2AW7_041_G887_C910 | G | G | A | G | U | A | C | G | * | U | A | A | A | A | C | |||||||||||||||||||||
| IL_95652.3_Instance_3 IL_95652.3_IL_3U5F_057_G1111_C1134 | G | G | A | G | U | A | U | G | U | G | A | A | A | C | ||||||||||||||||||||||
| IL_95652.3_Sequence_3 IL_95652.3_IL_3U5F_057_G_1111_C_1134 | G | G | A | G | U | A | U | G | * | U | G | A | A | A | C | |||||||||||||||||||||
| IL_95652.3_Instance_4 IL_95652.3_IL_4BPP_052_G1083_C1107 | G | A | A | G | U | A | U | G | U | G | A | A | A | C | ||||||||||||||||||||||
| IL_95652.3_Sequence_4 IL_95652.3_IL_4BPP_052_G_1083_C_1107 | G | A | A | G | U | A | U | G | * | U | G | A | A | A | C |
1 2 s35 1 14 cWW 2 3 s33 2 12 s33 2 13 tSH 2 14 s55 3 4 s55 3 5 s55 3 11 s53 3 12 tHH 4 5 cSH 4 10 s33 5 6 s35 5 10 s33 5 11 tWH 6 7 s35 6 10 tHS 6 11 s55 7 8 s35 8 9 cWW 9 10 s35 11 12 s35 12 13 s35 13 14 s35 10 5 6BPh 4 11 6BPh 3 12 6BPh 14 13 7BPh 13 2 6BR 6 10 6BRJAR3D SCFG/MRF model for IL_95652.3:
Character Definition | A,C,G,U,* // Define characters here InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Initial node G887 - C910 from junction BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.003876703,0.055283349,0.004488645,0.073569181,0.000000000],[0.006541094,0.022376317,0.079237697,0.005043447,0.000000000],[0.004432143,0.610609112,0.000817354,0.010483940,0.000000000],[0.073144353,0.037059067,0.009043524,0.003994075,0.000000000],[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 [14] // Basepair G887 - C910 cWW BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.130969856,0.127242150,0.001382179,0.007812668,0.000000000],[0.120901106,0.102549889,0.001382179,0.001382179,0.000000000],[0.160425389,0.001382179,0.008196369,0.087318529,0.000000000],[0.125458163,0.120832807,0.001382179,0.001382179,0.000000000],[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 [2] | Right Index [13] // Basepair G888 - A909 tSH BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.570678958,0.107433541,0.026568743,0.026609119,0.000000000],[0.009819045,0.000760311,0.065362604,0.054006351,0.000000000],[0.004749819,0.063087677,0.001862668,0.000760311,0.000000000],[0.004672114,0.062108118,0.000760311,0.000760311,0.000000000],[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 [3] | Right Index [12] // Basepair A889 - A908 tHH ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [11] | Norm Constant [0.471704422088098] // Cluster node G890:U891 and A907:A907 Interaction | Interacting Bases [2,3] | Pair Probability [[0.025472342,0.005342148,0.026204408,0.005342148,0.000000000],[0.053063396,0.044352700,0.035460347,0.005342148,0.000000000],[0.005342148,0.005342148,0.062519909,0.024919560,0.000000000],[0.572676343,0.005342148,0.065903626,0.057374481,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U891 - A907 tWH Interaction | Interacting Bases [1,2] | Pair Probability [[0.054073450,0.055705351,0.003037987,0.002513558,0.000000000],[0.052305533,0.060757431,0.000646153,0.061231574,0.000000000],[0.036981281,0.020223322,0.041338982,0.490768639,0.000000000],[0.004652840,0.054184209,0.000646153,0.060933536,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G890 - U891 cSH 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 [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] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.137917373,0.045760669,0.311458334,0.047613612,0.000000000],[0.114554217,0.039460194,0.002849476,0.045859042,0.000000000],[0.001348900,0.000524797,0.014332810,0.000524797,0.000000000],[0.009454491,0.000524797,0.227291694,0.000524797,0.000000000],[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 [6] | Right Index [10] // Basepair A892 - G906 tHS FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000] | Position [1] | Left Index [7] | Right Index [9] // Fixed node on left 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 [0.0000249735224443] | Pair Probability [[0.016183114,0.304321651,0.015271658,0.043813033,0.000000000],[0.014196807,0.011327490,0.037477687,0.015135201,0.000000000],[0.014933673,0.043446980,0.003387233,0.377184865,0.000000000],[0.037192849,0.016768018,0.014870400,0.034489340,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [9] // Basepair G894 - U905 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 truncationSequences of instances from IL_95652.3:
> IL_95652.3 IL_1FJG_034 G 887 C 910 GGAGUACG*UGAAAC > IL_95652.3 IL_2AW7_041 G 887 C 910 GGAGUACG*UAAAAC > IL_95652.3 IL_3U5F_057 G 1111 C 1134 GGAGUAUG*UGAAAC > IL_95652.3 IL_4BPP_052 G 1083 C 1107 GAAGUAUG*UGAAAC