Alignment of IL_31504.1 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
4
I

14
4

7
15
4
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16
4

8
17
4
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18
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9
19
4
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20
4

10
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4
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22
4

11
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4
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4

12
25
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26
4

13
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5
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28
6


29
5
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30
4

14
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4
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32
4

15
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34
4

16
35
3
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36
3

17
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2
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38
2

18
39
1
I


In
acceptance
region

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score
Full
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distance
Interior
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Alignment
score
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IL_31504.1_Instance_1 IL_31504.1,IL_4V9F_014,G501_C491GAGGCGAAAUAGAGCGUACC
IL_31504.1_Sequence_1 IL_31504.14V9F_G501_C491GAGGCGAAAUAGAGC*GUACCtrue100000.00

Conserved interactions between motif group positions in IL_31504.1:
1 2 s35 
1 18 cWW 
2 3 s35 
2 17 cWW 
3 4 s35 
3 15 cWS 
3 16 tSH 
4 5 s35 
4 11 bif 
4 15 s55 
5 6 s35 
5 9 tWH 
6 9 s55 
6 10 tSH 
7 8 s35 
8 10 s35 
9 10 s53 
9 11 s35 
11 14 tSS 
11 15 s35 
12 14 s53 
12 15 tHH 
13 14 cWW 
16 17 s35 
17 18 s35 
6 9 6BPh
12 15 6BPh
16 3 6BR
8 6 7BR
3 15 6BR
JAR3D SCFG/MRF model for IL_31504.1:
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 [18] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009830065,0.020472507,0.011193821,0.203314028,0.000000000],[0.017266777,0.009639366,0.205036802,0.013415526,0.000000000],[0.011069507,0.220897605,0.002109966,0.027030175,0.000000000],[0.200711998,0.013924020,0.023693165,0.010394672,0.000000000],[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 [18] // Basepair G501 - C491 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.013958323,0.310268183,0.012182537,0.032389778,0.000000000],[0.012235413,0.011726251,0.024580362,0.012106270,0.000000000],[0.011896483,0.029143924,0.003003672,0.274859274,0.000000000],[0.025778993,0.013284394,0.012704593,0.199881551,0.000000000],[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 [2] | Right Index [17] // Basepair A502 - C490 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000000000000000000000145428340716098441685768] | Num Left Bases [11] | Num Right Bases [3] | Left Index [3] | Right Index [16] | Norm Constant [0.016791583515372] // Cluster node 4V9F|1|0|G|503:4V9F|1|0|C|515 and 4V9F|1|0|G|487:4V9F|1|0|A|489
Interaction  | Interacting Bases [9,12] | 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 4V9F|1|0|G|512 - 4V9F|1|0|G|487 tSS 
Interaction  | Interacting Bases [11,12] | 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 4V9F|1|0|C|515 - 4V9F|1|0|G|487 cWW 
Interaction  | Interacting Bases [1,13] | Pair Probability [[0.028639612,0.026641307,0.028329055,0.029620074,0.000000000],[0.025585386,0.024110226,0.021492269,0.024577439,0.000000000],[0.063264876,0.006020808,0.029037104,0.611981755,0.000000000],[0.021611744,0.020957404,0.016761760,0.021369182,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|G|503 - 4V9F|1|0|U|488 cWS 
Interaction  | Interacting Bases [10,13] | Pair Probability [[0.022419310,0.046882232,0.387198968,0.468236079,0.000000000],[0.003041982,0.000654764,0.003012792,0.053906011,0.000000000],[0.003144044,0.003062387,0.000654764,0.000654764,0.000000000],[0.002933041,0.002889332,0.000654764,0.000654764,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|A|513 - 4V9F|1|0|U|488 tHH 
Interaction  | Interacting Bases [1,14] | Pair Probability [[0.055450269,0.058701583,0.000665644,0.003137180,0.000000000],[0.055862225,0.058565654,0.000665644,0.000665644,0.000000000],[0.342722747,0.003328218,0.016270599,0.282486523,0.000000000],[0.061897309,0.058249476,0.000665644,0.000665644,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|G|503 - 4V9F|1|0|A|489 tSH 
Interaction  | Interacting Bases [3,7] | Pair Probability [[0.031021441,0.003624252,0.103678615,0.003624252,0.000000000],[0.372326222,0.026405017,0.003624252,0.003624252,0.000000000],[0.003624252,0.012653299,0.032591280,0.033407624,0.000000000],[0.036446633,0.003624252,0.016294714,0.313429642,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|C|505 - 4V9F|1|0|A|509 tWH 
Interaction  | Interacting Bases [4,8] | Pair Probability [[0.044130649,0.046718239,0.000529759,0.002496756,0.000000000],[0.044458508,0.046610059,0.000529759,0.000529759,0.000000000],[0.380732303,0.003708313,0.018128765,0.314747597,0.000000000],[0.049261589,0.046358426,0.000529759,0.000529759,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|G|506 - 4V9F|1|0|A|511 tSH 
Interaction  | Interacting Bases [2,9] | Pair Probability [[0.286859111,0.207254157,0.003021830,0.003021830,0.000000000],[0.012680128,0.008875223,0.003021830,0.003021830,0.000000000],[0.003021830,0.003021830,0.312083968,0.142029115,0.000000000],[0.003021830,0.003021830,0.003021830,0.003021830,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|G|504 - 4V9F|1|0|G|512 bif 
Interaction  | Interacting Bases [5,5] | 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 4V9F|1|0|A|507
Interaction  | Interacting Bases [6,6] | 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]] // Left strand conserved insertion 4V9F|1|0|A|508
Insertion    | Location [7] | 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 7 in cluster node
Insertion    | Location [10] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000]// Insertion after nucleotide 12, 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 [14] | Right Index [13] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [14] | Right Index [14] | 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_31504.1:
> IL_31504.1  4V9F G  501 C  491
GAGGCGAAAUAGAGC*GUACC