Alignment of HL_85461.1 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
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4
2

2
5
3
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6
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3
7
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8
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4
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10
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5
11
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6
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14
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7
15
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16
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8
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18
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9
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10
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11
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12
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14
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3
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30
2

15
31
1
I


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Cutoff
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Alignment
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HL_85461.1_Instance_1 HL_85461.1,HL_8CRE_206,G701_C720GGUAGCCAUUUAUGGCGAAC
HL_85461.1_Sequence_1 HL_85461.18CRE_G701_C720GGUAGCCAUUUAUGGCGAACtrue100000.00

Conserved interactions between motif group positions in HL_85461.1:
1 2 s33 
1 15 cWW 
2 15 cHW 
3 5 perp 
4 5 s35 
4 13 s33 
4 14 s55 
5 6 s35 
6 7 perp 
6 8 perp 
7 12 perp 
10 11 s35 
11 12 s33 
13 5 7BR
4 13 6BR
JAR3D SCFG/MRF model for HL_85461.1:
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 [15] // Initial node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [1] | Right Index [15] | Norm Constant [0.250147856423620] // Cluster node 8CRE|1|CM|G|701:8CRE|1|CM|G|702 and 8CRE|1|CM|C|720:8CRE|1|CM|C|720
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.009830065,0.020472507,0.011193821,0.203314028,0.000000000],[0.017266777,0.009639366,0.205036802,0.013415526,0.000000000],[0.011069507,0.220897605,0.002109966,0.027030175,0.000000000],[0.200711998,0.013924020,0.023693165,0.010394672,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|G|701 - 8CRE|1|CM|C|720 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.061881188,0.061881188,0.061881188,0.061881188,0.000000000],[0.061881188,0.061881188,0.061881188,0.061881188,0.000000000],[0.061881188,0.071782178,0.061881188,0.061881188,0.000000000],[0.061881188,0.061881188,0.061881188,0.061881188,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|G|702 - 8CRE|1|CM|C|720 cHW 
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [14] // New Initial node after Cluster
HairpinNode  | Num Bases [12] | Left Index [3] | Right Index [14] | Norm Constant [0.999999999999998] // Hairpin node U703:A719
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U703
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.785714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[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 A704
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G705
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C706
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C707
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A708
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U709
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U710
Interaction  | Interacting Bases [9,9] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G714
Interaction  | Interacting Bases [10,10] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G715
Interaction  | Interacting Bases [11,11] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.785714286,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[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 C716
Interaction  | Interacting Bases [12,12] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A719
Insertion    | Location [8] | Length Distribution [0.000000000,0.000000000,0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.300000000,0.100000000,0.100000000,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 10, position 8
Insertion    | Location [11] | Length Distribution [0.000000000,0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000]// Insertion in Hairpin after nucleotide 13, position 11
Sequences of instances from HL_85461.1:
> HL_85461.1  8CRE G  701 C  720
GGUAGCCAUUUAUGGCGAAC