Alignment of IL_17765.1 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
3
I

6
3

3
7
3
I

8
3

4
9
3
I

10
3

5
11
3
I

12
3

6
13
3
I

14
3

7
15
3
I

16
3

8
17
3
I

18
3

9
19
3
I

20
3

10
21
4
I

22
5


23
4
I

24
3

11
25
3
I

26
3

12
27
3
I

28
3

13
29
2
I

30
2

14
31
1
I


In
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Cutoff
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Interior
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Alignment
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IL_17765.1_Instance_1 IL_17765.1,IL_3D2V_002,C26_G13CUGAGAAAGUCGGUG
IL_17765.1_Sequence_1 IL_17765.13D2V_C26_G13CUGAGAAAGUC*GGUGtrue100000.00

Conserved interactions between motif group positions in IL_17765.1:
1 2 s35 
1 14 cWW 
2 3 s35 
2 6 tWH 
3 5 s33 
3 6 s55 
4 5 s35 
4 10 cSS 
5 12 tSS 
6 14 s35 
7 13 s33 
8 9 s53 
8 13 cHW 
9 10 s55 
9 12 cHW 
10 11 cWW 
11 12 s35 
12 13 s35 
3 6 6BPh
7 14 2BPh
JAR3D SCFG/MRF model for IL_17765.1:
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 [14] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | 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]] | 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 [14] // Basepair C26 - G13 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000000000000001191720873277651707035468314865] | Num Left Bases [9] | Num Right Bases [3] | Left Index [2] | Right Index [13] | Norm Constant [0.101806870731090] // Cluster node 3D2V|1|A|U|27:3D2V|1|A|C|36 and 3D2V|1|A|G|10:3D2V|1|A|U|12
Interaction  | Interacting Bases [9,10] | 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 3D2V|1|A|C|36 - 3D2V|1|A|G|10 cWW 
Interaction  | Interacting Bases [4,11] | Pair Probability [[0.021020407,0.017594599,0.020098875,0.012637885,0.000000000],[0.002461033,0.002461033,0.216453963,0.002461033,0.000000000],[0.239241614,0.002461033,0.256004269,0.197260125,0.000000000],[0.002461033,0.002461033,0.002461033,0.002461033,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3D2V|1|A|G|30 - 3D2V|1|A|G|11 tSS 
Interaction  | Interacting Bases [8,11] | Pair Probability [[0.004966430,0.004966430,0.206503547,0.017165095,0.000000000],[0.004966430,0.052642128,0.004966430,0.004966430,0.000000000],[0.051077026,0.004966430,0.506544030,0.015536138,0.000000000],[0.042074794,0.017912101,0.004966430,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3D2V|1|A|G|34 - 3D2V|1|A|G|11 cHW 
Interaction  | Interacting Bases [7,12] | Pair Probability [[0.003098658,0.003098658,0.011416052,0.319766810,0.000000000],[0.003098658,0.014901162,0.003098658,0.003098658,0.000000000],[0.013353226,0.003098658,0.010709656,0.286715797,0.000000000],[0.013415874,0.293495075,0.003098658,0.014535741,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3D2V|1|A|A|33 - 3D2V|1|A|U|12 cHW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.018961504,0.004196211,0.019694625,0.004196211,0.000000000],[0.042198433,0.338134433,0.004196211,0.004196211,0.000000000],[0.004196211,0.010058595,0.031911832,0.018663303,0.000000000],[0.429522110,0.004196211,0.024345914,0.041331983,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3D2V|1|A|U|27 - 3D2V|1|A|A|31 tWH 
Interaction  | Interacting Bases [3,9] | Pair Probability [[0.081591666,0.095215600,0.082006787,0.080836575,0.000000000],[0.075904306,0.083072861,0.003458357,0.075094816,0.000000000],[0.078139289,0.003393533,0.007809038,0.077291685,0.000000000],[0.071822400,0.041801731,0.062580800,0.079980554,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3D2V|1|A|A|29 - 3D2V|1|A|C|36 cSS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.833333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3D2V|1|A|G|28
Interaction  | Interacting Bases [6,6] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3D2V|1|A|A|32
Insertion    | Location [8] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 9, position 8 in cluster node
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 [11] | Right Index [10] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [11] | Right Index [11] | 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_17765.1:
> IL_17765.1  3D2V C   26 G   13
CUGAGAAAGUC*GGUG