Alignment of IL_84409.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_84409.1
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
2
I

8
2

4
9
2
I

10
2

5
11
2
I

12
2

6
13
2
I

14
2

7
15
2
I

16
2

8
17
2
I

18
2

9
19
2
I

20
2

10
21
2
I

22
2

11
23
2
I

24
2

12
25
3
I

26
4

13
27
4
I

28
5


29
4
I

30
4

14
31
3
I

32
2

15
33
2
I

34
2

16
35
2
I

36
2

17
37
2
I

38
2

18
39
2
I

40
2

19
41
2
I

42
2

20
43
2
I

44
2

21
45
2
I

46
2

22
47
2
I

48
2

23
49
1
I


In
acceptance
region

Cutoff
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Full
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Interior
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Alignment
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IL_84409.1_Instance_1 IL_84409.1,IL_1NBS_010,C184_G226CACAGUGACGAAGUAGUGGAACGCG
IL_84409.1_Sequence_1 IL_84409.11NBS_C184_G226CACAGUGACGAAGU*AGUGGAACGCGtrue100000.00

Conserved interactions between motif group positions in IL_84409.1:
1 19 tSS 
1 23 cWW 
2 3 s35 
2 18 tHH 
3 4 s35 
4 5 s35 
4 8 tWH 
4 16 cSS 
5 20 tSW 
6 7 s35 
6 12 cWS 
6 13 s55 
7 11 cSS 
7 12 s55 
7 15 cHW 
7 20 s33 
8 9 cSH 
8 19 s33 
8 20 s55 
9 21 s55 
9 22 cWH 
9 23 s35 
10 11 s35 
10 21 cHW 
11 12 s35 
11 21 s53 
12 13 s35 
13 14 cWW 
14 15 s35 
15 16 s35 
16 17 s35 
16 20 tWH 
17 20 s55 
18 19 s35 
20 21 cSH 
4 2 7BPh
5 8 6BPh
10 8 6BPh
17 20 6BPh
19 1 6BR
10 7 6BR
JAR3D SCFG/MRF model for IL_84409.1:
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 [23] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000000000000000000000000000000000000011361589] | Num Left Bases [12] | Num Right Bases [9] | Left Index [1] | Right Index [23] | Norm Constant [0.000021674562286] // Cluster node 1NBS|1|B|C|184:1NBS|1|B|G|196 and 1NBS|1|B|G|217:1NBS|1|B|G|226
Interaction  | Interacting Bases [7,13] | 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 1NBS|1|B|G|190 - 1NBS|1|B|G|217 cHW 
Interaction  | Interacting Bases [4,14] | Pair Probability [[0.182515075,0.189130397,0.188336532,0.209508482,0.000000000],[0.025620151,0.027220148,0.001139121,0.025015907,0.000000000],[0.026251560,0.001114163,0.003092545,0.025986527,0.000000000],[0.023668144,0.021956376,0.023814207,0.025630666,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|A|187 - 1NBS|1|B|U|218 cSS 
Interaction  | Interacting Bases [2,16] | Pair Probability [[0.019674940,0.022627159,0.420271327,0.346678609,0.000000000],[0.018725299,0.004103703,0.017645274,0.043903004,0.000000000],[0.033745492,0.017830048,0.004103703,0.004103703,0.000000000],[0.019705139,0.018675191,0.004103703,0.004103703,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|A|185 - 1NBS|1|B|G|220 tHH 
Interaction  | Interacting Bases [1,17] | Pair Probability [[0.061881188,0.061881188,0.061881188,0.061881188,0.000000000],[0.071782178,0.061881188,0.061881188,0.061881188,0.000000000],[0.061881188,0.061881188,0.061881188,0.061881188,0.000000000],[0.061881188,0.061881188,0.061881188,0.061881188,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|C|184 - 1NBS|1|B|A|221 tSS 
Interaction  | Interacting Bases [5,18] | Pair Probability [[0.071773872,0.071430006,0.000892096,0.004313658,0.000000000],[0.083480414,0.003933530,0.000892096,0.003566586,0.000000000],[0.634367958,0.006244670,0.006244670,0.020478373,0.000000000],[0.077201799,0.003877011,0.007019357,0.004283906,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|G|188 - 1NBS|1|B|A|222 tSW 
Interaction  | Interacting Bases [10,19] | Pair Probability [[0.024752475,0.024752475,0.024752475,0.024752475,0.000000000],[0.024752475,0.024752475,0.024752475,0.024752475,0.000000000],[0.173267327,0.183168317,0.173267327,0.173267327,0.000000000],[0.024752475,0.024752475,0.024752475,0.024752475,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|G|193 - 1NBS|1|B|C|223 cHW 
