Alignment of IL_47087.1 sequences from 3D to the JAR3D model

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The correspondence between sequences from 3D structures and the motif group is shown in blue and the JAR3D alignment of the sequences to the motif group is shown in black. Occasionally the two disagree, in which case the JAR3D alignment is shown in red.

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 9 6	13 9 I	14 9 7	15 9 I	16 9 8	17 10 I	18 11	19 10 I	20 9 9	21 9 I	22 9 10	23 2 I	24 2 11	25 1 I	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_47087.1_Instance_1 IL_47087.1,IL_3P59_003,G51_C112		G		G		A		A		C		U		A		C				G		C		C
IL_47087.1_Sequence_1 IL_47087.13P59_G51_C112		G		G		A		A		C		U		A		C		*		G		C		C		true	100	0	0	0.00

Conserved interactions between motif group positions in IL_47087.1:

1 2 s35 
1 11 cWW 
2 3 s35 
2 11 s55 
3 4 s35 
5 7 cSH 
5 9 tWH 
6 7 s35 
7 8 s35 
7 10 cWW 
8 9 cWW 
9 10 s35 
11 9 7BPh
6 5 7BR

JAR3D SCFG/MRF model for IL_47087.1:

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 [11] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.003861747,0.056298454,0.004397499,0.079872036,0.000000000],[0.006783263,0.026507815,0.080548829,0.005270297,0.000000000],[0.004348662,0.590132004,0.000828901,0.010618820,0.000000000],[0.078849827,0.038290418,0.009307874,0.004083553,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [11] // Basepair G51 - C112 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Position [1] | Left Index [2] | Right Index [10] // Fixed node on left for 3P59|1|E|G|52
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left for 3P59|1|E|A|53
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [4] | Right Index [10] // Fixed node on left for 3P59|1|E|A|54
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [10] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [4] | Num Right Bases [2] | Left Index [5] | Right Index [10] | Norm Constant [0.015089947498055] // Cluster node 3P59|1|E|C|55:3P59|1|E|C|58 and 3P59|1|F|G|110:3P59|1|F|C|111
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.061881188,0.061881188,0.061881188,0.061881188,0.000000000],[0.061881188,0.061881188,0.071782178,0.061881188,0.000000000],[0.061881188,0.061881188,0.061881188,0.061881188,0.000000000],[0.061881188,0.061881188,0.061881188,0.061881188,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3P59|1|E|C|55 - 3P59|1|F|G|110 tWH 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3P59|1|E|C|58 - 3P59|1|F|G|110 cWW 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.013958323,0.310268183,0.012182537,0.032389778,0.000000000],[0.012235413,0.011726251,0.024580362,0.012106270,0.000000000],[0.011896483,0.029143924,0.003003672,0.274859274,0.000000000],[0.025778993,0.013284394,0.012704593,0.199881551,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3P59|1|E|A|57 - 3P59|1|F|C|111 cWW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.110380675,0.105269562,0.005717769,0.037273020,0.000000000],[0.130005463,0.104189678,0.001201045,0.010129477,0.000000000],[0.010623361,0.001201045,0.098039136,0.072282348,0.000000000],[0.112884724,0.103241206,0.001201045,0.096360446,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3P59|1|E|C|55 - 3P59|1|E|A|57 cSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.785714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3P59|1|E|U|56
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [8] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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 truncation

Sequences of instances from IL_47087.1:> IL_47087.1 3P59 G 51 C 112 GGAACUAC*GCC