Alignment of IL_90057.1 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
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
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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
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_90057.1_Instance_1 IL_90057.1_IL_1NBS_003_C184_G226CACAGUGACGAAGUAGUGGAACGCG
IL_90057.1_Sequence_1 IL_90057.1_IL_1NBS_003_C184_G226CACAGUGACGAAGU*AGUGGAACGCGtrue100000.00
IL_90057.1_Instance_2 IL_90057.1_IL_1NBS_010_C184_G226CACAGUGACGAAGUAGUGGAACGCG
IL_90057.1_Sequence_2 IL_90057.1_IL_1NBS_010_C184_G226CACAGUGACGAAGU*AGUGGAACGCGtrue100000.00

Conserved interactions between motif group positions in IL_90057.1:
1 19 tSS 
1 23 cWW 
2 3 s35 
2 18 tHH 
3 4 s35 
4 5 s35 
4 8 tWH 
4 16 cSS 
4 20 tWW 
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 17 tWS 
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
1 9 7BPh
17 20 6BPh
19 1 6BR
10 7 6BR
9 8 7BR
21 20 7BR
JAR3D SCFG/MRF model for IL_90057.1:
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 [23] // Initial node C184 - G226 from junction 
ClusterNode  | Deletion Probability [0.000000000000000000000000000000000000000000000000000011624274] | Num Left Bases [12] | Num Right Bases [9] | Left Index [1] | Right Index [23] | Norm Constant [0.000050680706613] // Cluster node C184:G196 and G217:G226
Interaction  | Interacting Bases [7,13] | Pair Probability [[0.004749905,0.004749905,0.036692280,0.019008418,0.000000000],[0.004749905,0.044695720,0.004749905,0.004749905,0.000000000],[0.048133976,0.221179392,0.494598316,0.014613106,0.000000000],[0.027827322,0.025102721,0.004749905,0.039649321,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G190 - G217 cHW 
Interaction  | Interacting Bases [4,14] | Pair Probability [[0.181988495,0.181795261,0.173934281,0.209629097,0.000000000],[0.023908124,0.022702883,0.001969550,0.024591260,0.000000000],[0.024882546,0.023911658,0.021881535,0.024573721,0.000000000],[0.025123882,0.011025252,0.022013973,0.026068482,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A187 - U218 cSS 
Interaction  | Interacting Bases [8,15] | Pair Probability [[0.008947363,0.079325473,0.616028953,0.005161128,0.000000000],[0.075466431,0.003967145,0.162538428,0.003586090,0.000000000],[0.000852030,0.003849229,0.005964211,0.004747888,0.000000000],[0.004064644,0.003498027,0.019386766,0.002616194,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A191 - G219 tWS 
Interaction  | Interacting Bases [2,16] | Pair Probability [[0.020789531,0.016955835,0.436057743,0.349753317,0.000000000],[0.017600079,0.004164499,0.017933588,0.044394026,0.000000000],[0.017216889,0.021322694,0.004164499,0.004164499,0.000000000],[0.017579165,0.019574638,0.004164499,0.004164499,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A185 - G220 tHH 
Interaction  | Interacting Bases [1,17] | Pair Probability [[0.024509804,0.024509804,0.024509804,0.024509804,0.000000000],[0.191176471,0.171568627,0.171568627,0.171568627,0.000000000],[0.024509804,0.024509804,0.024509804,0.024509804,0.000000000],[0.024509804,0.024509804,0.024509804,0.024509804,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C184 - A221 tSS 
Interaction  | Interacting Bases [4,18] | Pair Probability [[0.742873018,0.067910692,0.007232652,0.034263267,0.000000000],[0.009713775,0.004002376,0.003143155,0.003947390,0.000000000],[0.001033236,0.003141446,0.097606567,0.005654000,0.000000000],[0.004895843,0.003947466,0.005659243,0.004975874,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A187 - A222 tWW 
Interaction  | Interacting Bases [5,18] | Pair Probability [[0.008947363,0.075466431,0.000852030,0.004064644,0.000000000],[0.079325473,0.003967145,0.003849229,0.003498027,0.000000000],[0.616028953,0.162538428,0.005964211,0.019386766,0.000000000],[0.005161128,0.003586090,0.004747888,0.002616194,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G188 - A222 tSW 
