| 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 2 2 | 5 2 I | 6 2 3 | 7 2 I | 8 2 4 | 9 2 I | 10 2 5 | 11 2 I | 12 2 6 | 13 2 I | 14 2 7 | 15 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_39334.4_Instance_1 HL_39334.4_HL_4WF9_023_C789_G798 | C | G | U | U | G | A | A | AA | G | |||||||||||
| HL_39334.4_Sequence_1 HL_39334.4_HL_4WF9_023_C789_G798 | C | G | U | U | G | A | A | AA | G | true | 97 | 0 | 0 | 0.46 | ||||||
| HL_39334.4_Instance_2 HL_39334.4_HL_7A0S_022_U757_A766 | U | G | C | U | G | A | A | AC | A | |||||||||||
| HL_39334.4_Sequence_2 HL_39334.4_HL_7A0S_022_U757_A766 | U | G | C | U | G | A | A | AC | A | true | 89 | 0 | 0 | 1.62 | ||||||
| HL_39334.4_Instance_3 HL_39334.4_HL_4Y4O_125_G744_C753 | G | G | A | U | G | C | A | AA | C | |||||||||||
| HL_39334.4_Sequence_3 HL_39334.4_HL_4Y4O_125_G744_C753 | G | G | A | U | G | C | A | AA | C | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_39334.4_Instance_4 HL_39334.4_HL_4V9F_024_U837_A846 | U | C | C | U | A | C | A | AU | A | |||||||||||
| HL_39334.4_Sequence_4 HL_39334.4_HL_4V9F_024_U837_A846 | U | C | C | U | A | C | A | AU | A | true | 83 | 0 | 0 | 2.54 | ||||||
| HL_39334.4_Instance_5 HL_39334.4_HL_5TBW_020_A876_U885 | A | C | G | U | G | C | A | AA | U | |||||||||||
| HL_39334.4_Sequence_5 HL_39334.4_HL_5TBW_020_A876_U885 | A | C | G | U | G | C | A | AA | U | true | 100 | 0 | 0 | 0.05 |
1 2 s35 1 7 cWW 2 3 s35 2 4 s33 2 6 tSW 2 7 s55 4 6 s33 5 6 s35 5 7 cWS 6 7 s55 6 2 7BR 4 3 2BRJAR3D SCFG/MRF model for HL_39334.4:
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 [7] // Initial node C789 - G798 from junction HairpinNode | Num Bases [7] | Left Index [1] | Right Index [7] | Norm Constant [0.249973259348243] // Hairpin node C789:G798 Interaction | Interacting Bases [2,6] | Pair Probability [[0.161671308,0.158976612,0.001984076,0.009657096,0.000000000],[0.209780801,0.008874447,0.001984076,0.007985973,0.000000000],[0.221911551,0.001984076,0.001984076,0.006483107,0.000000000],[0.173619805,0.008756591,0.014756162,0.009590242,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G790 - A795 tSW Interaction | Interacting Bases [1,7] | Pair Probability [[0.009057963,0.018354800,0.010060520,0.203200943,0.000000000],[0.019230394,0.009423090,0.203835059,0.011564523,0.000000000],[0.010064286,0.203344265,0.002002830,0.029053534,0.000000000],[0.214301711,0.011434067,0.034939147,0.010132867,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction C789 - G798 cWW Interaction | Interacting Bases [5,7] | Pair Probability [[0.104247946,0.091635700,0.103157231,0.092253245,0.000000000],[0.163558958,0.163026387,0.002395318,0.163725761,0.000000000],[0.023016496,0.002395318,0.027010747,0.010380352,0.000000000],[0.012877755,0.018619515,0.009694589,0.012004682,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction A794 - G798 cWS Interaction | Interacting Bases [3,3] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.357142857,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.214285714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U791 Interaction | Interacting Bases [4,4] | Pair Probability [[0.203703704,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.018518519,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.759259259,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.018518519,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G793 Insertion | Location [3] | Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Letter Distribution [0.071428571,0.071428571,0.071428571,0.785714286,0.000000000]// Insertion in Hairpin after nucleotide 3, position 3 Insertion | Location [6] | Length Distribution [0.000000000,0.009799118,0.979911808,0.009799118,0.000489956] | Letter Distribution [0.708333333,0.125000000,0.041666667,0.125000000,0.000000000]// Insertion in Hairpin after nucleotide 6, position 6Sequences of instances from HL_39334.4:
> HL_39334.4 HL_4WF9_023 C 789 G 798 CGUUGAAAAG > HL_39334.4 HL_7A0S_022 U 757 A 766 UGCUGAAACA > HL_39334.4 HL_4Y4O_125 G 744 C 753 GGAUGCAAAC > HL_39334.4 HL_4V9F_024 U 837 A 846 UCCUACAAUA > HL_39334.4 HL_5TBW_020 A 876 U 885 ACGUGCAAAU