| 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_41207.1_Instance_1 HL_41207.1_HL_6MJ0_006_U12_A20 | U | C | U | U | U | A | A | A | A | |||||||||||||||
| HL_41207.1_Sequence_1 HL_41207.1_HL_6MJ0_006_U12_A20 | U | C | U | U | U | A | A | A | A | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_41207.1_Instance_2 HL_41207.1_HL_4V88_219_A1550_U1561 | A | U | U | G | U | A | A | UUA | U | U | ||||||||||||||
| HL_41207.1_Sequence_2 HL_41207.1_HL_4V88_219_A_1550_U_1561 | A | U | U | G | U | A | A | UUA | U | U | true | 80 | 0 | 0 | 3.26 |
1 2 s35 1 9 cWW 2 3 s35 2 8 cSW 3 4 s35 3 7 tWH 3 8 s53 4 7 s55 5 6 s35 6 7 s53 7 8 s33 8 9 s35JAR3D SCFG/MRF model for HL_41207.1:
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 U12 - A20 from junction BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009158630,0.019777652,0.009912226,0.210022087,0.000000000],[0.019781061,0.009705967,0.195573829,0.010701870,0.000000000],[0.009912241,0.195571919,0.002042701,0.038130662,0.000000000],[0.210028228,0.010701362,0.038153583,0.010825982,0.000000000],[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 U12 - A20 cWW BasepairNode | Deletion Probability [0.0000000071284465] | Pair Probability [[0.181283883,0.017605843,0.016457592,0.007138737,0.000000000],[0.206888803,0.015627556,0.001970849,0.007621878,0.000000000],[0.181066470,0.001970849,0.048802153,0.006071725,0.000000000],[0.177593635,0.015233353,0.008720755,0.105945918,0.000000000],[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 [0.481347774,0.012033694,0.012635379,0.481347774,0.012033694,0.000601685] | Right Letter Distribution [0.300000000,0.100000000,0.100000000,0.500000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair C13 - A19 cSW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.017068734,0.003777338,0.017728674,0.003777338,0.000000000],[0.037986112,0.304381264,0.003777338,0.003777338,0.000000000],[0.003777338,0.009054529,0.028726337,0.016800299,0.000000000],[0.486468209,0.003777338,0.021915662,0.037206152,0.000000000],[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 U14 - A18 tWH HairpinNode | Num Bases [3] | Left Index [4] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node U15:A17 Interaction | Interacting Bases [1,1] | 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 U15 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],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U16 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 A17Sequences of instances from HL_41207.1:
> HL_41207.1 HL_6MJ0_006 U 12 A 20 UCUUUAAAA > HL_41207.1 HL_4V88_219 A 1550 U 1561 AUUGUAAUUAUU