| 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 6 I | 10 7 5 | 11 7 I | 12 8 | 13 7 I | 14 7 6 | 15 4 I | 16 4 7 | 17 3 I | 18 3 8 | 19 2 I | 20 2 9 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_68909.1_Instance_1 IL_68909.1,IL_1J2B_001,G943_C929 | G | G | A | G | G | C | G | C | C | |||||||||||||||||
| IL_68909.1_Sequence_1 IL_68909.11J2B_G943_C929 | G | G | A | G | G | * | C | G | C | C | true | 88 | 0 | 0 | 1.21 | |||||||||||
| IL_68909.1_Instance_2 IL_68909.1,IL_8CRE_111,G2835_U2798 | G | A | U | U | C | G | G | C | U | |||||||||||||||||
| IL_68909.1_Sequence_2 IL_68909.18CRE_G_2835_U_2798 | G | A | U | U | C | * | G | G | C | U | true | 91 | 0 | 0 | 0.95 | |||||||||||
| IL_68909.1_Instance_3 IL_68909.1,IL_8CRE_009,G161_C259 | G | U | A | U | C | G | U | U | C | |||||||||||||||||
| IL_68909.1_Sequence_3 IL_68909.18CRE_G161_C259 | G | U | A | U | C | * | G | U | U | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_68909.1_Instance_4 IL_68909.1,IL_4DB2_001,G6_C8 | G | G | C | C | C | G | G | G | C | |||||||||||||||||
| IL_68909.1_Sequence_4 IL_68909.14DB2_G6_C8 | G | G | C | C | C | * | G | G | G | C | true | 84 | 0 | 0 | 1.65 | |||||||||||
| IL_68909.1_Instance_5 IL_68909.1,IL_8CRE_101,C2422_G2481 | C | A | U | G | G | U | A | U | A | G | ||||||||||||||||
| IL_68909.1_Sequence_5 IL_68909.18CRE_C_2422_G_2481 | C | A | U | G | G | * | U | A | U | A | G | true | 62 | 0 | 0 | 3.95 | ||||||||||
| IL_68909.1_Instance_6 IL_68909.1,IL_4PHY_006,G17_C34 | G | A | U | C | A | C | G | G | A | A | C | |||||||||||||||
| IL_68909.1_Sequence_6 IL_68909.14PHY_G17_C34 | G | A | U | C | A | C | * | G | G | A | A | C | true | 56 | 0 | 0 | 4.53 |
1 2 s35 1 9 cWW 2 3 s35 2 8 cWW 2 9 s55 3 4 s35 3 7 cWW 4 5 s35 5 6 cWW 5 7 s55 6 7 s35 8 9 s35JAR3D SCFG/MRF model for IL_68909.1:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [9] // Initial node BasepairNode | Deletion Probability [0.0000097596267952] | Pair Probability [[0.010314056,0.063361168,0.011165057,0.174595639,0.000000000],[0.016420899,0.009731951,0.179035235,0.013043747,0.000000000],[0.011056644,0.210999173,0.002195769,0.082400211,0.000000000],[0.165657257,0.013499233,0.021652982,0.014870977,0.000000000],[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 [0.826344012,0.171868555,0.001718686,0.000068747] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [1] | Right Index [9] // Basepair G943 - C929 cWW BasepairNode | Deletion Probability [0.0000097596267952] | Pair Probability [[0.154836587,0.153392826,0.019758913,0.097087008,0.000000000],[0.014845222,0.011427970,0.063031146,0.015276731,0.000000000],[0.016940995,0.075070742,0.035394807,0.087596551,0.000000000],[0.062228923,0.016707513,0.016892981,0.159511085,0.000000000],[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 [0.826344012,0.171868555,0.001718686,0.000068747] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [2] | Right Index [8] // Basepair G944 - C928 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.013655430,0.014484361,0.099903376,0.134962891,0.000000000],[0.082274911,0.013104784,0.116470566,0.019079598,0.000000000],[0.087339607,0.103957221,0.002528776,0.017655349,0.000000000],[0.126148077,0.019049935,0.138980106,0.010405012,0.000000000],[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 [7] // Basepair A945 - G927 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.312500000,0.312500000,0.312500000,0.000000000] | Position [1] | Left Index [4] | Right Index [6] // Fixed node on left for 1J2B|1|C|C|929 InitialNode | Left Length Distribution [0.826344012,0.171868555,0.001718686,0.000068747] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010219218,0.061835778,0.011107030,0.173377702,0.000000000],[0.017950372,0.009812717,0.210199288,0.013287507,0.000000000],[0.011117080,0.179880118,0.002195997,0.080812972,0.000000000],[0.166918894,0.013258429,0.023245708,0.014781190,0.000000000],[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 G947 - C926 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_68909.1:
> IL_68909.1 1J2B G 943 C 929 GGAGG*CGCC > IL_68909.1 8CRE G 2835 U 2798 GAUUC*GGCU > IL_68909.1 8CRE G 161 C 259 GUAUC*GUUC > IL_68909.1 4DB2 G 6 C 8 GGCCC*GGGC > IL_68909.1 8CRE C 2422 G 2481 CAUGG*UAUAG > IL_68909.1 4PHY G 17 C 34 GAUCAC*GGAAC