| 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 6 3 | 7 5 I | 8 5 4 | 9 4 I | 10 3 5 | 11 2 I | 12 2 6 | 13 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_43527.1_Instance_1 HL_43527.1_HL_4PQV_002_C28_G34 | C | G | C | C | G | A | G | |||||||||||
| HL_43527.1_Sequence_1 HL_43527.1_HL_4PQV_002_C28_G34 | C | G | C | C | G | A | G | true | 92 | 0 | 0 | 0.77 | ||||||
| HL_43527.1_Instance_2 HL_43527.1_HL_4Y4O_168_C2701_G2706 | C | U | C | C | A | G | ||||||||||||
| HL_43527.1_Sequence_2 HL_43527.1_HL_4Y4O_168_C_2701_G_2706 | C | U | C | C | A | G | true | 100 | 0 | 0 | 0.00 |
1 6 cWW 2 3 s35 2 4 cSH 3 4 s35 4 5 s35 5 6 s35JAR3D SCFG/MRF model for HL_43527.1:
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 [6] // Initial node C28 - G34 from junction BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [1] | Right Index [6] // Basepair C28 - G34 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Position [2] | Left Index [2] | 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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [4] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.082442164,0.088350897,0.007680972,0.084139219,0.000000000],[0.084342963,0.086292904,0.000981194,0.011079913,0.000000000],[0.012396638,0.099911675,0.089503806,0.079842104,0.000000000],[0.084200391,0.107923341,0.000981194,0.079930624,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [4] // Basepair G29 - C31 cSH HairpinNode | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node C30:C30 Interaction | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.625000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C30Sequences of instances from HL_43527.1:
> HL_43527.1 HL_4PQV_002 C 28 G 34 CGCCGAG > HL_43527.1 HL_4Y4O_168 C 2701 G 2706 CUCCAG