| 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 3 3 | 7 3 I | 8 3 4 | 9 3 I | 10 3 5 | 11 3 I | 12 3 6 | 13 3 I | 14 3 7 | 15 2 I | 16 2 8 | 17 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_72451.4_Instance_1 HL_72451.4_HL_4Y4O_130_G978_C985 | G | G | A | A | C | A | A | C | ||||||||||||||
| HL_72451.4_Sequence_1 HL_72451.4_HL_4Y4O_130_G978_C985 | G | G | A | A | C | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| HL_72451.4_Instance_2 HL_72451.4_HL_4V9F_029_G1076_C1083 | G | G | A | A | C | A | A | C | ||||||||||||||
| HL_72451.4_Sequence_2 HL_72451.4_HL_4V9F_029_G_1076_C_1083 | G | G | A | A | C | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| HL_72451.4_Instance_3 HL_72451.4_HL_7A0S_027_G989_C996 | G | A | A | A | C | A | A | C | ||||||||||||||
| HL_72451.4_Sequence_3 HL_72451.4_HL_7A0S_027_G989_C996 | G | A | A | A | C | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| HL_72451.4_Instance_4 HL_72451.4_HL_5J7L_160_G978_C985 | G | A | A | A | C | A | A | C | ||||||||||||||
| HL_72451.4_Sequence_4 HL_72451.4_HL_5J7L_160_G978_C985 | G | A | A | A | C | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| HL_72451.4_Instance_5 HL_72451.4_HL_4WF9_028_G1022_C1029 | G | A | A | A | C | A | G | C | ||||||||||||||
| HL_72451.4_Sequence_5 HL_72451.4_HL_4WF9_028_G_1022_C_1029 | G | A | A | A | C | A | G | C | true | 88 | 0 | 0 | 1.30 | |||||||||
| HL_72451.4_Instance_6 HL_72451.4_HL_5TBW_026_G1148_C1155 | G | G | A | U | G | A | A | C | ||||||||||||||
| HL_72451.4_Sequence_6 HL_72451.4_HL_5TBW_026_G_1148_C_1155 | G | G | A | U | G | A | A | C | true | 74 | 0 | 0 | 2.85 |
1 2 s35 1 8 cWW 2 5 s33 2 8 s55 3 4 s35 4 5 perp 6 7 s35 5 4 7BPh 8 7 7BPhJAR3D SCFG/MRF model for HL_72451.4:
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 [8] // Initial node G978 - C985 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003679589,0.053642867,0.004190070,0.076104487,0.000000000],[0.006463298,0.025257446,0.076749356,0.005021698,0.000000000],[0.004143537,0.609465400,0.000789802,0.010117932,0.000000000],[0.075130495,0.036484266,0.008868823,0.003890933,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair G978 - C985 cWW HairpinNode | Num Bases [6] | Left Index [2] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node G979:A984 Interaction | Interacting Bases [1,1] | Pair Probability [[0.437500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.437500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G979 Interaction | Interacting Bases [2,2] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A980 Interaction | Interacting Bases [3,3] | Pair Probability [[0.687500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.187500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A981 Interaction | Interacting Bases [4,4] | Pair Probability [[0.011363636,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.806818182,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.170454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.011363636,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C982 Interaction | Interacting Bases [5,5] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A983 Interaction | Interacting Bases [6,6] | Pair Probability [[0.687500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.187500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A984Sequences of instances from HL_72451.4:
> HL_72451.4 HL_4Y4O_130 G 978 C 985 GGAACAAC > HL_72451.4 HL_4V9F_029 G 1076 C 1083 GGAACAAC > HL_72451.4 HL_7A0S_027 G 989 C 996 GAAACAAC > HL_72451.4 HL_5J7L_160 G 978 C 985 GAAACAAC > HL_72451.4 HL_4WF9_028 G 1022 C 1029 GAAACAGC > HL_72451.4 HL_5TBW_026 G 1148 C 1155 GGAUGAAC