Interaction  | Interacting Bases [9,20] | Pair Probability [[0.061881188,0.061881188,0.061881188,0.061881188,0.000000000],[0.061881188,0.061881188,0.071782178,0.061881188,0.000000000],[0.061881188,0.061881188,0.061881188,0.061881188,0.000000000],[0.061881188,0.061881188,0.061881188,0.061881188,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|C|192 - 1NBS|1|B|G|224 cWH 
Interaction  | Interacting Bases [1,21] | 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 1NBS|1|B|C|184 - 1NBS|1|B|G|226 cWW 
Interaction  | Interacting Bases [4,8] | Pair Probability [[0.500586469,0.004906855,0.432872759,0.004906855,0.000000000],[0.005999965,0.002974708,0.000700979,0.000700979,0.000000000],[0.000700979,0.001736421,0.025766190,0.007503062,0.000000000],[0.003167529,0.000700979,0.003359793,0.003415476,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|A|187 - 1NBS|1|B|A|191 tWH 
Interaction  | Interacting Bases [8,9] | Pair Probability [[0.104166825,0.124612443,0.005621093,0.043860124,0.000000000],[0.100542670,0.099286043,0.001147115,0.009317734,0.000000000],[0.010004306,0.001147115,0.104180479,0.094225112,0.000000000],[0.104547355,0.103291070,0.001147115,0.092903402,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|A|191 - 1NBS|1|B|C|192 cSH 
Interaction  | Interacting Bases [7,11] | Pair Probability [[0.083071528,0.077827995,0.079676854,0.073574035,0.000000000],[0.086320773,0.084839186,0.003406498,0.011604013,0.000000000],[0.099703595,0.003481632,0.007719409,0.061927698,0.000000000],[0.084731846,0.078131797,0.078751916,0.085231224,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|G|190 - 1NBS|1|B|A|195 cSS 
Interaction  | Interacting Bases [6,12] | Pair Probability [[0.007621108,0.007878219,0.007225892,0.008042656,0.000000000],[0.011893482,0.011962372,0.002557227,0.012112360,0.000000000],[0.009982001,0.002557227,0.009162302,0.007119248,0.000000000],[0.212206128,0.210847785,0.265623667,0.213208328,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|U|189 - 1NBS|1|B|G|196 cWS 
Interaction  | Interacting Bases [14,18] | 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 1NBS|1|B|U|218 - 1NBS|1|B|A|222 tWH 
Interaction  | Interacting Bases [18,19] | Pair Probability [[0.104166825,0.124612443,0.005621093,0.043860124,0.000000000],[0.100542670,0.099286043,0.001147115,0.009317734,0.000000000],[0.010004306,0.001147115,0.104180479,0.094225112,0.000000000],[0.104547355,0.103291070,0.001147115,0.092903402,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|A|222 - 1NBS|1|B|C|223 cSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 1NBS|1|B|C|186
Interaction  | Interacting Bases [15,15] | 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]] // Right strand conserved insertion 1NBS|1|B|G|219
Insertion    | Location [10] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 10, position 10 in cluster node
Insertion    | Location [20] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 22, position 20 in cluster node
InitialNode  | 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 [13] | Right Index [14] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009123784,0.017718471,0.010008206,0.198264936,0.000000000],[0.022262210,0.009929018,0.198931998,0.011154256,0.000000000],[0.010027726,0.196386049,0.002064490,0.023275738,0.000000000],[0.216349992,0.010477281,0.053822220,0.010203624,0.000000000],[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 [13] | Right Index [14] // Basepair U197 - A216 cWW 
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_84409.1:
> IL_84409.1  1NBS C  184 G  226
CACAGUGACGAAGU*AGUGGAACGCG