| 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 7 I | 9 8 4 | 10 8 I | 11 8 5 | 12 8 I | 13 8 6 | 14 8 I | 15 8 7 | 16 7 I | 17 6 8 | 18 3 I | 19 3 9 | 20 2 I | 21 2 10 | 22 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_32255.1_Instance_1 HL_32255.1_HL_4V88_209_U1055_G1064 | U | U | U | U | U | U | A | A | U | G | |||||||||||||||||
| HL_32255.1_Sequence_1 HL_32255.1_HL_4V88_209_U_1055_G_1064 | U | U | U | U | U | U | A | A | U | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 10 cWW 2 9 cWW 2 10 s55 3 6 s33 4 6 cWW 5 6 perp 6 7 cSS 7 8 s53 8 9 s55 9 10 s35 7 6 2BRJAR3D SCFG/MRF model for HL_32255.1:
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 [10] // Initial node U1055 - G1064 from junction BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.011357495,0.014122426,0.014418960,0.037643649,0.000000000],[0.305533580,0.028227484,0.042773463,0.016192886,0.000000000],[0.014734624,0.037492866,0.003338882,0.014817277,0.000000000],[0.087046211,0.014824487,0.343789173,0.013686536,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair U1055 - G1064 cWW BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.015580470,0.285764820,0.013910732,0.024295965,0.000000000],[0.017220118,0.018567546,0.020767248,0.015270770,0.000000000],[0.013620185,0.021155527,0.004294262,0.054860011,0.000000000],[0.021224145,0.016538232,0.017602771,0.439327198,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [9] // Basepair U1056 - U1063 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left InitialNode | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [2] | Left Index [4] | Right Index [8] // Fixed node on right 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 [4] | Right Index [7] // New Initial node after Fixed node HairpinNode | Num Bases [4] | Left Index [4] | Right Index [7] | Norm Constant [0.275565987730353] // Hairpin node U1058:A1061 Interaction | Interacting Bases [1,3] | Pair Probability [[0.015580470,0.285764820,0.013910732,0.024295965,0.000000000],[0.017220118,0.018567546,0.020767248,0.015270770,0.000000000],[0.013620185,0.021155527,0.004294262,0.054860011,0.000000000],[0.021224145,0.016538232,0.017602771,0.439327198,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U1058 - U1060 cWW Interaction | Interacting Bases [3,4] | Pair Probability [[0.076146696,0.074822471,0.076666471,0.069121724,0.000000000],[0.078906659,0.079495189,0.003253861,0.064122585,0.000000000],[0.078575452,0.003326749,0.009031637,0.069548293,0.000000000],[0.093178774,0.073057805,0.075892455,0.074853180,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U1060 - A1061 cSS Interaction | Interacting Bases [2,2] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U1059Sequences of instances from HL_32255.1:
> HL_32255.1 HL_4V88_209 U 1055 G 1064 UUUUUUAAUG