Alignment of IL_00555.1 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
3

3
7
3
I

8
3

4
9
4
I

10
5


11
4
I

12
3

5
13
2
I

14
2

6
15
1
I


In
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IL_00555.1_Instance_1 IL_00555.1,IL_8P9A_324,A2520_U2587AUGAAGCGGGU
IL_00555.1_Sequence_1 IL_00555.18P9A_A_2520_U_2587AUGAAGC*GGGUtrue100000.00
IL_00555.1_Instance_2 IL_00555.1,IL_8CRE_106,A2498_U2559AUGAAGCGGGU
IL_00555.1_Sequence_2 IL_00555.18CRE_A_2498_U_2559AUGAAGC*GGGUtrue100000.00

Conserved interactions between motif group positions in IL_00555.1:
1 2 s35 
1 6 cWW 
2 3 cWS 
3 6 s35 
4 5 cWW
JAR3D SCFG/MRF model for IL_00555.1:
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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000000005912491] | Pair Probability [[0.009282926,0.022010543,0.009914366,0.223723012,0.000000000],[0.017518170,0.009580259,0.194165974,0.010358839,0.000000000],[0.009895067,0.196683142,0.002041152,0.053213779,0.000000000],[0.196023621,0.011028161,0.023012614,0.011548375,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.083333333,0.083333333,0.750000000,0.083333333,0.000000000] | Left Index [1] | Right Index [6] // Basepair A2520 - U2587 cWW 
ClusterNode  | Deletion Probability [0.000000000000000076180842891157205953625402643352350634502873] | Num Left Bases [3] | Num Right Bases [1] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Cluster node 8P9A|1|AR|U|2521:8P9A|1|AR|C|2526 and 8P9A|1|AR|G|2584:8P9A|1|AR|G|2584
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|C|2526 - 8P9A|1|AR|G|2584 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.008335090,0.008456775,0.008103673,0.008758894,0.000000000],[0.015122597,0.014345643,0.003255280,0.015476731,0.000000000],[0.010786459,0.002334730,0.009842452,0.008380535,0.000000000],[0.253080851,0.210591316,0.193742704,0.229386269,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|U|2521 - 8P9A|1|AR|A|2523 cWS 
Insertion    | Location [1] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000]// Insertion after nucleotide 2, position 1 in cluster node
Insertion    | Location [2] | Length Distribution [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.416666667,0.083333333,0.416666667,0.083333333,0.000000000]// Insertion after nucleotide 3, position 2 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 [5] | Right Index [4] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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_00555.1:
> IL_00555.1  8P9A A 2520 U 2587
AUGAAGC*GGGU
> IL_00555.1  8CRE A 2498 U 2559
AUGAAGC*GGGU