Alignment of IL_15052.4 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
3
I

8
4

4
9
4
I

10
5


11
4
I

12
4

5
13
3
I

14
2

6
15
1
I


In
acceptance
region

Cutoff
score
Full
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distance
Interior
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Alignment
score
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IL_15052.4_Instance_1 IL_15052.4,IL_3MXH_005,A61_U77AAACGU
IL_15052.4_Sequence_1 IL_15052.43MXH_A61_U77AAAC*GUtrue100000.00
IL_15052.4_Instance_2 IL_15052.4,IL_3IWN_005,A51_U72AAACGU
IL_15052.4_Sequence_2 IL_15052.43IWN_A51_U72AAAC*GUtrue100000.00
IL_15052.4_Instance_3 IL_15052.4,IL_5J7L_052,C1129_G1143CAGCGG
IL_15052.4_Sequence_3 IL_15052.45J7L_C_1129_G_1143CAGC*GGtrue97000.33
IL_15052.4_Instance_4 IL_15052.4,IL_4LFB_049,C1128_G1143CCAGCGG
IL_15052.4_Sequence_4 IL_15052.44LFB_C_1128_G_1143CCAGC*GGtrue69002.93
IL_15052.4_Instance_5 IL_15052.4,IL_5J7L_007,U70_A98UAACGA
IL_15052.4_Sequence_5 IL_15052.45J7L_U70_A98UAAC*GAtrue99000.05
IL_15052.4_Instance_6 IL_15052.4,IL_3RW6_001,U53_A8UAAUAA
IL_15052.4_Sequence_6 IL_15052.43RW6_U53_A8UAAU*AAtrue97000.24
IL_15052.4_Instance_7 IL_15052.4,IL_8OI5_136,G49_C29GUAGCC
IL_15052.4_Sequence_7 IL_15052.48OI5_G49_C29GUAG*CCtrue97000.26
IL_15052.4_Instance_8 IL_15052.4,IL_8P9A_366,G49_C29GUAGCC
IL_15052.4_Sequence_8 IL_15052.48P9A_G49_C29GUAG*CCtrue97000.26

Conserved interactions between motif group positions in IL_15052.4:
1 2 cSH 
1 6 cWW 
2 3 s35 
3 4 s35 
3 6 cWS 
4 5 cWW 
5 6 s35
JAR3D SCFG/MRF model for IL_15052.4:
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
ClusterNode  | Deletion Probability [0.0000000003110069] | Num Left Bases [3] | Num Right Bases [1] | Left Index [1] | Right Index [6] | Norm Constant [0.063001153906314] // Cluster node 3MXH|1|R|A|61:3MXH|1|R|A|63 and 3MXH|1|R|U|77:3MXH|1|R|U|77
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.008874834,0.018163668,0.009886445,0.207536427,0.000000000],[0.018165448,0.009130305,0.208151098,0.011446284,0.000000000],[0.009886458,0.208149880,0.001951325,0.029866332,0.000000000],[0.207539466,0.011446018,0.029877333,0.009928679,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3MXH|1|R|A|61 - 3MXH|1|R|U|77 cWW 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.170467240,0.166301040,0.136971357,0.205943433,0.000000000],[0.019820634,0.017474116,0.002085912,0.017096107,0.000000000],[0.072315416,0.002085912,0.148434418,0.009860109,0.000000000],[0.008027459,0.008438658,0.006786122,0.007892067,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3MXH|1|R|A|63 - 3MXH|1|R|U|77 cWS 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.119745586,0.094479268,0.004908919,0.020690521,0.000000000],[0.119288416,0.091354616,0.001054420,0.008300314,0.000000000],[0.008518046,0.001054420,0.087230987,0.130059640,0.000000000],[0.137288177,0.089788077,0.001054420,0.085184173,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3MXH|1|R|A|61 - 3MXH|1|R|A|62 cSH 
Insertion    | Location [1] | Length Distribution [0.869396619,0.129517605,0.001046999,0.000038778] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 1, position 1 in cluster node
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008994017,0.016952215,0.010258508,0.188051808,0.000000000],[0.018608027,0.009147540,0.240841489,0.012580721,0.000000000],[0.010304402,0.210675231,0.001968173,0.022892025,0.000000000],[0.199180633,0.012323190,0.027633566,0.009588455,0.000000000],[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 [4] | Right Index [5] // Basepair C64 - G76 cWW 
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_15052.4:
> IL_15052.4  3MXH A   61 U   77
AAAC*GU
> IL_15052.4  3IWN A   51 U   72
AAAC*GU
> IL_15052.4  5J7L C 1129 G 1143
CAGC*GG
> IL_15052.4  4LFB C 1128 G 1143
CCAGC*GG
> IL_15052.4  5J7L U   70 A   98
UAAC*GA
> IL_15052.4  3RW6 U   53 A    8
UAAU*AA
> IL_15052.4  8OI5 G   49 C   29
GUAG*CC
> IL_15052.4  8P9A G   49 C   29
GUAG*CC