| 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 2 I | 10 2 5 | 11 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_70970.1_Instance_1 HL_70970.1_HL_4V9F_004_U125_A129 | U | C | U | A | A | |||||||||||
| HL_70970.1_Sequence_1 HL_70970.1_HL_4V9F_004_U125_A129 | U | C | U | A | A | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_70970.1_Instance_2 HL_70970.1_HL_5J7L_163_G1171_C1178 | G | C | UUA | U | G | C | ||||||||||
| HL_70970.1_Sequence_2 HL_70970.1_HL_5J7L_163_G_1171_C_1178 | G | C | UUA | U | G | C | true | 73 | 0 | 0 | 2.59 |
1 2 perp 1 5 cWW 2 4 perp 4 5 s35JAR3D SCFG/MRF model for HL_70970.1:
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 [5] // Initial node U125 - A129 from junction BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009384013,0.018908278,0.010497082,0.198820958,0.000000000],[0.019570724,0.009688269,0.200004160,0.012164451,0.000000000],[0.010445199,0.211498280,0.002066765,0.024906359,0.000000000],[0.211388534,0.012081037,0.038377715,0.010198176,0.000000000],[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 [5] // Basepair U125 - A129 cWW HairpinNode | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node C126:A128 Interaction | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.625000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[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 C126 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 U127 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],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[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 A128 Insertion | Location [1] | Length Distribution [0.481347774,0.012033694,0.012635379,0.481347774,0.012033694,0.000601685] | Letter Distribution [0.300000000,0.100000000,0.100000000,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1Sequences of instances from HL_70970.1:
> HL_70970.1 HL_4V9F_004 U 125 A 129 UCUAA > HL_70970.1 HL_5J7L_163 G 1171 C 1178 GCUUAUGC