| 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 | 15 7 I | 16 7 7 | 17 6 I | 18 6 8 | 19 5 I | 20 5 9 | 21 4 I | 22 4 10 | 23 3 I | 24 3 11 | 25 2 I | 26 2 12 | 27 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_47444.3_Instance_1 IL_47444.3_IL_1DUH_002_U45_G64 | U | C | A | G | G | U | A | A | G | C | A | G | ||||||||||||||||||||
| IL_47444.3_Sequence_1 IL_47444.3_IL_1DUH_002_U45_G64 | U | C | A | G | G | U | * | A | A | G | C | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| IL_47444.3_Instance_2 IL_47444.3_IL_1DUH_004_U45_G64 | U | C | A | G | G | U | A | A | G | C | A | G | ||||||||||||||||||||
| IL_47444.3_Sequence_2 IL_47444.3_IL_1DUH_004_U45_G64 | U | C | A | G | G | U | * | A | A | G | C | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| IL_47444.3_Instance_3 IL_47444.3_IL_2PXV_002_U146_G165 | U | C | A | G | G | U | A | A | G | C | A | G | ||||||||||||||||||||
| IL_47444.3_Sequence_3 IL_47444.3_IL_2PXV_002_U146_G165 | U | C | A | G | G | U | * | A | A | G | C | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| IL_47444.3_Instance_4 IL_47444.3_IL_1LNT_002_U4_G21 | U | C | A | G | G | U | A | A | G | C | A | G | ||||||||||||||||||||
| IL_47444.3_Sequence_4 IL_47444.3_IL_1LNT_002_U4_G21 | U | C | A | G | G | U | * | A | A | G | C | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| IL_47444.3_Instance_5 IL_47444.3_IL_1MFQ_007_C190_G209 | C | C | A | G | G | U | G | A | G | C | A | G | ||||||||||||||||||||
| IL_47444.3_Sequence_5 IL_47444.3_IL_1MFQ_007_C190_G209 | C | C | A | G | G | U | * | G | A | G | C | A | G | true | 90 | 0 | 0 | 1.77 | ||||||||||||||
| IL_47444.3_Instance_6 IL_47444.3_IL_2XXA_015_U40_G59 | U | C | A | G | A | G | C | A | G | C | A | G | ||||||||||||||||||||
| IL_47444.3_Sequence_6 IL_47444.3_IL_2XXA_015_U40_G59 | U | C | A | G | A | G | * | C | A | G | C | A | G | true | 93 | 0 | 0 | 1.34 | ||||||||||||||
| IL_47444.3_Instance_7 IL_47444.3_IL_3U5H_127_C3161_G3289 | C | C | A | C | A | C | G | C | G | U | G | G | ||||||||||||||||||||
| IL_47444.3_Sequence_7 IL_47444.3_IL_3U5H_127_C_3161_G_3289 | C | C | A | C | A | C | * | G | C | G | U | G | G | true | 44 | 0 | 0 | 10.01 | ||||||||||||||
| IL_47444.3_Instance_8 IL_47444.3_IL_4FAW_007_U214_A163 | U | A | C | A | G | A | U | A | G | G | U | A | ||||||||||||||||||||
| IL_47444.3_Sequence_8 IL_47444.3_IL_4FAW_007_U214_A163 | U | A | C | A | G | A | * | U | A | G | G | U | A | true | 54 | 0 | 0 | 8.21 | ||||||||||||||
| IL_47444.3_Instance_9 IL_47444.3_IL_1D4R_002_G12_C17 | G | G | G | A | G | C | G | G | G | A | G | C | ||||||||||||||||||||
| IL_47444.3_Sequence_9 IL_47444.3_IL_1D4R_002_G12_C17 | G | G | G | A | G | C | * | G | G | G | A | G | C | true | 51 | 0 | 0 | 8.91 |
1 2 s35 1 12 cWW 2 9 s33 2 11 tSH 3 4 s35 3 10 tHW 3 11 s55 4 5 s35 4 9 tHS 4 10 s55 5 6 s35 5 8 cWW 5 9 s55 6 7 cWW 7 8 s35 8 9 s35 9 10 s35 10 11 s35 11 12 s35 9 3 6BPh 2 10 6BPhJAR3D SCFG/MRF model for IL_47444.3:
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 [12] // Initial node U45 - G64 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.010861630,0.015518619,0.012759211,0.101819593,0.000000000],[0.173445935,0.011997144,0.128406679,0.014433747,0.000000000],[0.012959429,0.115200367,0.002728704,0.018324658,0.000000000],[0.115535013,0.013473421,0.240394114,0.012141736,0.000000000],[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 [12] // Basepair U45 - G64 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.050489329,0.042183614,0.000520707,0.027051559,0.000000000],[0.419540607,0.255029502,0.027381659,0.003644947,0.000000000],[0.043601253,0.000520707,0.027349873,0.006066193,0.000000000],[0.048627321,0.046951315,0.000520707,0.000520707,0.000000000],[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 [11] // Basepair C46 - A63 tSH BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.017695077,0.279180118,0.002241342,0.045999899,0.000000000],[0.002241342,0.010605986,0.025978054,0.002241342,0.000000000],[0.149311367,0.207805235,0.015309849,0.010728810,0.000000000],[0.002241342,0.002241342,0.023148360,0.203030532,0.000000000],[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 [10] // Basepair A47 - C62 tHW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008241149,0.006583009,0.079647297,0.005438157,0.000000000],[0.004483626,0.004166170,0.030377634,0.004738347,0.000000000],[0.000948703,0.000948703,0.719138102,0.000948703,0.000000000],[0.088506880,0.000948703,0.043936112,0.000948703,0.000000000],[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 [9] // Basepair G48 - G61 tHS BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.095476982,0.063682634,0.259729097,0.017796169,0.000000000],[0.012936191,0.005797560,0.018701505,0.032815706,0.000000000],[0.307844781,0.019297171,0.025207837,0.051425081,0.000000000],[0.016902877,0.034170536,0.014254373,0.023961499,0.000000000],[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 [8] // Basepair G49 - A60 cWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009252775,0.018190197,0.010372744,0.181878762,0.000000000],[0.051344320,0.009257883,0.190042721,0.011475298,0.000000000],[0.010430036,0.179189206,0.002156526,0.022148569,0.000000000],[0.212757301,0.011207133,0.068104341,0.012192189,0.000000000],[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 [6] | Right Index [7] // Basepair U50 - A59 cWW HairpinNode | Num Bases [1] | Left Index [7] | Right Index [7] | 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_47444.3:
> IL_47444.3 IL_1DUH_002 U 45 G 64 UCAGGU*AAGCAG > IL_47444.3 IL_1DUH_004 U 45 G 64 UCAGGU*AAGCAG > IL_47444.3 IL_2PXV_002 U 146 G 165 UCAGGU*AAGCAG > IL_47444.3 IL_1LNT_002 U 4 G 21 UCAGGU*AAGCAG > IL_47444.3 IL_1MFQ_007 C 190 G 209 CCAGGU*GAGCAG > IL_47444.3 IL_2XXA_015 U 40 G 59 UCAGAG*CAGCAG > IL_47444.3 IL_3U5H_127 C 3161 G 3289 CCACAC*GCGUGG > IL_47444.3 IL_4FAW_007 U 214 A 163 UACAGA*UAGGUA > IL_47444.3 IL_1D4R_002 G 12 C 17 GGGAGC*GGGAGC