| 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_94386.1_Instance_1 HL_94386.1_HL_6N5P_002_G58_C64 | G | U | G | A | A | G | C | |||||||||||
| HL_94386.1_Sequence_1 HL_94386.1_HL_6N5P_002_G58_C64 | G | U | G | A | A | G | C | true | 76 | 0 | 0 | 2.27 | ||||||
| HL_94386.1_Instance_2 HL_94386.1_HL_2A64_001_G31_C36 | G | G | U | U | U | C | ||||||||||||
| HL_94386.1_Sequence_2 HL_94386.1_HL_2A64_001_G31_C36 | G | G | U | U | U | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_94386.1_Instance_3 HL_94386.1_HL_361D_001_G86_C90 | G | G | C | G | A | C | ||||||||||||
| HL_94386.1_Sequence_3 HL_94386.1_HL_361D_001_G86_C90 | G | G | C | G | A | C | true | 95 | 0 | 0 | 0.51 | |||||||
| HL_94386.1_Instance_4 HL_94386.1_HL_5TBW_012_C543_G548 | C | C | U | C | G | G | ||||||||||||
| HL_94386.1_Sequence_4 HL_94386.1_HL_5TBW_012_C543_G548 | C | C | U | C | G | G | true | 99 | 0 | 0 | 0.10 |
1 2 s35 1 6 cWW 5 6 s35JAR3D SCFG/MRF model for HL_94386.1:
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 [6] // Initial node G58 - C64 from junction BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009498175,0.019104591,0.010841350,0.196828520,0.000000000],[0.017548139,0.009402467,0.210196267,0.013152764,0.000000000],[0.010780994,0.232320656,0.002049218,0.025441577,0.000000000],[0.195565178,0.013399649,0.023821386,0.010049069,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair G58 - C64 cWW HairpinNode | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node U59:G63 Interaction | Interacting Bases [1,1] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U59 Interaction | Interacting Bases [2,2] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.416666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A61 Interaction | Interacting Bases [3,3] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A62 Interaction | Interacting Bases [4,4] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G63 Insertion | Location [1] | Length Distribution [0.741082411,0.255227552,0.003536285,0.000153752] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1Sequences of instances from HL_94386.1:
> HL_94386.1 HL_6N5P_002 G 58 C 64 GUGAAGC > HL_94386.1 HL_2A64_001 G 31 C 36 GGUUUC > HL_94386.1 HL_361D_001 G 86 C 90 GGCGAC > HL_94386.1 HL_5TBW_012 C 543 G 548 CCUCGG