Alignment of IL_81516.2 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
3
I

22
3

11
23
3
I

24
3

12
25
4
I

26
5


27
4
I

28
3

13
29
3
I

30
3

14
31
3
I

32
3

15
33
2
I

34
2

16
35
1
I


In
acceptance
region

Cutoff
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Full
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distance
Interior
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Alignment
score
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IL_81516.2_Instance_1 IL_81516.2,IL_5J7L_255,G496_C484GAGUGAAAAAGAACGAAC
IL_81516.2_Sequence_1 IL_81516.25J7L_G496_C484GAGUGAAAAAGAAC*GAACtrue100000.00
IL_81516.2_Instance_2 IL_81516.2,IL_7A0S_009,G506_C495GAGUGAAAGAGAACGAAC
IL_81516.2_Sequence_2 IL_81516.27A0S_G506_C495GAGUGAAAGAGAAC*GAACtrue96000.85
IL_81516.2_Instance_3 IL_81516.2,IL_9DFE_012,G496_C484GAGUGAAAUAGAGCGAAC
IL_81516.2_Sequence_3 IL_81516.29DFE_G496_C484GAGUGAAAUAGAGC*GAACtrue93001.64
IL_81516.2_Instance_4 IL_81516.2,IL_4WF9_015,G541_C530GAGUGAAAUAGAACGCAC
IL_81516.2_Sequence_4 IL_81516.24WF9_G541_C530GAGUGAAAUAGAAC*GCACtrue97000.71
IL_81516.2_Instance_5 IL_81516.2,IL_8P9A_243,G390_C379GAGUGAAAAAGUACGAAC
IL_81516.2_Sequence_5 IL_81516.28P9A_G390_C379GAGUGAAAAAGUAC*GAACtrue92001.75
IL_81516.2_Instance_6 IL_81516.2,IL_8CRE_015,G390_C379GAGUGAAAAAGUACGAAC
IL_81516.2_Sequence_6 IL_81516.28CRE_G390_C379GAGUGAAAAAGUAC*GAACtrue92001.75

