| 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 5 2 | 5 5 I | 6 12 3 | 7 12 I | 8 13 | 9 12 I | 10 12 4 | 11 11 I | 12 10 5 | 13 9 I | 14 8 6 | 15 7 I | 16 6 7 | 17 5 I | 18 5 8 | 19 4 I | 20 3 9 | 21 2 I | 22 2 10 | 23 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_35043.1_Instance_1 IL_35043.1_IL_1GID_006_G134_C189 | G | U | A | U | A | A | U | A | A | G | C | |||||||||||||||||
| IL_35043.1_Sequence_1 IL_35043.1_IL_1GID_006_G134_C189 | G | U | A | * | U | A | A | U | A | A | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_35043.1_Instance_2 IL_35043.1_IL_1GID_013_G134_C189 | G | U | A | U | A | A | U | A | A | G | C | |||||||||||||||||
| IL_35043.1_Sequence_2 IL_35043.1_IL_1GID_013_G134_C189 | G | U | A | * | U | A | A | U | A | A | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_35043.1_Instance_3 IL_35043.1_IL_1X8W_005_G134_C189 | G | U | A | U | A | A | U | A | A | G | C | |||||||||||||||||
| IL_35043.1_Sequence_3 IL_35043.1_IL_1X8W_005_G134_C189 | G | U | A | * | U | A | A | U | A | A | G | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 10 cWW 2 3 s35 2 8 cWH 3 4 cWW 3 8 s53 4 8 s33 4 9 perp 5 6 s35 5 9 s53 8 10 s55 8 4 2BRJAR3D SCFG/MRF model for IL_35043.1:
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 [10] // Initial node G134 - C189 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.010096111,0.020567805,0.011689796,0.191596493,0.000000000],[0.017034996,0.008324961,0.206359029,0.013134669,0.000000000],[0.011542646,0.241989936,0.002128637,0.027303363,0.000000000],[0.190490110,0.013787581,0.023552083,0.010401784,0.000000000],[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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair G134 - C189 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [2] | Left Index [2] | Right Index [9] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.006848383,0.001369677,0.006793156,0.004887194,0.000000000],[0.006848383,0.014650494,0.006720759,0.074754976,0.000000000],[0.030042562,0.001369677,0.005481244,0.001369677,0.000000000],[0.713964488,0.001369677,0.109749071,0.013780587,0.000000000],[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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair U135 - A187 cWH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000] | Left Index [3] | Right Index [6] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [3] | Right Index [6] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [3] | Right Index [5] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [4] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009161066,0.024198359,0.009714577,0.241850087,0.000000000],[0.019887785,0.009212929,0.190364960,0.010177246,0.000000000],[0.009698024,0.191470616,0.002127239,0.027515312,0.000000000],[0.204743936,0.010249221,0.023357727,0.016270918,0.000000000],[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 [3] | Right Index [4] // Basepair A136 - U182 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 truncationSequences of instances from IL_35043.1:
> IL_35043.1 IL_1GID_006 G 134 C 189 GUA*UAAUAAGC > IL_35043.1 IL_1GID_013 G 134 C 189 GUA*UAAUAAGC > IL_35043.1 IL_1X8W_005 G 134 C 189 GUA*UAAUAAGC