| 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 5 3 | 7 6 I | 8 7 4 | 9 8 I | 10 9 5 | 11 9 I | 12 10 | 13 9 I | 14 9 6 | 15 2 I | 16 2 7 | 17 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_29346.2_Instance_1 IL_29346.2,IL_5J7L_036,G774_C805 | G | G | G | A | G | U | C | |||||||||||||||
| IL_29346.2_Sequence_1 IL_29346.25J7L_G774_C805 | G | G | G | A | G | * | U | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_29346.2_Instance_2 IL_29346.2,IL_4LFB_032,G774_C805 | G | G | G | A | G | U | C | |||||||||||||||
| IL_29346.2_Sequence_2 IL_29346.24LFB_G774_C805 | G | G | G | A | G | * | U | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_29346.2_Instance_3 IL_29346.2,IL_3PDR_001,C163_G22 | C | G | A | U | U | G | C | G | ||||||||||||||
| IL_29346.2_Sequence_3 IL_29346.23PDR_C163_G22 | C | G | A | U | U | G | * | C | G | true | 53 | 0 | 0 | 4.48 |
1 2 s35 1 7 cWW 2 3 s35 2 7 s55 4 5 s35 5 6 cWW 7 6 7BPhJAR3D SCFG/MRF model for IL_29346.2:
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 [7] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.005672504,0.042448635,0.006493750,0.117833868,0.000000000],[0.011127546,0.020534877,0.131347442,0.007997558,0.000000000],[0.006502467,0.465760787,0.001231693,0.014687879,0.000000000],[0.118016323,0.029417282,0.014921870,0.006005517,0.000000000],[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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair G774 - C805 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 [6] // Fixed node on left for 5J7L|1|AA|G|775 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 [6] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.500000000,0.100000000,0.000000000] | Position [1] | Left Index [3] | Right Index [6] // Fixed node on left for 5J7L|1|AA|G|776 InitialNode | Left Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [6] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.100000000,0.300000000,0.000000000] | Position [1] | Left Index [4] | Right Index [6] // Fixed node on left for 5J7L|1|AA|A|777 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 [6] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.013670424,0.202694703,0.013111240,0.122296464,0.000000000],[0.014703520,0.011594218,0.091070574,0.013895076,0.000000000],[0.012868105,0.106114901,0.002831594,0.242445403,0.000000000],[0.089753694,0.014939126,0.017249809,0.030761150,0.000000000],[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 G778 - U804 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_29346.2:
> IL_29346.2 5J7L G 774 C 805 GGGAG*UC > IL_29346.2 4LFB G 774 C 805 GGGAG*UC > IL_29346.2 3PDR C 163 G 22 CGAUUG*CG