| 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 7 4 | 9 8 I | 10 9 5 | 11 10 I | 12 11 6 | 13 12 I | 14 13 7 | 15 13 I | 16 14 | 17 13 I | 18 13 8 | 19 2 I | 20 2 9 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_39526.4_Instance_1 IL_39526.4_IL_2NOK_001_G52_C111 | G | A | A | C | U | A | C | G | C | |||||||||||||||||
| IL_39526.4_Sequence_1 IL_39526.4_IL_2NOK_001_G52_C111 | G | A | A | C | U | A | C | * | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_39526.4_Instance_2 IL_39526.4_IL_2NOK_005_G52_C111 | G | A | A | C | U | A | C | G | C | |||||||||||||||||
| IL_39526.4_Sequence_2 IL_39526.4_IL_2NOK_005_G52_C111 | G | A | A | C | U | A | C | * | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_39526.4_Instance_3 IL_39526.4_IL_2PN4_002_G52_C111 | G | A | A | C | U | A | C | G | C | |||||||||||||||||
| IL_39526.4_Sequence_3 IL_39526.4_IL_2PN4_002_G52_C111 | G | A | A | C | U | A | C | * | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_39526.4_Instance_4 IL_39526.4_IL_3P59_001_G52_C111 | G | A | A | C | U | A | C | G | C | |||||||||||||||||
| IL_39526.4_Sequence_4 IL_39526.4_IL_3P59_001_G52_C111 | G | A | A | C | U | A | C | * | G | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 9 cWW 2 3 s35 2 9 s55 3 4 s35 6 7 s35 7 8 cWW 9 8 7BPh 6 4 7BRJAR3D SCFG/MRF model for IL_39526.4:
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 [9] // Initial node G52 - C111 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 [9] // Basepair G52 - C111 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // 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 [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // 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 [4] | Right Index [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [4] | Right Index [8] // 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 [5] | Right Index [8] // New Initial node after Fixed 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 [8] // 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 [6] | Right Index [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.931818182,0.022727273,0.022727273,0.022727273,0.000000000] | Position [1] | Left Index [6] | Right Index [8] // 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 [7] | Right Index [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009837906,0.016874612,0.011433973,0.188696651,0.000000000],[0.020374159,0.008402684,0.249321155,0.013657771,0.000000000],[0.011579737,0.204416164,0.002108596,0.023330341,0.000000000],[0.189792617,0.013011006,0.027046303,0.010116326,0.000000000],[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 [7] | Right Index [8] // Basepair C58 - G110 cWW HairpinNode | Num Bases [1] | Left Index [8] | Right Index [8] | 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_39526.4:
> IL_39526.4 IL_2NOK_001 G 52 C 111 GAACUAC*GC > IL_39526.4 IL_2NOK_005 G 52 C 111 GAACUAC*GC > IL_39526.4 IL_2PN4_002 G 52 C 111 GAACUAC*GC > IL_39526.4 IL_3P59_001 G 52 C 111 GAACUAC*GC