Alignment of IL_37015.1 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
3
I

14
4

7
15
4
I

16
5

8
17
5
I

18
6


19
5
I

20
5

9
21
4
I

22
4

10
23
3
I

24
2

11
25
2
I

26
2

12
27
2
I

28
2

13
29
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_37015.1_Instance_1 IL_37015.1,IL_5J7L_248,C97_G85CGUUAUAACGUAAG
IL_37015.1_Sequence_1 IL_37015.15J7L_C97_G85CGUUAUAAC*GUAAGtrue100000.00

Conserved interactions between motif group positions in IL_37015.1:
1 2 s35 
1 6 cSS 
1 13 cWW 
2 3 s35 
2 12 tSS 
2 13 s55 
4 5 s53 
5 11 s53 
5 12 tHH 
6 7 s35 
6 11 tHS 
6 12 s55 
6 13 tSS 
7 8 s35 
7 10 tHS 
8 9 cWW 
9 10 s35 
10 11 s35 
4 3 7BR
11 5 6BR
JAR3D SCFG/MRF model for IL_37015.1:
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 [13] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000000009533766986221214533025748902239021246] | Num Left Bases [6] | Num Right Bases [3] | Left Index [1] | Right Index [13] | Norm Constant [0.002631750717555] // Cluster node 5J7L|1|DA|C|97:5J7L|1|DA|A|103 and 5J7L|1|DA|A|83:5J7L|1|DA|G|85
Interaction  | Interacting Bases [6,7] | Pair Probability [[0.490885373,0.093275450,0.080135126,0.086621764,0.000000000],[0.056132539,0.038208747,0.000961969,0.086439173,0.000000000],[0.004809844,0.000961969,0.008356384,0.000961969,0.000000000],[0.029330166,0.000961969,0.020995590,0.000961969,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|103 - 5J7L|1|DA|A|83 tHS 
Interaction  | Interacting Bases [2,8] | Pair Probability [[0.021644907,0.017792930,0.020496934,0.013012017,0.000000000],[0.002614097,0.002614097,0.227437495,0.002614097,0.000000000],[0.271310703,0.002614097,0.254121285,0.153270951,0.000000000],[0.002614097,0.002614097,0.002614097,0.002614097,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|98 - 5J7L|1|DA|A|84 tSS 
Interaction  | Interacting Bases [5,8] | Pair Probability [[0.198669318,0.151650079,0.009050375,0.009233541,0.000000000],[0.166069526,0.001887683,0.160926363,0.017936931,0.000000000],[0.009411467,0.158869742,0.004711656,0.001887683,0.000000000],[0.012821277,0.093098993,0.001887683,0.001887683,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|101 - 5J7L|1|DA|A|84 tHH 
Interaction  | Interacting Bases [1,9] | 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 5J7L|1|DA|C|97 - 5J7L|1|DA|G|85 cWW 
Interaction  | Interacting Bases [6,9] | Pair Probability [[0.191916759,0.191457524,0.206852541,0.181565662,0.000000000],[0.001969516,0.001969516,0.020408579,0.001969516,0.000000000],[0.015442820,0.001969516,0.016084729,0.160515261,0.000000000],[0.001969516,0.001969516,0.001969516,0.001969516,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|103 - 5J7L|1|DA|G|85 tSS 
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.074958370,0.074522986,0.072592901,0.075257560,0.000000000],[0.093663030,0.076039825,0.003534873,0.067669678,0.000000000],[0.079480999,0.003480647,0.006829583,0.080842831,0.000000000],[0.075739436,0.073025027,0.072599406,0.069762848,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|97 - 5J7L|1|DA|A|103 cSS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|DA|U|99
Interaction  | Interacting Bases [4,4] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.785714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|DA|U|100
Insertion    | Location [5] | 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 5, position 5 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 [7] | Right Index [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.121583738,0.122053423,0.125556588,0.144924515,0.000000000],[0.111055049,0.114840499,0.001350235,0.124802948,0.000000000],[0.001350235,0.001350235,0.008345120,0.001350235,0.000000000],[0.006642085,0.001350235,0.112094623,0.001350235,0.000000000],[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 [7] | Right Index [10] // Basepair A104 - U82 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | 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]] | 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 [8] | Right Index [9] // Basepair C105 - G81 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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_37015.1:
> IL_37015.1  5J7L C   97 G   85
CGUUAUAAC*GUAAG