| 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 7 6 | 15 2 I | 16 2 7 | 17 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_01080.1_Instance_1 IL_01080.1_IL_1S72_016_U548_A608 | U | A | C | A | A | G | C | G | A | |||||||||||||
| IL_01080.1_Sequence_1 IL_01080.1_IL_1S72_016_U548_A608 | U | A | C | A | A | G | * | C | G | A | true | 82 | 0 | 0 | 1.69 | |||||||
| IL_01080.1_Instance_2 IL_01080.1_IL_2AW7_068_U1445_G1457 | U | A | A | C | G | A | G | |||||||||||||||
| IL_01080.1_Sequence_2 IL_01080.1_IL_2AW7_068_U_1445_G_1457 | U | A | A | C | * | G | A | G | true | 95 | 0 | 0 | 0.46 | |||||||||
| IL_01080.1_Instance_3 IL_01080.1_IL_2PXV_001_U139_A169 | U | A | C | C | A | G | C | A | A | |||||||||||||
| IL_01080.1_Sequence_3 IL_01080.1_IL_2PXV_001_U139_A169 | U | A | C | C | A | G | * | C | A | A | true | 82 | 0 | 0 | 1.69 | |||||||
| IL_01080.1_Instance_4 IL_01080.1_IL_1FJG_057_G1491_C1409 | G | A | A | G | C | A | C | |||||||||||||||
| IL_01080.1_Sequence_4 IL_01080.1_IL_1FJG_057_G_1491_C_1409 | G | A | A | G | * | C | A | C | true | 100 | 0 | 0 | 0.00 |
1 7 cWW 2 3 s35 4 5 cWW 4 6 s55 5 6 s35 6 7 s35JAR3D SCFG/MRF model for IL_01080.1:
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 [7] // Initial node U548 - A608 from junction BasepairNode | Deletion Probability [0.0000016375373120] | Pair Probability [[0.010162074,0.018592568,0.011523352,0.158593139,0.000000000],[0.093953024,0.010674378,0.157255289,0.012623241,0.000000000],[0.011581455,0.166407753,0.002448287,0.022155131,0.000000000],[0.183202760,0.012332159,0.115614732,0.012880655,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Left Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | 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 [7] // Basepair U548 - A608 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.416666667,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [2] | Right Index [6] // 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 [3] | Right Index [6] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.583333333,0.250000000,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [3] | Right Index [6] // Fixed node on left InitialNode | Left Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Left Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [6] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.583333333,0.083333333,0.250000000,0.083333333,0.000000000] | Position [2] | Left Index [4] | 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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009958751,0.019496181,0.011541539,0.189489827,0.000000000],[0.017746938,0.008284356,0.215611394,0.013170723,0.000000000],[0.011468679,0.238062912,0.002108276,0.026113208,0.000000000],[0.188942010,0.013494008,0.024255791,0.010255407,0.000000000],[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 [4] | Right Index [5] // Basepair G553 - C606 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 truncationSequences of instances from IL_01080.1:
> IL_01080.1 IL_1S72_016 U 548 A 608 UACAAG*CGA > IL_01080.1 IL_2AW7_068 U 1445 G 1457 UAAC*GAG > IL_01080.1 IL_2PXV_001 U 139 A 169 UACCAG*CAA > IL_01080.1 IL_1FJG_057 G 1491 C 1409 GAAG*CAC