| 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 4 I | 8 5 4 | 9 5 I | 10 5 5 | 11 5 I | 12 5 6 | 13 4 I | 14 4 7 | 15 3 I | 16 3 8 | 17 2 I | 18 2 9 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_08748.1_Instance_1 HL_08748.1_HL_4V9F_032_A1274_U1282 | A | C | U | C | A | U | A | C | U | |||||||||||||||
| HL_08748.1_Sequence_1 HL_08748.1_HL_4V9F_032_A_1274_U_1282 | A | C | U | C | A | U | A | C | U | true | 91 | 0 | 0 | 1.24 | ||||||||||
| HL_08748.1_Instance_2 HL_08748.1_HL_4WF9_039_A1673_U1681 | A | U | G | A | G | A | A | U | U | |||||||||||||||
| HL_08748.1_Sequence_2 HL_08748.1_HL_4WF9_039_A_1673_U_1681 | A | U | G | A | G | A | A | U | U | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 9 cWW 2 3 s35 2 8 cWW 3 5 s33 3 7 tSH 4 5 s35 5 7 s35 6 8 perp 6 9 perp 7 8 s35 8 9 s35 3 6 6BPhJAR3D SCFG/MRF model for HL_08748.1:
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 A1274 - U1282 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 [9] // Basepair A1274 - U1282 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.014025201,0.257239276,0.012522138,0.021870700,0.000000000],[0.015501176,0.115644582,0.018694225,0.013746415,0.000000000],[0.012260594,0.019043745,0.003865601,0.049383789,0.000000000],[0.019105514,0.014887357,0.015845632,0.396364055,0.000000000],[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 [8] // Basepair C1275 - C1281 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.045082454,0.044351636,0.000520299,0.002505376,0.000000000],[0.045334528,0.045021438,0.000520299,0.000520299,0.000000000],[0.217394406,0.002093995,0.010570186,0.177251098,0.000000000],[0.214804909,0.189892275,0.002068399,0.002068399,0.000000000],[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 [3] | Right Index [7] // Basepair U1276 - A1280 tSH HairpinNode | Num Bases [3] | Left Index [4] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node C1277:U1279 Interaction | Interacting Bases [1,1] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[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 C1277 Interaction | Interacting Bases [2,2] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[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 A1278 Interaction | Interacting Bases [3,3] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U1279Sequences of instances from HL_08748.1:
> HL_08748.1 HL_4V9F_032 A 1274 U 1282 ACUCAUACU > HL_08748.1 HL_4WF9_039 A 1673 U 1681 AUGAGAAUU