Alignment of HL_08602.1 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
2

2
5
2
I

6
2

3
7
2
I

8
2

4
9
2
I

10
2

5
11
3
I

12
4

6
13
5
I

14
6

7
15
6
I

16
7

8
17
7
I

18
7

9
19
6
I

20
6

10
21
3
I

22
2

11
23
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
HL_08602.1_Instance_1 HL_08602.1,HL_4WFL_002,C42_G54CAAUCCGCUCUAG
HL_08602.1_Sequence_1 HL_08602.14WFL_C42_G54CAAUCCGCUCUAGtrue100000.00

Conserved interactions between motif group positions in HL_08602.1:
1 2 s35 
1 5 cSS 
1 11 cWW 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
7 10 cSS 
9 10 s55 
11 6 2BR
6 11 2BR
JAR3D SCFG/MRF model for HL_08602.1:
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 [11] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000076270135889769347254524013854470196433658662] | Num Left Bases [5] | Num Right Bases [1] | Left Index [1] | Right Index [11] | Norm Constant [0.249358129285457] // Cluster node 4WFL|1|A|C|42:4WFL|1|A|C|47 and 4WFL|1|A|G|54:4WFL|1|A|G|54
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.004779407,0.008570624,0.027472582,0.099626418,0.000000000],[0.010161837,0.004867687,0.533557704,0.006911397,0.000000000],[0.005556221,0.101773100,0.005236567,0.011760459,0.000000000],[0.100917975,0.006658998,0.067084168,0.005064856,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WFL|1|A|C|42 - 4WFL|1|A|G|54 cWW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.078640160,0.080072651,0.077688369,0.078498279,0.000000000],[0.074652149,0.092134428,0.003369305,0.072302146,0.000000000],[0.077101580,0.003305185,0.007983630,0.076026938,0.000000000],[0.070376178,0.066021161,0.066765764,0.075062078,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WFL|1|A|C|42 - 4WFL|1|A|C|47 cSS 
Interaction  | Interacting Bases [2,2] | 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]] // Left strand conserved insertion 4WFL|1|A|A|43
Interaction  | Interacting Bases [3,3] | 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]] // Left strand conserved insertion 4WFL|1|A|A|44
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]] // Left strand conserved insertion 4WFL|1|A|C|46
Insertion    | Location [3] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 3, position 3 in cluster node
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 [6] | Right Index [10] // Initial node 4WFL|1|A|G|48 - 4WFL|1|A|A|53 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.071428571,0.785714286,0.071428571,0.000000000] | Position [1] | Left Index [6] | Right Index [10] // Fixed node on left for 4WFL|1|A|C|47
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000001156129129] | Pair Probability [[0.074958370,0.074522986,0.072592901,0.075257560,0.000000000],[0.093663030,0.076039825,0.003534873,0.067669678,0.000000000],[0.079480999,0.003480647,0.006829583,0.080842831,0.000000000],[0.075739436,0.073025027,0.072599406,0.069762848,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [0.045351474,0.907029478,0.045351474,0.002267574] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [7] | Right Index [10] // Basepair C49 - A53 cSS 
HairpinNode  | Num Bases [2] | Left Index [8] | Right Index [9] | Norm Constant [1.000000000000000] // Hairpin node U50:C51
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 U50
Interaction  | Interacting Bases [2,2] | 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 C51
Sequences of instances from HL_08602.1:
> HL_08602.1  4WFL C   42 G   54
CAAUCCGCUCUAG