Alignment of IL_52743.1 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
2

2
5
2
I

6
2

3
7
2
I

8
2

4
9
3
I

10
4

5
11
5
I

12
6

6
13
6
I

14
6

7
15
7
I

16
8


17
7
I

18
6

8
19
6
I

20
6

9
21
3
I

22
2

10
23
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_52743.1_Instance_1 IL_52743.1,IL_5NWQ_002,G29_C20GACAAGAUAC
IL_52743.1_Sequence_1 IL_52743.15NWQ_G29_C20GACAAGA*UACtrue100000.00

Conserved interactions between motif group positions in IL_52743.1:
1 4 tSW 
1 10 cWW 
2 3 s35 
3 4 s35 
4 5 s35 
5 6 s35 
6 8 tSH 
6 9 cSW 
7 8 cWW 
7 9 s55 
8 9 s35 
9 10 s35 
3 2 7BPh
10 9 7BPh
JAR3D SCFG/MRF model for IL_52743.1:
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 [10] // Initial node
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [1] | Right Index [10] | Norm Constant [0.241220344742765] // Cluster node 5NWQ|1|A|G|29:5NWQ|1|A|A|32 and 5NWQ|1|A|C|20:5NWQ|1|A|C|20
Interaction  | Interacting Bases [1,5] | 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]] // Cluster Interaction 5NWQ|1|A|G|29 - 5NWQ|1|A|C|20 cWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.166586913,0.165788799,0.002070551,0.010011986,0.000000000],[0.193757756,0.009129710,0.002070551,0.008278035,0.000000000],[0.216956090,0.002070551,0.002070551,0.006790033,0.000000000],[0.179185112,0.008998530,0.016291903,0.009942930,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5NWQ|1|A|G|29 - 5NWQ|1|A|A|32 tSW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5NWQ|1|A|A|30
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.833333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5NWQ|1|A|C|31
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 [5] | Right Index [9] // Initial node 5NWQ|1|A|A|33 - 5NWQ|1|A|A|19 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [5] | Right Index [9] // Fixed node on left for 5NWQ|1|A|A|30
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 [6] | Right Index [9] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [2] | Num Right Bases [2] | Left Index [6] | Right Index [9] | Norm Constant [0.064907758104499] // Cluster node 5NWQ|1|A|G|34:5NWQ|1|A|A|35 and 5NWQ|1|A|U|18:5NWQ|1|A|A|19
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.053818499,0.067941945,0.002465838,0.014965233,0.000000000],[0.031217389,0.030696053,0.002465838,0.002465838,0.000000000],[0.209290967,0.002465838,0.017668093,0.256484744,0.000000000],[0.204710348,0.098411704,0.002465838,0.002465838,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5NWQ|1|A|G|34 - 5NWQ|1|A|U|18 tSH 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.009374836,0.022228469,0.010012528,0.216037101,0.000000000],[0.017691617,0.009675113,0.196088410,0.010461402,0.000000000],[0.009993038,0.198630499,0.002061361,0.053740648,0.000000000],[0.197964449,0.011137350,0.023240462,0.011662716,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5NWQ|1|A|A|35 - 5NWQ|1|A|U|18 cWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.218661090,0.014620617,0.019969329,0.007807710,0.000000000],[0.206663216,0.011999471,0.002249461,0.008266368,0.000000000],[0.234847085,0.002249461,0.027362667,0.006356246,0.000000000],[0.208475927,0.012213416,0.010584145,0.007673792,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5NWQ|1|A|G|34 - 5NWQ|1|A|A|19 cSW 
InitialNode  | Left Length Distribution [0.952380952,0.047619048] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.952380952,0.047619048] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [7] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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_52743.1:
> IL_52743.1  5NWQ G   29 C   20
GACAAGA*UAC