Alignment of IL_02359.3 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
3
I

8
4

4
9
4
I

10
5


11
4
I

12
4

5
13
3
I

14
2

6
15
2
I

16
2

7
17
2
I

18
2

8
19
2
I

20
2

9
21
2
I

22
2

10
23
2
I

24
2

11
25
2
I

26
2

12
27
2
I

28
2

13
29
2
I

30
2

14
31
2
I

32
2

15
33
2
I

34
2

16
35
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
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distance

Alignment
score
deficit
IL_02359.3_Instance_1 IL_02359.3_IL_2QBG_016_G481_C509GAACGAGUGAAAAAGAAC
IL_02359.3_Sequence_1 IL_02359.3_IL_2QBG_016_G481_C509GAAC*GAGUGAAAAAGAACtrue100000.00
IL_02359.3_Instance_2 IL_02359.3_IL_4IOA_009_G492_C519GAACGAGUGAAAGAGAAC
IL_02359.3_Sequence_2 IL_02359.3_IL_4IOA_009_G492_C519GAAC*GAGUGAAAGAGAACtrue98000.51
IL_02359.3_Instance_3 IL_02359.3_IL_3V2F_014_G481_C509GAACGAGUGAAAUAGAGC
IL_02359.3_Sequence_3 IL_02359.3_IL_3V2F_014_G481_C509GAAC*GAGUGAAAUAGAGCtrue94001.36
IL_02359.3_Instance_4 IL_02359.3_IL_4A1B_012_G375_C400GAACGGGCUAAAAGAC
IL_02359.3_Sequence_4 IL_02359.3_IL_4A1B_012_G375_C400GAAC*GGGCUAAAAGACtrue78005.25
IL_02359.3_Instance_5 IL_02359.3_IL_3U5H_015_G376_C403GAACGAGUGAAAAAGUAC
IL_02359.3_Sequence_5 IL_02359.3_IL_3U5H_015_G376_C403GAAC*GAGUGAAAAAGUACtrue88002.85

