Alignment of HL_66853.7 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
4

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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HL_66853.7_Instance_1 HL_66853.7,HL_8UO6_005,C13_G22CAGUCGGUAG
HL_66853.7_Sequence_1 HL_66853.78UO6_C13_G22CAGUCGGUAGtrue94001.01
HL_66853.7_Instance_2 HL_66853.7,HL_8UO6_001,C13_G22CAGUCGGUAG
HL_66853.7_Sequence_2 HL_66853.78UO6_C13_G22CAGUCGGUAGtrue94001.01
HL_66853.7_Instance_3 HL_66853.7,HL_8S95_001,C13_G22CAGUCGGUAG
HL_66853.7_Sequence_3 HL_66853.78S95_C13_G22CAGUCGGUAGtrue94001.01
HL_66853.7_Instance_4 HL_66853.7,HL_4YCO_001,C13_G22CAGUCGGUAG
HL_66853.7_Sequence_4 HL_66853.74YCO_C13_G22CAGUCGGUAGtrue94001.01
HL_66853.7_Instance_5 HL_66853.7,HL_6CU1_003,C58_G66CAAUGGUAG
HL_66853.7_Sequence_5 HL_66853.76CU1_C58_G66CAAUGGUAGtrue92001.34
HL_66853.7_Instance_6 HL_66853.7,HL_4WJ4_001,C13_G22CAGUCGGUAG
HL_66853.7_Sequence_6 HL_66853.74WJ4_C13_G22CAGUCGGUAGtrue94001.01
HL_66853.7_Instance_7 HL_66853.7,HL_4MGN_002,C13_G21CAGUGGUAG
HL_66853.7_Sequence_7 HL_66853.74MGN_C13_G21CAGUGGUAGtrue100000.00
HL_66853.7_Instance_8 HL_66853.7,HL_4YCP_001,C13_G22CAAUUGGUAG
HL_66853.7_Sequence_8 HL_66853.74YCP_C13_G22CAAUUGGUAGtrue90001.69
HL_66853.7_Instance_9 HL_66853.7,HL_6UGG_004,C12_G22CAGUCGGUUAG
HL_66853.7_Sequence_9 HL_66853.76UGG_C12_G22CAGUCGGUUAGtrue76003.96
HL_66853.7_Instance_10 HL_66853.7,HL_7E8O_001,C13_G21CAGUGGUAG
HL_66853.7_Sequence_10 HL_66853.77E8O_C13_G21CAGUGGUAGtrue100000.00
HL_66853.7_Instance_11 HL_66853.7,HL_7UZ0_001,C13_G21CAGUGGUAG
HL_66853.7_Sequence_11 HL_66853.77UZ0_C13_G21CAGUGGUAGtrue100000.00

Conserved interactions between motif group positions in HL_66853.7:
1 7 cWW 
2 3 s35 
2 6 cWS 
2 7 s55 
4 5 cSH
JAR3D SCFG/MRF model for HL_66853.7:
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 [[0.008763342,0.015714778,0.010074541,0.182671298,0.000000000],[0.018632366,0.008925211,0.291130597,0.012672481,0.000000000],[0.010187681,0.186607373,0.001920315,0.021563540,0.000000000],[0.185039448,0.012209691,0.024600607,0.009286731,0.000000000],[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 C13 - G22 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.301170538,0.185870650,0.196425553,0.189864663,0.000000000],[0.014851023,0.012112735,0.002020714,0.012292797,0.000000000],[0.020081070,0.002020714,0.025737398,0.009612078,0.000000000],[0.007214040,0.007609905,0.006022181,0.007093939,0.000000000],[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 A14 - A21 cWS 
HairpinNode  | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node G15:U20
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.071283328,0.072634441,0.003993667,0.070984637,0.000000000],[0.053217661,0.080199949,0.000884266,0.071133447,0.000000000],[0.062280392,0.000884266,0.075971462,0.207110458,0.000000000],[0.072389355,0.071954791,0.000884266,0.084193615,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G19 - U20 cSH 
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.192307692,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.730769231,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G15
Insertion    | Location [1] | Length Distribution [0.000000000,0.001637633,0.363145074,0.632126261,0.002947739,0.000143293] | Letter Distribution [0.016129032,0.209677419,0.370967742,0.403225806,0.000000000]// Insertion in Hairpin after nucleotide 3, position 1
Insertion    | Location [2] | Length Distribution [0.904811823,0.094550986,0.000616637,0.000020555] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 4, position 2
Sequences of instances from HL_66853.7:
> HL_66853.7  8UO6 C   13 G   22
CAGUCGGUAG
> HL_66853.7  8UO6 C   13 G   22
CAGUCGGUAG
> HL_66853.7  8S95 C   13 G   22
CAGUCGGUAG
> HL_66853.7  4YCO C   13 G   22
CAGUCGGUAG
> HL_66853.7  6CU1 C   58 G   66
CAAUGGUAG
> HL_66853.7  4WJ4 C   13 G   22
CAGUCGGUAG
> HL_66853.7  4MGN C   13 G   21
CAGUGGUAG
> HL_66853.7  4YCP C   13 G   22
CAAUUGGUAG
> HL_66853.7  6UGG C   12 G   22
CAGUCGGUUAG
> HL_66853.7  7E8O C   13 G   21
CAGUGGUAG
> HL_66853.7  7UZ0 C   13 G   21
CAGUGGUAG