Alignment of HL_40252.4 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
3

2
5
3
I

6
4

3
7
4
I

8
5

4
9
4
I

10
4

5
11
3
I

12
3

6
13
2
I

14
2

7
15
1
I


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Alignment
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HL_40252.4_Instance_1 HL_40252.4,HL_4JYZ_001,C912_G923CAAGCGGUAAG
HL_40252.4_Sequence_1 HL_40252.44JYZ_C912_G923CAAGCGGUAAGtrue100000.00
HL_40252.4_Instance_2 HL_40252.4,HL_8JOZ_001,C12_G23CGAGCGGUUGAAG
HL_40252.4_Sequence_2 HL_40252.48JOZ_C12_G23CGAGCGGUUGAAGtrue88001.95
HL_40252.4_Instance_3 HL_40252.4,HL_1F7U_001,C912_G923CCAAUGGUCACG
HL_40252.4_Sequence_3 HL_40252.41F7U_C912_G923CCAAUGGUCACGtrue81003.16
HL_40252.4_Instance_4 HL_40252.4,HL_9QRP_001,C12_G24CGAGUGGCUGAAG
HL_40252.4_Sequence_4 HL_40252.49QRP_C12_G24CGAGUGGCUGAAGtrue88001.95
HL_40252.4_Instance_5 HL_40252.4,HL_1QTQ_001,C912_G923CAAGCGGUAAG
HL_40252.4_Sequence_5 HL_40252.41QTQ_C912_G923CAAGCGGUAAGtrue100000.00

Conserved interactions between motif group positions in HL_40252.4:
1 2 s35 
1 7 cWW 
2 3 s35 
2 6 tSH 
2 7 s55 
3 4 s35 
3 5 cWS 
3 6 s55 
6 7 s35 
6 2 6BR
JAR3D SCFG/MRF model for HL_40252.4:
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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009264105,0.016612765,0.010650229,0.193109658,0.000000000],[0.019697072,0.009435223,0.250623774,0.013396622,0.000000000],[0.010769834,0.197270651,0.002030047,0.022795742,0.000000000],[0.195613131,0.012907388,0.026006356,0.009817401,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [1] | Right Index [7] // Basepair C912 - G923 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.156307084,0.066342815,0.001479679,0.008134770,0.000000000],[0.135110444,0.122478729,0.001479679,0.001479679,0.000000000],[0.153018183,0.001479679,0.010417714,0.072732466,0.000000000],[0.135126772,0.131452947,0.001479679,0.001479679,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [2] | Right Index [6] // Basepair A913 - A922 tSH 
BasepairNode | Deletion Probability [0.0000000000000001] | Pair Probability [[0.261237426,0.196491830,0.207649871,0.200714073,0.000000000],[0.015699653,0.012804891,0.002136184,0.012995242,0.000000000],[0.021228560,0.002136184,0.027208107,0.010161340,0.000000000],[0.007626271,0.008044757,0.006366306,0.007499307,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [0.000000000,0.000000000,0.000000000,0.003919647,0.393924547,0.203821656,0.394120529,0.004017638,0.000195982] | Right Letter Distribution [0.018518519,0.203703704,0.462962963,0.314814815,0.000000000] | Left Index [3] | Right Index [5] // Basepair A914 - A921 cWS 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G915:G915
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.642857143,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G915
Sequences of instances from HL_40252.4:
> HL_40252.4  4JYZ C  912 G  923
CAAGCGGUAAG
> HL_40252.4  8JOZ C   12 G   23
CGAGCGGUUGAAG
> HL_40252.4  1F7U C  912 G  923
CCAAUGGUCACG
> HL_40252.4  9QRP C   12 G   24
CGAGUGGCUGAAG
> HL_40252.4  1QTQ C  912 G  923
CAAGCGGUAAG