Alignment of IL_24499.1 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
3
I

10
4

5
11
4
I

12
5

6
13
6
I

14
9

7
15
9
I

16
9

8
17
10
I

18
11


19
10
I

20
9

9
21
8
I

22
7

10
23
4
I

24
4

11
25
3
I

26
2

12
27
1
I


In
acceptance
region

Cutoff
score
Full
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distance
Interior
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distance
Alignment
score
deficit
IL_24499.1_Instance_1 IL_24499.1,IL_7ELQ_001,A6_U41AGAAGCGUAAUU
IL_24499.1_Sequence_1 IL_24499.17ELQ_A6_U41AGAAGCGU*AAUUtrue100000.00

Conserved interactions between motif group positions in IL_24499.1:
1 12 cWW 
2 3 s35 
3 4 s35 
4 5 s35 
4 12 cWS 
5 6 s35 
5 11 cWS 
6 7 s35 
7 8 cSH 
8 9 cWW 
9 10 s35 
10 11 s35 
11 12 s35
JAR3D SCFG/MRF model for IL_24499.1:
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 [12] // Initial node
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [1] | Right Index [12] | Norm Constant [0.248326495507515] // Cluster node 7ELQ|1|A|A|6:7ELQ|1|A|A|9 and 7ELQ|1|A|U|41:7ELQ|1|A|U|41
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.009374836,0.022228469,0.010012528,0.216037101,0.000000000],[0.017691617,0.009675113,0.196088410,0.010461402,0.000000000],[0.009993038,0.198630499,0.002061361,0.053740648,0.000000000],[0.197964449,0.011137350,0.023240462,0.011662716,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7ELQ|1|A|A|6 - 7ELQ|1|A|U|41 cWW 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.180519376,0.173124567,0.178058238,0.202026315,0.000000000],[0.017157494,0.013878938,0.001921253,0.014064519,0.000000000],[0.024883181,0.001921253,0.155093256,0.009451832,0.000000000],[0.007207709,0.007559536,0.006042475,0.007090057,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7ELQ|1|A|A|9 - 7ELQ|1|A|U|41 cWS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 7ELQ|1|A|G|7
Interaction  | Interacting Bases [3,3] | 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 7ELQ|1|A|A|8
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 [5] | Right Index [11] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000224390099112] | 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]] | 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 [5] | Right Index [11] // Basepair G10 - U40 cWS 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [6] | Right Index [10] // Fixed node on left for 7ELQ|1|A|C|11
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [2] | Left Index [7] | Right Index [10] // Fixed node on right for 7ELQ|1|A|A|39
InitialNode  | Left Length Distribution [1.000000000] | 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 [9] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [7] | Right Index [9] | Norm Constant [0.256882541264744] // Cluster node 7ELQ|1|A|G|12:7ELQ|1|A|U|13 and 7ELQ|1|A|A|38:7ELQ|1|A|A|38
Interaction  | Interacting Bases [2,3] | 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]] // Cluster Interaction 7ELQ|1|A|U|13 - 7ELQ|1|A|A|38 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.080081996,0.081599880,0.004486614,0.079746437,0.000000000],[0.059786442,0.090099217,0.000993413,0.079913615,0.000000000],[0.069967806,0.000993413,0.085348797,0.109242244,0.000000000],[0.081324543,0.080836340,0.000993413,0.094585831,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7ELQ|1|A|G|12 - 7ELQ|1|A|U|13 cSH 
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 [9] | Right Index [8] // New Initial node after Cluster
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_24499.1:
> IL_24499.1  7ELQ A    6 U   41
AGAAGCGU*AAUU