| 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 13 4 | 9 13 I | 10 14 | 11 13 I | 12 13 5 | 13 12 I | 14 11 6 | 15 10 I | 16 9 7 | 17 8 I | 18 7 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_52173.1_Instance_1 IL_52173.1_IL_1J2B_001_C926_G947 | C | G | C | C | G | G | A | G | G | |||||||||||||||||
| IL_52173.1_Sequence_1 IL_52173.1_IL_1J2B_001_C926_G947 | C | G | C | C | * | G | G | A | G | G | true | 86 | 0 | 0 | 1.58 | |||||||||||
| IL_52173.1_Instance_2 IL_52173.1_IL_1MFQ_001_U117_A234 | U | A | A | G | C | A | G | U | A | |||||||||||||||||
| IL_52173.1_Sequence_2 IL_52173.1_IL_1MFQ_001_U117_A234 | U | A | A | G | * | C | A | G | U | A | true | 91 | 0 | 0 | 1.04 | |||||||||||
| IL_52173.1_Instance_3 IL_52173.1_IL_1U6B_004_G119_C100 | G | A | A | G | C | A | A | G | C | |||||||||||||||||
| IL_52173.1_Sequence_3 IL_52173.1_IL_1U6B_004_G119_C100 | G | A | A | G | * | C | A | A | G | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 9 cWW 2 3 s35 2 9 s55 3 4 s35 4 5 cWW 4 6 s55 5 6 s35 6 7 s35 7 8 s35 8 9 s35JAR3D SCFG/MRF model for IL_52173.1:
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 [9] // Initial node C926 - G947 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009685694,0.019182219,0.010986155,0.195803621,0.000000000],[0.020623118,0.008749922,0.213456437,0.012400460,0.000000000],[0.010991697,0.213086471,0.002130191,0.024759915,0.000000000],[0.208179451,0.012376361,0.026149698,0.011438589,0.000000000],[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 [9] // Basepair C926 - G947 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // Fixed node on left InitialNode | 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 [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 [0.500000000,0.300000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left InitialNode | 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 [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 [0.100000000,0.100000000,0.500000000,0.300000000,0.000000000] | Position [2] | Left Index [4] | Right Index [8] // 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 [4] | Right Index [7] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | Position [2] | Left Index [4] | 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 [0.993970181,0.005999820,0.000029999] | 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 [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | 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 [0.993970181,0.005999820,0.000029999] | 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 [[0.010041880,0.019391351,0.011641525,0.191240548,0.000000000],[0.018213986,0.008378062,0.218250356,0.013353236,0.000000000],[0.011592485,0.230126887,0.002128781,0.026054525,0.000000000],[0.190871828,0.013570829,0.024804352,0.010339370,0.000000000],[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 C929 - G943 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_52173.1:
> IL_52173.1 IL_1J2B_001 C 926 G 947 CGCC*GGAGG > IL_52173.1 IL_1MFQ_001 U 117 A 234 UAAG*CAGUA > IL_52173.1 IL_1U6B_004 G 119 C 100 GAAG*CAAGC