| 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 3 I | 6 4 3 | 7 5 I | 8 8 4 | 9 8 I | 10 9 5 | 11 9 I | 12 9 6 | 13 9 I | 14 9 7 | 15 8 I | 16 8 8 | 17 7 I | 18 6 9 | 19 3 I | 20 3 10 | 21 2 I | 22 2 11 | 23 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_90620.1_Instance_1 HL_90620.1_HL_3IVN_003_A49_U59 | A | A | C | C | G | U | A | A | A | A | U | |||||||||||||||||
| HL_90620.1_Sequence_1 HL_90620.1_HL_3IVN_003_A49_U59 | A | A | C | C | G | U | A | A | A | A | U | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| HL_90620.1_Instance_2 HL_90620.1_HL_6P2H_002_A59_U69 | A | A | C | C | G | U | A | A | A | A | U | |||||||||||||||||
| HL_90620.1_Sequence_2 HL_90620.1_HL_6P2H_002_A59_U69 | A | A | C | C | G | U | A | A | A | A | U | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 11 cWW 2 3 s35 2 10 cWW 2 11 s55 3 4 s35 4 8 cSW 5 6 cSH 6 7 s53 7 8 s35 8 9 s35 9 10 s35 10 11 s35JAR3D SCFG/MRF model for HL_90620.1:
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 [11] // Initial node A49 - U59 from junction BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009282926,0.022010543,0.009914366,0.223723012,0.000000000],[0.017518170,0.009580259,0.194165974,0.010358839,0.000000000],[0.009895067,0.196683142,0.002041152,0.053213779,0.000000000],[0.196023621,0.011028161,0.023012614,0.011548375,0.000000000],[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 [1] | Right Index [11] // Basepair A49 - U59 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.615264647,0.027680686,0.049320315,0.027089794,0.000000000],[0.018530781,0.010338068,0.027182752,0.026285801,0.000000000],[0.037714972,0.027750896,0.005956568,0.029081265,0.000000000],[0.026324389,0.029605623,0.020261781,0.021611660,0.000000000],[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 [10] // Basepair A50 - A58 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [4] | 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 [0.991950402,0.007999600,0.000049998] | 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 BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.199412271,0.019366427,0.018103352,0.007852611,0.000000000],[0.236401213,0.017190312,0.002167934,0.008384066,0.000000000],[0.199173117,0.002167934,0.053682368,0.006678898,0.000000000],[0.195352999,0.016756688,0.009592831,0.007716981,0.000000000],[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 [4] | Right Index [8] // Basepair C52 - A56 cSW HairpinNode | Num Bases [3] | Left Index [5] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node G53:A55 Interaction | Interacting Bases [1,2] | Pair Probability [[0.079296878,0.080799881,0.004442628,0.078964610,0.000000000],[0.059200300,0.089215891,0.000983673,0.079130149,0.000000000],[0.069281848,0.000983673,0.084512044,0.117975163,0.000000000],[0.080527243,0.080043827,0.000983673,0.093658519,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G53 - U54 cSH Interaction | Interacting Bases [3,3] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A55Sequences of instances from HL_90620.1:
> HL_90620.1 HL_3IVN_003 A 49 U 59 AACCGUAAAAU > HL_90620.1 HL_6P2H_002 A 59 U 69 AACCGUAAAAU