Conserved interactions between motif group positions in IL_02359.3:
1 14 tSS 
1 15 s35 
1 16 cWW 
2 6 cSW 
2 14 s53 
2 15 tHH 
3 4 s35 
3 6 tHS 
4 5 cWW 
4 6 s55 
5 6 s35 
6 7 s35 
7 8 s35 
7 14 bif 
8 9 s35 
8 12 tWH 
9 11 s33 
9 12 s55 
9 13 tSH 
10 11 s35 
11 13 s35 
12 13 s53 
12 14 s35 
15 2 6BPh
4 3 7BPh
9 12 6BPh
3 6 6BR
11 9 7BR
2 14 6BR
JAR3D SCFG/MRF model for IL_02359.3:
Character Definition | A,C,G,U,* // Define characters here
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [16] // Initial node G481 - C509 from junction 
ClusterNode  | Deletion Probability [0.000000000000000000000000000000000001211008282206275700000000] | Num Left Bases [3] | Num Right Bases [11] | Left Index [1] | Right Index [16] | Norm Constant [0.013279958585473] // Cluster node G481:A483 and A497:C509
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.478443015,0.036369758,0.158610950,0.021176618,0.000000000],[0.078468636,0.005641642,0.025667140,0.006056960,0.000000000],[0.072220953,0.005571037,0.012040718,0.003489910,0.000000000],[0.079476498,0.005921929,0.006958079,0.003886159,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A482 - A497 cSW 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.183582475,0.141922579,0.138423704,0.137696516,0.000000000],[0.124538656,0.072141506,0.001499413,0.132557529,0.000000000],[0.001499413,0.001499413,0.012018634,0.001499413,0.000000000],[0.011041404,0.001499413,0.037080518,0.001499413,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A483 - A497 tHS 
Interaction  | Interacting Bases [1,12] | Pair Probability [[0.010983645,0.013785681,0.023402995,0.013491197,0.000000000],[0.002396565,0.002396565,0.002396565,0.002396565,0.000000000],[0.215473637,0.222077550,0.287275572,0.194337201,0.000000000],[0.002396565,0.002396565,0.002396565,0.002396565,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G481 - G506 tSS 
Interaction  | Interacting Bases [2,13] | Pair Probability [[0.740587879,0.040267265,0.009958255,0.042726002,0.000000000],[0.018144708,0.000398962,0.034298065,0.028339038,0.000000000],[0.008777237,0.033104331,0.000977408,0.000398962,0.000000000],[0.008633645,0.032590321,0.000398962,0.000398962,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A482 - A507 tHH 
Interaction  | Interacting Bases [1,14] | Pair Probability [[0.009903804,0.020176037,0.011467133,0.187947036,0.000000000],[0.016710520,0.008166390,0.202428381,0.012884484,0.000000000],[0.011322786,0.256428223,0.002088092,0.026783299,0.000000000],[0.186861727,0.013524960,0.023103472,0.010203655,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G481 - C509 cWW 
Interaction  | Interacting Bases [6,10] | Pair Probability [[0.024041325,0.004721629,0.048139148,0.004721629,0.000000000],[0.100431499,0.037456340,0.073399645,0.004721629,0.000000000],[0.004721629,0.004721629,0.052877132,0.024792127,0.000000000],[0.466250249,0.004721629,0.054559658,0.089723102,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U499 - A503 tWH 
Interaction  | Interacting Bases [7,11] | Pair Probability [[0.043376023,0.048520582,0.000511343,0.002468182,0.000000000],[0.043801785,0.044536745,0.000511343,0.000511343,0.000000000],[0.333835603,0.002967386,0.014466878,0.243064083,0.000000000],[0.117854180,0.101327801,0.001123361,0.001123361,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G500 - A505 tSH 
Interaction  | Interacting Bases [5,12] | Pair Probability [[0.032556401,0.250925245,0.004078006,0.004078006,0.000000000],[0.015466579,0.013181622,0.004078006,0.004078006,0.000000000],[0.004078006,0.004078006,0.455419622,0.191670474,0.000000000],[0.004078006,0.004078006,0.004078006,0.004078006,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G498 - G506 bif 
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.785714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A501
Interaction  | Interacting Bases [9,9] | Pair Probability [[0.944444444,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.018518519,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.018518519,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.018518519,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A502
Insertion    | Location [10] | Length Distribution [0.204221895,0.787432499,0.007952872,0.000392734] | Letter Distribution [0.416666667,0.083333333,0.250000000,0.250000000,0.000000000]// Insertion after nucleotide 12, position 10 in cluster node
Insertion    | Location [13] | Length Distribution [0.204221895,0.787432499,0.007952872,0.000392734] | Letter Distribution [0.583333333,0.083333333,0.250000000,0.083333333,0.000000000]// Insertion after nucleotide 15, position 13 in cluster node
InitialNode  | 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 [4] | Right Index [5] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003776012,0.006476861,0.004388619,0.072426074,0.000000000],[0.054740466,0.022575992,0.614148123,0.036695147,0.000000000],[0.004444567,0.078459581,0.000809327,0.008954716,0.000000000],[0.072846731,0.004993921,0.010380987,0.003882877,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // Basepair C484 - G496 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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_02359.3:
> IL_02359.3 IL_2QBG_016 G  481 C  509
GAAC*GAGUGAAAAAGAAC
> IL_02359.3 IL_4IOA_009 G  492 C  519
GAAC*GAGUGAAAGAGAAC
> IL_02359.3 IL_3V2F_014 G  481 C  509
GAAC*GAGUGAAAUAGAGC
> IL_02359.3 IL_4A1B_012 G  375 C  400
GAAC*GGGCUAAAAGAC
> IL_02359.3 IL_3U5H_015 G  376 C  403
GAAC*GAGUGAAAAAGUAC