| 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 7 4 | 9 7 I | 10 8 5 | 11 8 I | 12 8 6 | 13 8 I | 14 8 7 | 15 7 I | 16 7 8 | 17 6 I | 18 5 9 | 19 4 I | 20 4 10 | 21 3 I | 22 3 11 | 23 2 I | 24 2 12 | 25 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_70658.1_Instance_1 HL_70658.1,HL_4LVW_001,A33_U45 | A | A | U | G | G | G | A | U | G | U | C | G | U | |||||||||||||||||
| HL_70658.1_Sequence_1 HL_70658.14LVW_A33_U45 | A | A | U | G | G | G | A | U | G | U | C | G | U | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| HL_70658.1_Instance_2 HL_70658.1,HL_8P9A_160,A2252_U2264 | A | G | U | A | A | C | U | A | U | G | A | C | U | |||||||||||||||||
| HL_70658.1_Sequence_2 HL_70658.18P9A_A_2252_U_2264 | A | G | U | A | A | C | U | A | U | G | A | C | U | true | 95 | 0 | 0 | 0.90 |
1 2 s35 1 12 cWW 2 3 s35 2 11 cWW 2 12 s55 3 9 s33 3 10 tWH 4 8 tHW 4 9 s55 4 10 s55 5 6 s35 6 7 s35 7 8 s35 8 9 s35 9 10 s35 10 11 s35 11 12 s35JAR3D SCFG/MRF model for HL_70658.1:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [12] // Initial node 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 [12] // Basepair A33 - U45 cWW BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.027077160,0.013263515,0.336823218,0.015884116,0.000000000],[0.012952078,0.008821255,0.017156401,0.038551963,0.000000000],[0.314186837,0.116279553,0.003270193,0.014431498,0.000000000],[0.015853196,0.040733305,0.014122327,0.010593386,0.000000000],[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 [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Left Index [2] | Right Index [11] // Basepair A34 - G44 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.017326970,0.003556121,0.030852816,0.003556121,0.000000000],[0.307537579,0.041497220,0.003556121,0.003556121,0.000000000],[0.003556121,0.011127273,0.022868597,0.033545912,0.000000000],[0.133957684,0.003556121,0.014533182,0.365416038,0.000000000],[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 [10] // Basepair U35 - U42 tWH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [2] | Left Index [4] | Right Index [9] // Fixed node on right for 4LVW|1|A|G|41 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 [0.0000015195492620] | Pair Probability [[0.017068734,0.037986112,0.003777338,0.387537728,0.000000000],[0.003777338,0.304381264,0.009054529,0.003777338,0.000000000],[0.017728674,0.003777338,0.028726337,0.120846144,0.000000000],[0.003777338,0.003777338,0.016800299,0.037206152,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | 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 G36 - U40 tHW HairpinNode | Num Bases [3] | Left Index [5] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node G37:A39 Interaction | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[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 G37 Interaction | Interacting Bases [2,2] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G38 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 A39Sequences of instances from HL_70658.1:
> HL_70658.1 4LVW A 33 U 45 AAUGGGAUGUCGU > HL_70658.1 8P9A A 2252 U 2264 AGUAACUAUGACU