Conserved interactions between motif group positions in IL_81516.2:
1 2 s35 
1 16 cWW 
2 3 s35 
2 14 cWS 
2 15 tSH 
2 16 s55 
3 4 s35 
3 10 bif 
4 5 s35 
4 8 tWH 
5 7 s33 
5 8 s55 
5 9 tSH 
6 7 s35 
7 9 s35 
8 9 s53 
8 10 s35 
10 13 tSS 
10 14 s35 
11 13 s53 
11 14 tHH 
12 13 cWW 
15 16 s35 
5 8 6BPh
11 14 6BPh
16 15 7BPh
15 2 6BR
7 5 7BR
JAR3D SCFG/MRF model for IL_81516.2:
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 [16] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003679589,0.053642867,0.004190070,0.076104487,0.000000000],[0.006463298,0.025257446,0.076749356,0.005021698,0.000000000],[0.004143537,0.609465400,0.000789802,0.010117932,0.000000000],[0.075130495,0.036484266,0.008868823,0.003890933,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [16] // Basepair G496 - C484 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000000000000000000000151268825322266833831369] | Num Left Bases [11] | Num Right Bases [3] | Left Index [2] | Right Index [15] | Norm Constant [0.005678442180201] // Cluster node 5J7L|1|DA|A|497:5J7L|1|DA|C|509 and 5J7L|1|DA|G|481:5J7L|1|DA|A|483
Interaction  | Interacting Bases [9,12] | Pair Probability [[0.020028879,0.016764665,0.019150815,0.012041759,0.000000000],[0.002344946,0.002344946,0.206243870,0.002344946,0.000000000],[0.227956632,0.002344946,0.291098408,0.187955402,0.000000000],[0.002344946,0.002344946,0.002344946,0.002344946,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|506 - 5J7L|1|DA|G|481 tSS 
Interaction  | Interacting Bases [11,12] | Pair Probability [[0.009176708,0.016456041,0.010549755,0.191287868,0.000000000],[0.019511251,0.009346211,0.257693361,0.013270239,0.000000000],[0.010668232,0.195409608,0.002010896,0.022580688,0.000000000],[0.193767724,0.012785620,0.025761014,0.009724784,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|509 - 5J7L|1|DA|G|481 cWW 
Interaction  | Interacting Bases [1,13] | Pair Probability [[0.255486950,0.206401155,0.203351950,0.197013984,0.000000000],[0.016065555,0.013327012,0.002111047,0.013414598,0.000000000],[0.020426943,0.002111047,0.031068959,0.009926371,0.000000000],[0.007554652,0.007985333,0.006326349,0.007428094,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|497 - 5J7L|1|DA|A|482 cWS 
Interaction  | Interacting Bases [10,13] | Pair Probability [[0.388045295,0.332153463,0.018827954,0.023585663,0.000000000],[0.037274805,0.000540626,0.045519613,0.015373214,0.000000000],[0.002638001,0.045342292,0.001154794,0.000540626,0.000000000],[0.067172032,0.020750368,0.000540626,0.000540626,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|507 - 5J7L|1|DA|A|482 tHH 
Interaction  | Interacting Bases [1,14] | Pair Probability [[0.226839908,0.019867145,0.001702361,0.010380907,0.000000000],[0.165066191,0.067616638,0.001702361,0.001702361,0.000000000],[0.141812235,0.001702361,0.014787991,0.037155137,0.000000000],[0.153291403,0.152968278,0.001702361,0.001702361,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|497 - 5J7L|1|DA|A|483 tSH 
Interaction  | Interacting Bases [3,7] | Pair Probability [[0.018067094,0.003998277,0.018765634,0.003998277,0.000000000],[0.040207941,0.322184696,0.003998277,0.003998277,0.000000000],[0.003998277,0.009584133,0.030406557,0.017782958,0.000000000],[0.456431444,0.003998277,0.023197522,0.039382361,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|499 - 5J7L|1|DA|A|503 tWH 
Interaction  | Interacting Bases [4,8] | Pair Probability [[0.042049014,0.044514549,0.000504770,0.002378984,0.000000000],[0.042361408,0.044411471,0.000504770,0.000504770,0.000000000],[0.409943044,0.003533393,0.017273635,0.299901013,0.000000000],[0.046937930,0.044171708,0.000504770,0.000504770,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|500 - 5J7L|1|DA|A|505 tSH 
Interaction  | Interacting Bases [2,9] | Pair Probability [[0.273328021,0.197478018,0.002879291,0.002879291,0.000000000],[0.012082009,0.008456580,0.002879291,0.002879291,0.000000000],[0.002879291,0.002879291,0.344532838,0.135329628,0.000000000],[0.002879291,0.002879291,0.002879291,0.002879291,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|498 - 5J7L|1|DA|G|506 bif 
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|DA|A|501
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.953125000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.015625000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.015625000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.015625000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|DA|A|502
Insertion    | Location [7] | Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Letter Distribution [0.437500000,0.062500000,0.187500000,0.312500000,0.000000000]// Insertion after nucleotide 8, position 7 in cluster node
Insertion    | Location [10] | Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Letter Distribution [0.687500000,0.062500000,0.187500000,0.062500000,0.000000000]// Insertion after nucleotide 11, position 10 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 [13] | Right Index [12] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [13] | Right Index [13] | 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_81516.2:
> IL_81516.2  5J7L G  496 C  484
GAGUGAAAAAGAAC*GAAC
> IL_81516.2  7A0S G  506 C  495
GAGUGAAAGAGAAC*GAAC
> IL_81516.2  9DFE G  496 C  484
GAGUGAAAUAGAGC*GAAC
> IL_81516.2  4WF9 G  541 C  530
GAGUGAAAUAGAAC*GCAC
> IL_81516.2  8P9A G  390 C  379
GAGUGAAAAAGUAC*GAAC
> IL_81516.2  8CRE G  390 C  379
GAGUGAAAAAGUAC*GAAC