| 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 4 3 | 7 4 I | 8 4 4 | 9 4 I | 10 4 5 | 11 3 I | 12 3 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_80705.1_Instance_1 HL_80705.1_HL_3NKB_001_C20_G28 | C | U | C | C | U | C | G | C | G | |||||||||||
| HL_80705.1_Sequence_1 HL_80705.1_HL_3NKB_001_C20_G28 | C | U | C | C | U | C | G | C | G | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_80705.1_Instance_2 HL_80705.1_HL_4PR6_001_C119_G128 | C | U | C | C | U | C | G | CU | G | |||||||||||
| HL_80705.1_Sequence_2 HL_80705.1_HL_4PR6_001_C119_G128 | C | U | C | C | U | C | G | CU | G | true | 93 | 0 | 0 | 1.20 |
1 2 s35 1 7 cWW 2 5 s35 2 6 tWW 2 7 s55 3 4 s35 5 6 s53 6 7 s55 5 4 7BPh 5 2 7BRJAR3D SCFG/MRF model for HL_80705.1:
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 [7] // Initial node C20 - G28 from junction BasepairNode | Deletion Probability [0.0000000083615247] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[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 [0.011890606,0.487514863,0.487514863,0.012485137,0.000594530] | Right Letter Distribution [0.100000000,0.500000000,0.100000000,0.300000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair C20 - G28 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.016132647,0.013222764,0.002925794,0.014423455,0.000000000],[0.268574183,0.013818458,0.012328290,0.013607089,0.000000000],[0.002925794,0.009504076,0.025714781,0.013537368,0.000000000],[0.234369790,0.014144852,0.312187293,0.032583365,0.000000000],[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 [2] | Right Index [6] // Basepair U21 - G26 tWW HairpinNode | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node C22:C25 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 C22 Interaction | Interacting Bases [2,2] | 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 C23 Interaction | Interacting Bases [3,3] | Pair Probability [[0.031250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.906250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.031250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C25 Insertion | Location [2] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion in Hairpin after nucleotide 4, position 2Sequences of instances from HL_80705.1:
> HL_80705.1 HL_3NKB_001 C 20 G 28 CUCCUCGCG > HL_80705.1 HL_4PR6_001 C 119 G 128 CUCCUCGCUG