| 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 4 I | 6 7 3 | 7 7 I | 8 8 4 | 9 9 I | 10 10 5 | 11 11 I | 12 12 6 | 13 12 I | 14 13 | 15 12 I | 16 12 7 | 17 7 I | 18 7 8 | 19 6 I | 20 5 9 | 21 2 I | 22 2 10 | 23 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_70627.3_Instance_1 IL_70627.3,IL_4GXY_004,G148_C80 | G | G | A | G | U | C | G | U | G | A | C | |||||||||||||||||
| IL_70627.3_Sequence_1 IL_70627.34GXY_G148_C80 | G | G | A | G | U | C | * | G | U | G | A | C | true | 99 | 0 | 0 | 0.14 | |||||||||||
| IL_70627.3_Instance_2 IL_70627.3,IL_6VMY_002,A297_U283 | A | G | A | G | C | C | G | U | A | A | U | |||||||||||||||||
| IL_70627.3_Sequence_2 IL_70627.36VMY_A297_U283 | A | G | A | G | C | C | * | G | U | A | A | U | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_70627.3_Instance_3 IL_70627.3,IL_4V9F_052,C1483_G1460 | C | G | A | A | A | U | G | C | U | A | A | G | ||||||||||||||||
| IL_70627.3_Sequence_3 IL_70627.34V9F_C_1483_G_1460 | C | G | A | A | A | U | G | * | C | U | A | A | G | true | 84 | 0 | 0 | 2.62 |
1 2 s35 1 10 cWW 2 9 s33 2 10 s55 3 6 s35 3 8 tHW 3 9 s55 4 5 s35 6 7 cWW 7 8 s35 8 9 s35 9 3 6BPh 6 5 7BPhJAR3D SCFG/MRF model for IL_70627.3:
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 [10] // Initial node BasepairNode | Deletion Probability [0.0000001200211660] | Pair Probability [[0.009425327,0.019602391,0.010550535,0.209161741,0.000000000],[0.018119710,0.009519290,0.209803050,0.012356683,0.000000000],[0.010544174,0.210633518,0.002053265,0.034146945,0.000000000],[0.196782200,0.012577586,0.024177876,0.010545706,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair G148 - C80 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left for 4GXY|1|A|U|77 InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.630434783,0.021739130,0.326086957,0.021739130,0.000000000] | Position [2] | Left Index [3] | Right Index [9] // Fixed node on right for 4GXY|1|A|G|151 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000038011627649] | Pair Probability [[0.018593320,0.041379046,0.004114731,0.440599350,0.000000000],[0.004114731,0.331568716,0.009863283,0.004114731,0.000000000],[0.019312206,0.004114731,0.031292185,0.023873178,0.000000000],[0.004114731,0.004114731,0.018300908,0.040529420,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [8] // Basepair A150 - U77 tHW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.500000000,0.100000000,0.000000000] | Position [1] | Left Index [4] | Right Index [7] // Fixed node on left for 4GXY|1|A|A|79 InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [7] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.300000000,0.100000000,0.500000000,0.000000000] | Position [1] | Left Index [5] | Right Index [7] // Fixed node on left for 4GXY|1|A|C|80 InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.005685123,0.011124657,0.006500758,0.117985306,0.000000000],[0.042435980,0.020774777,0.465628354,0.029408551,0.000000000],[0.006492041,0.131315512,0.001231369,0.014917984,0.000000000],[0.117802838,0.007995460,0.014683976,0.006017314,0.000000000],[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 C153 - G76 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_70627.3:
> IL_70627.3 4GXY G 148 C 80 GGAGUC*GUGAC > IL_70627.3 6VMY A 297 U 283 AGAGCC*GUAAU > IL_70627.3 4V9F C 1483 G 1460 CGAAAUG*CUAAG