| 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 5 I | 8 8 4 | 9 8 I | 10 9 5 | 11 9 I | 12 10 6 | 13 10 I | 14 11 | 15 10 I | 16 10 7 | 17 9 I | 18 9 8 | 19 8 I | 20 8 9 | 21 7 I | 22 6 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_34822.1_Instance_1 IL_34822.1,IL_3PDR_005,A60_U81 | A | A | A | A | A | U | G | C | C | A | A | U | ||||||||||||||||||||
| IL_34822.1_Sequence_1 IL_34822.13PDR_A60_U81 | A | A | A | A | A | U | * | G | C | C | A | A | U | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| IL_34822.1_Instance_2 IL_34822.1,IL_4V9F_057,C1578_G1618 | C | C | A | A | C | U | A | C | G | A | A | C | G | |||||||||||||||||||
| IL_34822.1_Sequence_2 IL_34822.14V9F_C_1578_G_1618 | C | C | A | A | C | U | * | A | C | G | A | A | C | G | true | 98 | 0 | 0 | 0.37 |
1 2 s35 1 12 cWW 2 3 perp 2 10 s55 2 11 tWH 3 4 s35 3 9 s33 3 10 s55 4 5 s35 4 9 tHS 5 6 s35 5 8 bif 6 7 cWW 7 8 s35 8 9 s35 10 11 s35 11 12 s35JAR3D SCFG/MRF model for IL_34822.1:
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 [12] // Initial node BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.009409752,0.019555960,0.010438919,0.211256183,0.000000000],[0.018897284,0.009646494,0.211374635,0.012074740,0.000000000],[0.010490831,0.199877935,0.002065453,0.038339992,0.000000000],[0.198695040,0.012157589,0.024891932,0.010827262,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Left Index [1] | Right Index [12] // Basepair A60 - U81 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.126855308,0.003262473,0.093329234,0.003262473,0.000000000],[0.336051234,0.023769222,0.003262473,0.003262473,0.000000000],[0.003262473,0.011390225,0.029337962,0.030072816,0.000000000],[0.032808466,0.003262473,0.014668147,0.282142548,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair A61 - A80 tWH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left for 3PDR|1|X|A|62 InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [4] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [4] | Right Index [10] // Fixed node on right for 3PDR|1|X|A|79 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.102496164,0.202188119,0.132843734,0.114413092,0.000000000],[0.108506004,0.108254748,0.001230398,0.107670315,0.000000000],[0.001230398,0.001230398,0.006015026,0.001230398,0.000000000],[0.005798870,0.001230398,0.104431541,0.001230398,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // Basepair A63 - C78 tHS BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.024411903,0.400092434,0.007118959,0.007118959,0.000000000],[0.028015685,0.414783946,0.007118959,0.007118959,0.000000000],[0.007118959,0.007118959,0.025285756,0.007118959,0.000000000],[0.007118959,0.007118959,0.036220688,0.007118959,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair A64 - C77 bif BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010140241,0.015764366,0.012093842,0.116797878,0.000000000],[0.162291053,0.018891209,0.119667900,0.013539516,0.000000000],[0.012259791,0.115792992,0.002675199,0.018859777,0.000000000],[0.155112826,0.012526856,0.201758582,0.011827971,0.000000000],[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 U65 - 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_34822.1:
> IL_34822.1 3PDR A 60 U 81 AAAAAU*GCCAAU > IL_34822.1 4V9F C 1578 G 1618 CCAACU*ACGAACG