Alignment of IL_43946.1 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
3
I

14
3

6
15
3
I

16
3

7
17
3
I

18
3

8
19
3
I

20
3

9
21
3
I

22
3

10
23
3
I

24
3

11
25
2
I

26
2

12
27
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_43946.1_Instance_1 IL_43946.1_IL_2VPL_001_G10_C40GGAGCGAGAAAC
IL_43946.1_Sequence_1 IL_43946.1_IL_2VPL_001_G10_C40GGAG*CGAGAAACtrue100000.00
IL_43946.1_Instance_2 IL_43946.1_IL_2HW8_001_G10_C29GGAGCGCGAAAC
IL_43946.1_Sequence_2 IL_43946.1_IL_2HW8_001_G10_C29GGAG*CGCGAAACtrue97000.51
IL_43946.1_Instance_3 IL_43946.1_IL_1U63_001_G10_C40GGAGCGAGAAAC
IL_43946.1_Sequence_3 IL_43946.1_IL_1U63_001_G10_C40GGAG*CGAGAAACtrue100000.00

Conserved interactions between motif group positions in IL_43946.1:
1 2 s35 
1 12 cWW 
2 11 tSH 
2 12 s55 
3 6 tSS 
3 11 s55 
4 5 cWW 
4 6 s55 
4 11 tSS 
5 6 s35 
5 11 cSS 
6 7 s35 
9 10 s35 
11 12 s35 
2 10 6BPh
12 11 7BPh
11 2 6BR
JAR3D SCFG/MRF model for IL_43946.1:
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 [12] // Initial node G10 - C40 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.003914340,0.055820081,0.004532224,0.074283445,0.000000000],[0.006604600,0.022593563,0.080006995,0.005092413,0.000000000],[0.004475173,0.606828618,0.000825289,0.010585725,0.000000000],[0.073854492,0.037418864,0.009131325,0.004032852,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair G10 - C40 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000000009765625000000002400000000000000000000] | Num Left Bases [3] | Num Right Bases [7] | Left Index [2] | Right Index [11] | Norm Constant [0.023942467794376] // Cluster node G11:G13 and C33:A39
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.010096111,0.020567805,0.011689796,0.191596493,0.000000000],[0.017034996,0.008324961,0.206359029,0.013134669,0.000000000],[0.011542646,0.241989936,0.002128637,0.027303363,0.000000000],[0.190490110,0.013787581,0.023552083,0.010401784,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G13 - C33 cWW 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.170737532,0.190302277,0.237397338,0.182598480,0.000000000],[0.002082711,0.002082711,0.002082711,0.002082711,0.000000000],[0.011429712,0.013192201,0.020338141,0.157342629,0.000000000],[0.002082711,0.002082711,0.002082711,0.002082711,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A12 - G34 tSS 
Interaction  | Interacting Bases [1,10] | Pair Probability [[0.043291794,0.050462128,0.000521611,0.002483845,0.000000000],[0.043676961,0.045779825,0.000521611,0.000521611,0.000000000],[0.394253847,0.003651276,0.017689667,0.303712878,0.000000000],[0.047056648,0.045333078,0.000521611,0.000521611,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G11 - A39 tSH 
Interaction  | Interacting Bases [3,10] | Pair Probability [[0.027174669,0.006091800,0.007184673,0.006169792,0.000000000],[0.006545922,0.001309184,0.001309184,0.001309184,0.000000000],[0.683718369,0.116457217,0.117707918,0.014548614,0.000000000],[0.006545922,0.001309184,0.001309184,0.001309184,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G13 - A39 tSS 
Interaction  | Interacting Bases [4,10] | Pair Probability [[0.142497337,0.029020812,0.028160651,0.028639375,0.000000000],[0.237947678,0.029183050,0.003573896,0.026829201,0.000000000],[0.151870031,0.030839869,0.028008649,0.031022245,0.000000000],[0.147267189,0.028710808,0.027554250,0.028874959,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C33 - A39 cSS 
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A35
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G36
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A37
Interaction  | Interacting Bases [9,9] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A38
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 [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_43946.1:
> IL_43946.1 IL_2VPL_001 G   10 C   40
GGAG*CGAGAAAC
> IL_43946.1 IL_2HW8_001 G   10 C   29
GGAG*CGCGAAAC
> IL_43946.1 IL_1U63_001 G   10 C   40
GGAG*CGAGAAAC