| 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_33172.1_Instance_1 HL_33172.1_HL_5HR6_002_C31_G39 | C | C | UUU | C | A | C | G | |||||||||
| HL_33172.1_Sequence_1 HL_33172.1_HL_5HR6_002_C31_G39 | C | C | UUU | C | A | C | G | true | 100 | 0 | 0 | 0.00 | ||||
| HL_33172.1_Instance_2 HL_33172.1_HL_5HR7_005_C31_G39 | C | C | UUU | C | A | C | G | |||||||||
| HL_33172.1_Sequence_2 HL_33172.1_HL_5HR7_005_C31_G39 | C | C | UUU | C | A | C | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 5 cWW 2 3 tSW 2 5 s55 3 5 s55JAR3D SCFG/MRF model for HL_33172.1:
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 C31 - G39 from junction BasepairNode | Deletion Probability [0.0000229437914523] | 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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair C31 - G39 cWW HairpinNode | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node C32:C38 Interaction | Interacting Bases [1,2] | Pair Probability [[0.033292797,0.015918921,0.004045587,0.020111209,0.000000000],[0.018484423,0.424166534,0.004045587,0.027480179,0.000000000],[0.017838263,0.004045587,0.004045587,0.016453279,0.000000000],[0.019369877,0.347846556,0.018566404,0.024289210,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction C32 - C36 tSW Interaction | Interacting Bases [3,3] | 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 C38 Insertion | Location [1] | Length Distribution [0.000000000,0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.062500000,0.062500000,0.062500000,0.812500000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1 Insertion | Location [2] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2Sequences of instances from HL_33172.1:
> HL_33172.1 HL_5HR6_002 C 31 G 39 CCUUUCACG > HL_33172.1 HL_5HR7_005 C 31 G 39 CCUUUCACG