| 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 5 4 | 9 5 I | 10 6 5 | 11 6 I | 12 7 6 | 13 7 I | 14 8 7 | 15 8 I | 16 9 8 | 17 9 I | 18 10 9 | 19 10 I | 20 11 | 21 10 I | 22 10 10 | 23 9 I | 24 9 11 | 25 8 I | 26 8 12 | 27 7 I | 28 7 13 | 29 6 I | 30 6 14 | 31 5 I | 32 5 15 | 33 4 I | 34 4 16 | 35 3 I | 36 3 17 | 37 2 I | 38 2 18 | 39 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_25230.3_Instance_1 IL_25230.3_IL_1DFU_001_C71_G105 | C | G | A | U | G | G | U | A | G | C | G | A | G | A | G | U | A | G | ||||||||||||||||||||||||||
| IL_25230.3_Sequence_1 IL_25230.3_IL_1DFU_001_C71_G105 | C | G | A | U | G | G | U | A | G | * | C | G | A | G | A | G | U | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||||||
| IL_25230.3_Instance_2 IL_25230.3_IL_2QBG_005_C71_G105 | C | G | A | U | G | G | U | A | G | C | G | A | G | A | G | U | A | G | ||||||||||||||||||||||||||
| IL_25230.3_Sequence_2 IL_25230.3_IL_2QBG_005_C71_G105 | C | G | A | U | G | G | U | A | G | * | C | G | A | G | A | G | U | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||||||
| IL_25230.3_Instance_3 IL_25230.3_IL_1FEU_001_C71_G105 | C | G | A | U | G | G | U | A | G | C | G | A | G | A | G | U | A | G | ||||||||||||||||||||||||||
| IL_25230.3_Sequence_3 IL_25230.3_IL_1FEU_001_C71_G105 | C | G | A | U | G | G | U | A | G | * | C | G | A | G | A | G | U | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||||||
| IL_25230.3_Instance_4 IL_25230.3_IL_3V2F_111_C71_G106 | C | G | A | U | G | G | U | A | C | G | G | A | G | A | G | U | A | G | ||||||||||||||||||||||||||
| IL_25230.3_Sequence_4 IL_25230.3_IL_3V2F_111_C71_G106 | C | G | A | U | G | G | U | A | C | * | G | G | A | G | A | G | U | A | G | true | 100 | 0 | 0 | 0.09 | ||||||||||||||||||||
| IL_25230.3_Instance_5 IL_25230.3_IL_4IOA_108_C73_G108 | C | A | A | U | G | A | U | A | C | G | A | A | A | A | G | U | C | G | ||||||||||||||||||||||||||
| IL_25230.3_Sequence_5 IL_25230.3_IL_4IOA_108_C73_G108 | C | A | A | U | G | A | U | A | C | * | G | A | A | A | A | G | U | C | G | true | 88 | 0 | 0 | 2.61 | ||||||||||||||||||||
| IL_25230.3_Instance_6 IL_25230.3_IL_364D_003_C97_G79 | C | G | A | G | A | G | U | A | G | C | G | A | U | G | G | U | A | G | ||||||||||||||||||||||||||
| IL_25230.3_Sequence_6 IL_25230.3_IL_364D_003_C97_G79 | C | G | A | G | A | G | U | A | G | * | C | G | A | U | G | G | U | A | G | true | 79 | 0 | 0 | 4.41 |
1 2 s35 1 18 cWW 2 16 s33 2 17 tSH 2 18 s55 3 4 s35 3 16 tHW 3 17 s55 4 5 s35 4 15 bif 5 6 s35 5 14 wat 5 15 s55 6 7 s35 6 13 bif 7 8 s35 7 11 s33 7 12 tWH 8 9 s35 8 11 tHS 8 12 s55 9 10 cWW 9 11 s55 10 11 s35 12 13 s35 13 14 s35 14 15 s35 15 16 s35 16 17 s35 17 18 s35 17 2 6BR 8 11 6BRJAR3D SCFG/MRF model for IL_25230.3:
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 [18] // Initial node C71 - G105 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009652285,0.016556223,0.011218237,0.185136336,0.000000000],[0.019989741,0.008244143,0.263484907,0.013400077,0.000000000],[0.011361251,0.200559255,0.002068811,0.022890146,0.000000000],[0.186211624,0.012765515,0.026535995,0.009925452,0.000000000],[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 [1] | Right Index [18] // Basepair C71 - G105 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.107319836,0.135968602,0.001300561,0.006167642,0.000000000],[0.108304840,0.114225444,0.001300561,0.001300561,0.000000000],[0.176511302,0.001300561,0.006274896,0.108168433,0.000000000],[0.116721758,0.112533879,0.001300561,0.001300561,0.000000000],[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 [17] // Basepair G72 - A104 tSH BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.024991732,0.052062200,0.005241353,0.580739054,0.000000000],[0.005241353,0.043515857,0.005241353,0.005241353,0.000000000],[0.025709985,0.034791284,0.061340288,0.064660161,0.000000000],[0.005241353,0.005241353,0.024449379,0.056291944,0.000000000],[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 [3] | Right Index [16] // Basepair A73 - U103 tHW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.023615491,0.017319894,0.003739651,0.003739651,0.000000000],[0.300657640,0.014674084,0.003739651,0.003739651,0.000000000],[0.003739651,0.003739651,0.220883287,0.003739651,0.000000000],[0.003739651,0.003739651,0.385453090,0.003739651,0.000000000],[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 [15] // Basepair U74 - G102 bif BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008042594,0.008042594,0.035974521,0.008042594,0.000000000],[0.008042594,0.008042594,0.008042594,0.008042594,0.000000000],[0.851429169,0.008042594,0.008042594,0.008042594,0.000000000],[0.008042594,0.008042594,0.008042594,0.008042594,0.000000000],[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 [5] | Right Index [14] // Basepair G75 - A101 wat BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.062609363,0.236721929,0.003847175,0.003847175,0.000000000],[0.014591112,0.012435492,0.003847175,0.003847175,0.000000000],[0.003847175,0.003847175,0.422453372,0.212716979,0.000000000],[0.003847175,0.003847175,0.003847175,0.003847175,0.000000000],[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 [6] | Right Index [13] // Basepair G76 - G100 bif BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.024991732,0.005241353,0.025709985,0.005241353,0.000000000],[0.052062200,0.043515857,0.034791284,0.005241353,0.000000000],[0.005241353,0.005241353,0.061340288,0.024449379,0.000000000],[0.580739054,0.005241353,0.064660161,0.056291944,0.000000000],[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 [7] | Right Index [12] // Basepair U77 - A99 tWH BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.124703280,0.115292115,0.176480473,0.121074897,0.000000000],[0.125065232,0.105032267,0.001336529,0.116620511,0.000000000],[0.001336529,0.001336529,0.007456337,0.001336529,0.000000000],[0.007169504,0.001336529,0.093086208,0.001336529,0.000000000],[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 [8] | Right Index [11] // Basepair A78 - G98 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009757676,0.018842539,0.011312047,0.185828079,0.000000000],[0.017698496,0.008140947,0.221507422,0.012975314,0.000000000],[0.011264395,0.242481786,0.002068532,0.025317133,0.000000000],[0.185469795,0.013186749,0.024102342,0.010046747,0.000000000],[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 [9] | Right Index [10] // Basepair G79 - C97 cWW HairpinNode | Num Bases [1] | Left Index [10] | Right Index [10] | 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_25230.3:
> IL_25230.3 IL_1DFU_001 C 71 G 105 CGAUGGUAG*CGAGAGUAG > IL_25230.3 IL_2QBG_005 C 71 G 105 CGAUGGUAG*CGAGAGUAG > IL_25230.3 IL_1FEU_001 C 71 G 105 CGAUGGUAG*CGAGAGUAG > IL_25230.3 IL_3V2F_111 C 71 G 106 CGAUGGUAC*GGAGAGUAG > IL_25230.3 IL_4IOA_108 C 73 G 108 CAAUGAUAC*GAAAAGUCG > IL_25230.3 IL_364D_003 C 97 G 79 CGAGAGUAG*CGAUGGUAG