| 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 2 I | 12 2 6 | 13 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_02733.4_Instance_1 HL_02733.4_HL_5J7L_203_C38_G44 | C | A | U | G | C | C | G | |||||||||||
| HL_02733.4_Sequence_1 HL_02733.4_HL_5J7L_203_C38_G44 | C | A | U | G | C | C | G | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_02733.4_Instance_2 HL_02733.4_HL_5FDV_069_C38_G44 | C | A | U | U | C | C | G | |||||||||||
| HL_02733.4_Sequence_2 HL_02733.4_HL_5FDV_069_C38_G44 | C | A | U | U | C | C | G | true | 92 | 0 | 0 | 1.10 | ||||||
| HL_02733.4_Instance_3 HL_02733.4_HL_1MJI_002_C38_G44 | C | A | U | G | C | C | G | |||||||||||
| HL_02733.4_Sequence_3 HL_02733.4_HL_1MJI_002_C38_G44 | C | A | U | G | C | C | G | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_02733.4_Instance_4 HL_02733.4_HL_4V9F_071_C37_G43 | C | A | U | C | C | C | G | |||||||||||
| HL_02733.4_Sequence_4 HL_02733.4_HL_4V9F_071_C37_G43 | C | A | U | C | C | C | G | true | 92 | 0 | 0 | 1.10 | ||||||
| HL_02733.4_Instance_5 HL_02733.4_HL_4WF9_066_C36_G42 | C | A | U | G | C | C | G | |||||||||||
| HL_02733.4_Sequence_5 HL_02733.4_HL_4WF9_066_C36_G42 | C | A | U | G | C | C | G | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_02733.4_Instance_6 HL_02733.4_HL_5TBW_185_C36_G41 | C | G | U | C | C | G | ||||||||||||
| HL_02733.4_Sequence_6 HL_02733.4_HL_5TBW_185_C36_G41 | C | G | U | C | C | G | true | 80 | 0 | 0 | 2.89 | |||||||
| HL_02733.4_Instance_7 HL_02733.4_HL_7A0S_069_C40_G46 | C | A | U | G | C | C | G | |||||||||||
| HL_02733.4_Sequence_7 HL_02733.4_HL_7A0S_069_C40_G46 | C | A | U | G | C | C | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 6 cWW 2 3 s35 2 6 s55 4 5 s35 3 6 6BPh 5 3 7BR 2 6 6BRJAR3D SCFG/MRF model for HL_02733.4:
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 [6] // Initial node C38 - G44 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009090944,0.016302246,0.010451159,0.189500131,0.000000000],[0.019328903,0.009258863,0.264630806,0.013146218,0.000000000],[0.010568529,0.193583350,0.001992102,0.022369654,0.000000000],[0.191956811,0.012666128,0.025520256,0.009633898,0.000000000],[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 [6] // Basepair C38 - G44 cWW HairpinNode | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A39:C43 Interaction | Interacting Bases [1,1] | Pair Probability [[0.824324324,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.013513514,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.148648649,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.013513514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A39 Interaction | Interacting Bases [2,2] | Pair Probability [[0.009803922,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.009803922,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.009803922,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.970588235,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U40 Interaction | Interacting Bases [3,3] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.833333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C42 Interaction | Interacting Bases [4,4] | Pair Probability [[0.013513514,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.959459459,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.013513514,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.013513514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C43 Insertion | Location [2] | Length Distribution [0.146977400,0.846630090,0.006090502,0.000302008] | Letter Distribution [0.062500000,0.187500000,0.562500000,0.187500000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2Sequences of instances from HL_02733.4:
> HL_02733.4 HL_5J7L_203 C 38 G 44 CAUGCCG > HL_02733.4 HL_5FDV_069 C 38 G 44 CAUUCCG > HL_02733.4 HL_1MJI_002 C 38 G 44 CAUGCCG > HL_02733.4 HL_4V9F_071 C 37 G 43 CAUCCCG > HL_02733.4 HL_4WF9_066 C 36 G 42 CAUGCCG > HL_02733.4 HL_5TBW_185 C 36 G 41 CGUCCG > HL_02733.4 HL_7A0S_069 C 40 G 46 CAUGCCG