Alignment of IL_33323.1 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
4

3
7
4
I

8
4

4
9
4
I

10
4

5
11
4
I

12
4

6
13
5
I

14
6


15
5
I

16
4

7
17
3
I

18
3

8
19
2
I

20
2

9
21
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_33323.1_Instance_1 IL_33323.1,IL_8D28_004,C20_G11CCCUUGCAG
IL_33323.1_Sequence_1 IL_33323.18D28_C20_G11CCCUUG*CAGtrue88001.64
IL_33323.1_Instance_2 IL_33323.1,IL_5J7L_021,C492_G442CAGAAGCAG
IL_33323.1_Sequence_2 IL_33323.15J7L_C492_G442CAGAAG*CAGtrue100000.00

Conserved interactions between motif group positions in IL_33323.1:
1 2 s35 
1 9 cWW 
2 3 s35 
2 8 cWW 
2 9 s55 
3 5 s35 
3 6 cSH 
4 5 s53 
5 6 s53 
6 7 cWW 
6 8 s55 
7 8 s35 
8 9 s35
JAR3D SCFG/MRF model for IL_33323.1:
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 [9] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[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 [1] | Right Index [9] // Basepair C20 - G11 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.551310107,0.025164260,0.044836650,0.024627086,0.000000000],[0.115776646,0.009398244,0.024711593,0.023896183,0.000000000],[0.034286338,0.025228088,0.005415062,0.026437514,0.000000000],[0.023931263,0.026914203,0.018419801,0.019646964,0.000000000],[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 [8] // Basepair C21 - A10 cWW 
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [3] | Right Index [7] | Norm Constant [0.249136979790658] // Cluster node 8D28|1|B|C|22:8D28|1|B|G|25 and 8D28|1|B|C|9:8D28|1|B|C|9
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8D28|1|B|G|25 - 8D28|1|B|C|9 cWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.081891091,0.089510988,0.005530002,0.081620772,0.000000000],[0.080452043,0.086529911,0.099916072,0.011403414,0.000000000],[0.012307770,0.000985591,0.108363034,0.084676822,0.000000000],[0.083029246,0.089904891,0.000985591,0.082892761,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8D28|1|B|C|22 - 8D28|1|B|G|25 cSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8D28|1|B|U|23
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8D28|1|B|U|24
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 [7] | Right Index [6] // New Initial node after Cluster
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 truncation
Sequences of instances from IL_33323.1:
> IL_33323.1  8D28 C   20 G   11
CCCUUG*CAG
> IL_33323.1  5J7L C  492 G  442
CAGAAG*CAG