| 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 5 2 | 5 5 I | 6 6 3 | 7 6 I | 8 7 4 | 9 7 I | 10 8 5 | 11 8 I | 12 9 | 13 8 I | 14 8 6 | 15 7 I | 16 7 7 | 17 6 I | 18 6 8 | 19 5 I | 20 5 9 | 21 4 I | 22 3 10 | 23 2 I | 24 2 11 | 25 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_53635.3_Instance_1 IL_53635.3_IL_3V2F_018_G674_C806 | G | A | A | A | C | G | A | G | A | U | A | G | C | |||||||||||||||||
| IL_53635.3_Sequence_1 IL_53635.3_IL_3V2F_018_G674_C806 | G | A | A | A | C | * | G | A | G | A | U | A | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_53635.3_Instance_2 IL_53635.3_IL_2QBG_021_G674_C806 | G | A | A | A | C | G | A | G | A | U | A | G | C | |||||||||||||||||
| IL_53635.3_Sequence_2 IL_53635.3_IL_2QBG_021_G674_C806 | G | A | A | A | C | * | G | A | G | A | U | A | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_53635.3_Instance_3 IL_53635.3_IL_1S72_025_G765_C899 | G | A | A | U | C | G | C | A | A | C | A | G | C | |||||||||||||||||
| IL_53635.3_Sequence_3 IL_53635.3_IL_1S72_025_G765_C899 | G | A | A | U | C | * | G | C | A | A | C | A | G | C | true | 82 | 0 | 0 | 3.62 | |||||||||||
| IL_53635.3_Instance_4 IL_53635.3_IL_4A1B_035_G830_C963 | G | A | A | A | G | C | U | A | G | U | A | G | C | |||||||||||||||||
| IL_53635.3_Sequence_4 IL_53635.3_IL_4A1B_035_G830_C963 | G | A | A | A | G | * | C | U | A | G | U | A | G | C | true | 84 | 0 | 0 | 3.11 | |||||||||||
| IL_53635.3_Instance_5 IL_53635.3_IL_4IOA_014_G687_C819 | G | A | A | A | C | G | A | G | A | U | A | G | C | |||||||||||||||||
| IL_53635.3_Sequence_5 IL_53635.3_IL_4IOA_014_G687_C819 | G | A | A | A | C | * | G | A | G | A | U | A | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_53635.3_Instance_6 IL_53635.3_IL_3U5H_029_G805_C938 | G | A | A | A | G | C | U | A | G | U | A | G | C | |||||||||||||||||
| IL_53635.3_Sequence_6 IL_53635.3_IL_3U5H_029_G805_C938 | G | A | A | A | G | * | C | U | A | G | U | A | G | C | true | 84 | 0 | 0 | 3.11 |
1 10 s33 1 11 cWW 2 3 s35 2 9 tHW 2 10 s55 3 8 tHW 4 5 s35 4 7 tWW 4 8 s55 5 6 cWW 6 7 s33 7 8 s55 8 9 s35 9 10 s35 10 2 6BRJAR3D SCFG/MRF model for IL_53635.3:
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 [11] // Initial node G674 - C806 from junction BasepairNode | Deletion Probability [0.0000001231336240] | Pair Probability [[0.009810372,0.019985697,0.011358953,0.186173951,0.000000000],[0.016552873,0.008089349,0.200518679,0.012762933,0.000000000],[0.011215968,0.263443051,0.002068393,0.026530626,0.000000000],[0.185098881,0.013397366,0.022885515,0.010107394,0.000000000],[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 [0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.062500000,0.062500000,0.812500000,0.062500000,0.000000000] | Left Index [1] | Right Index [11] // Basepair G674 - C806 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.953125000,0.015625000,0.015625000,0.015625000,0.000000000] | Position [2] | Left Index [2] | Right Index [10] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | 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 [2] | Right Index [9] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.024010722,0.093152721,0.004771130,0.487955535,0.000000000],[0.004771130,0.038171791,0.004771130,0.004771130,0.000000000],[0.044022502,0.066387877,0.053871957,0.055814147,0.000000000],[0.004771130,0.004771130,0.024540096,0.083445872,0.000000000],[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 [2] | Right Index [9] // Basepair A675 - U803 tHW BasepairNode | Deletion Probability [0.0000001231336240] | Pair Probability [[0.414957834,0.027524172,0.079529796,0.016623519,0.000000000],[0.003486342,0.012807437,0.003486342,0.003486342,0.000000000],[0.298959150,0.019956551,0.043185240,0.020639353,0.000000000],[0.003486342,0.003486342,0.031107565,0.017277672,0.000000000],[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 [0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.437500000,0.062500000,0.437500000,0.062500000,0.000000000] | Left Index [3] | Right Index [8] // Basepair A676 - A802 tHW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.360594839,0.031200513,0.003322930,0.091785179,0.000000000],[0.031239901,0.012871807,0.010108516,0.012694969,0.000000000],[0.003322930,0.010103019,0.313906749,0.018183499,0.000000000],[0.015745234,0.050716942,0.018200359,0.016002616,0.000000000],[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 [4] | Right Index [7] // Basepair A677 - A800 tWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009704981,0.017699381,0.011265142,0.185482208,0.000000000],[0.018844119,0.008192545,0.242496164,0.013187696,0.000000000],[0.011312823,0.221520521,0.002068672,0.024103639,0.000000000],[0.185840710,0.012976132,0.025319168,0.009986100,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [5] | Right Index [6] // Basepair C678 - G799 cWW HairpinNode | Num Bases [1] | Left Index [6] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node type * Interaction | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncationSequences of instances from IL_53635.3:
> IL_53635.3 IL_3V2F_018 G 674 C 806 GAAAC*GAGAUAGC > IL_53635.3 IL_2QBG_021 G 674 C 806 GAAAC*GAGAUAGC > IL_53635.3 IL_1S72_025 G 765 C 899 GAAUC*GCAACAGC > IL_53635.3 IL_4A1B_035 G 830 C 963 GAAAG*CUAGUAGC > IL_53635.3 IL_4IOA_014 G 687 C 819 GAAAC*GAGAUAGC > IL_53635.3 IL_3U5H_029 G 805 C 938 GAAAG*CUAGUAGC