Alignment of HL_89346.1 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
4
I

6
7

3
7
8
I

8
9

4
9
9
I

10
10

5
11
10
I

12
10

6
13
10
I

14
10

7
15
10
I

16
10

8
17
10
I

18
10

9
19
10
I

20
10

10
21
10
I

22
10

11
23
10
I

24
10

12
25
9
I

26
9

13
27
8
I

28
7

14
29
7
I

30
7

15
31
6
I

32
5

16
33
2
I

34
2

17
35
1
I


In
acceptance
region

Cutoff
score
Full
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distance
Interior
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Alignment
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HL_89346.1_Instance_1 HL_89346.1,HL_8P9A_224,A1691_U1710AGAAGGGGGCAACUCCAUCU
HL_89346.1_Sequence_1 HL_89346.18P9A_A_1691_U_1710AGAAGGGGGCAACUCCAUCUtrue89002.83
HL_89346.1_Instance_2 HL_89346.1,HL_6ZDU_005,C1268_G1286CUUCCCGAAUUGUGGAUAG
HL_89346.1_Sequence_2 HL_89346.16ZDU_C_1268_G_1286CUUCCCGAAUUGUGGAUAGtrue100000.00

Conserved interactions between motif group positions in HL_89346.1:
1 2 s35 
1 17 cWW 
2 3 s35 
2 17 s55 
3 4 s35 
3 14 cWW 
3 15 cWW 
4 5 s35 
4 13 cWW 
4 14 s33 
5 6 s35 
6 7 s35 
6 11 perp 
7 8 s35 
7 11 s53 
7 12 perp 
8 9 perp 
9 10 s55 
11 12 perp 
12 13 s35 
13 14 s35 
14 15 s35 
15 16 s35 
16 17 s55
JAR3D SCFG/MRF model for HL_89346.1:
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 [17] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009409752,0.019555960,0.010438919,0.211256183,0.000000000],[0.018897284,0.009646494,0.211374635,0.012074740,0.000000000],[0.010490831,0.199877935,0.002065453,0.038339992,0.000000000],[0.198695040,0.012157589,0.024891932,0.010827262,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [17] // Basepair A1691 - U1710 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000] | Position [1] | Left Index [2] | Right Index [16] // Fixed node on left for 8P9A|1|sR|G|1692
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [3] | Right Index [16] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [3] | Right Index [16] // Fixed node on right for 8P9A|1|sR|C|1706
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [15] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [3] | Right Index [15] | Norm Constant [0.260747313858006] // Cluster node 8P9A|1|sR|A|1693:8P9A|1|sR|A|1693 and 8P9A|1|sR|A|1707:8P9A|1|sR|U|1708
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.107143513,0.015949783,0.009009170,0.178473784,0.000000000],[0.020039957,0.008937886,0.179074258,0.010040818,0.000000000],[0.009026741,0.176782451,0.001858409,0.020952313,0.000000000],[0.195644824,0.009431421,0.048449592,0.009185080,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|A|1693 - 8P9A|1|sR|A|1707 cWW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.012355323,0.152486873,0.011844359,0.123890391,0.000000000],[0.017284732,0.013982885,0.107364811,0.012739948,0.000000000],[0.011690860,0.108815631,0.003146657,0.053767974,0.000000000],[0.108519843,0.013702127,0.020221404,0.228186183,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|A|1693 - 8P9A|1|sR|U|1708 cWW 
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [13] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.008669617,0.114477187,0.009966792,0.180717594,0.000000000],[0.018433089,0.008829754,0.199781606,0.012536946,0.000000000],[0.010078722,0.184611572,0.001899777,0.021332914,0.000000000],[0.183060417,0.012079106,0.024337499,0.009187408,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [13] // Basepair A1694 - C1706 cWW 
HairpinNode  | Num Bases [8] | Left Index [5] | Right Index [12] | Norm Constant [1.000000000000000] // Hairpin node G1695:C1705
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1695
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1696
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1697
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1698
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1699
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C1703
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U1704
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C1705
Insertion    | Location [5] | Length Distribution [0.011890606,0.475624257,0.023781213,0.476218787,0.011890606,0.000594530] | Letter Distribution [0.416666667,0.250000000,0.083333333,0.250000000,0.000000000]// Insertion in Hairpin after nucleotide 9, position 5
Insertion    | Location [7] | Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 11, position 7
Sequences of instances from HL_89346.1:
> HL_89346.1  8P9A A 1691 U 1710
AGAAGGGGGCAACUCCAUCU
> HL_89346.1  6ZDU C 1268 G 1286
CUUCCCGAAUUGUGGAUAG