Interaction  | Interacting Bases [10,19] | Pair Probability [[0.000194944,0.000974721,0.002275854,0.000956556,0.000000000],[0.000194944,0.081105411,0.000194944,0.000194944,0.000000000],[0.112944347,0.701912479,0.063543053,0.005338350,0.000000000],[0.001071393,0.012289112,0.000194944,0.016614002,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G193 - C223 cHW 
Interaction  | Interacting Bases [9,20] | Pair Probability [[0.000797307,0.000797307,0.065990589,0.004381919,0.000000000],[0.003986537,0.331715203,0.418261570,0.050261569,0.000000000],[0.009308076,0.000797307,0.037126635,0.000797307,0.000000000],[0.003912246,0.000797307,0.003119066,0.067950053,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C192 - G224 cWH 
Interaction  | Interacting Bases [1,21] | Pair Probability [[0.003887072,0.006667356,0.004517696,0.074556253,0.000000000],[0.056350480,0.023239991,0.602799539,0.037774416,0.000000000],[0.004575289,0.080767216,0.000833131,0.009218090,0.000000000],[0.074989282,0.005140801,0.010686310,0.003997079,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C184 - G226 cWW 
Interaction  | Interacting Bases [4,8] | Pair Probability [[0.519623131,0.005000153,0.428770720,0.005000153,0.000000000],[0.005639356,0.002624082,0.004088846,0.000714308,0.000000000],[0.000714308,0.000714308,0.008848111,0.006373548,0.000000000],[0.003405949,0.000714308,0.004228743,0.003539977,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A187 - A191 tWH 
Interaction  | Interacting Bases [8,9] | Pair Probability [[0.107358724,0.143107315,0.006419081,0.005362531,0.000000000],[0.110490754,0.103294657,0.001234995,0.106950551,0.000000000],[0.006103550,0.006664607,0.014614084,0.106469853,0.000000000],[0.061780476,0.116710780,0.001234995,0.102203046,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A191 - C192 cSH 
Interaction  | Interacting Bases [7,11] | Pair Probability [[0.072106438,0.068212864,0.069372989,0.069940665,0.000000000],[0.074749653,0.068873836,0.070120860,0.017346033,0.000000000],[0.098375108,0.008401879,0.032027853,0.066558883,0.000000000],[0.072098922,0.070130398,0.070288073,0.071395548,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G190 - A195 cSS 
Interaction  | Interacting Bases [6,12] | Pair Probability [[0.008423477,0.009919438,0.008066461,0.009502076,0.000000000],[0.014035600,0.014368927,0.013928497,0.014300052,0.000000000],[0.012447882,0.010476921,0.010369283,0.008576553,0.000000000],[0.250441890,0.022833380,0.320949650,0.271359911,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U189 - G196 cWS 
Interaction  | Interacting Bases [14,18] | Pair Probability [[0.023610727,0.004951724,0.024289290,0.004951724,0.000000000],[0.049185322,0.041111237,0.032868771,0.004951724,0.000000000],[0.004951724,0.004951724,0.057950718,0.023098344,0.000000000],[0.603906771,0.004951724,0.061087140,0.053181337,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U218 - A222 tWH 
Interaction  | Interacting Bases [18,19] | Pair Probability [[0.107358724,0.143107315,0.006419081,0.005362531,0.000000000],[0.110490754,0.103294657,0.001234995,0.106950551,0.000000000],[0.006103550,0.006664607,0.014614084,0.106469853,0.000000000],[0.061780476,0.116710780,0.001234995,0.102203046,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A222 - C223 cSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.625000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion C186
Insertion    | Location [10] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 10, position 10 in cluster node
Insertion    | Location [20] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 22, position 20 in cluster node
InitialNode  | 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 [13] | Right Index [14] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009116058,0.020135905,0.009819016,0.207298319,0.000000000],[0.024500257,0.009533097,0.193859401,0.010377090,0.000000000],[0.009835776,0.192739951,0.002153778,0.023649137,0.000000000],[0.234985657,0.010304218,0.027858593,0.013833748,0.000000000],[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_90057.1:
> IL_90057.1 IL_1NBS_003 C  184 G  226
CACAGUGACGAAGU*AGUGGAACGCG
> IL_90057.1 IL_1NBS_010 C  184 G  226
CACAGUGACGAAGU*AGUGGAACGCG