Alignment of HL_04171.7 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
5
I

8
8

4
9
8
I

10
8

5
11
9
I

12
10

6
13
9
I

14
8

7
15
7
I

16
6

8
17
3
I

18
3

9
19
2
I

20
2

10
21
1
I


In
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Alignment
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HL_04171.7_Instance_1 HL_04171.7,HL_4LX6_001,A30_U40AUGAUAUGGUU
HL_04171.7_Sequence_1 HL_04171.74LX6_A30_U40AUGAUAUGGUUtrue100000.00
HL_04171.7_Instance_2 HL_04171.7,HL_4XNR_001,A30_U40AUGAUAUGGUU
HL_04171.7_Sequence_2 HL_04171.74XNR_A30_U40AUGAUAUGGUUtrue100000.00
HL_04171.7_Instance_3 HL_04171.7,HL_1Y26_001,A30_U40AUGAUAUGGUU
HL_04171.7_Sequence_3 HL_04171.71Y26_A30_U40AUGAUAUGGUUtrue100000.00
HL_04171.7_Instance_4 HL_04171.7,HL_8KEB_001,A18_U28AUGAUAUGGUU
HL_04171.7_Sequence_4 HL_04171.78KEB_A18_U28AUGAUAUGGUUtrue100000.00
HL_04171.7_Instance_5 HL_04171.7,HL_3LA5_001,A30_U40AUGAUAUGGUU
HL_04171.7_Sequence_5 HL_04171.73LA5_A30_U40AUGAUAUGGUUtrue100000.00
HL_04171.7_Instance_6 HL_04171.7,HL_5SWD_004,A30_U40AUGAUAUGGUU
HL_04171.7_Sequence_6 HL_04171.75SWD_A30_U40AUGAUAUGGUUtrue100000.00
HL_04171.7_Instance_7 HL_04171.7,HL_3IVN_001,A21_U31AUGAUAUGGUU
HL_04171.7_Sequence_7 HL_04171.73IVN_A21_U31AUGAUAUGGUUtrue100000.00
HL_04171.7_Instance_8 HL_04171.7,HL_7KVT_001,A23_U33AUAAUAUGGUU
HL_04171.7_Sequence_8 HL_04171.77KVT_A23_U33AUAAUAUGGUUtrue95001.10
HL_04171.7_Instance_9 HL_04171.7,HL_4ATO_001,U15_A25UUACCGUAGUA
HL_04171.7_Sequence_9 HL_04171.74ATO_U15_A25UUACCGUAGUAtrue77004.64

Conserved interactions between motif group positions in HL_04171.7:
1 2 s35 
1 10 cWW 
2 3 s35 
2 9 cWW 
3 4 s35 
3 9 s55 
4 5 s35 
4 7 cSS 
5 7 cSS 
6 7 s55 
7 8 s35 
9 10 s35
JAR3D SCFG/MRF model for HL_04171.7:
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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008660927,0.020132690,0.009277219,0.263590965,0.000000000],[0.016863721,0.008991154,0.181989365,0.009764926,0.000000000],[0.009263175,0.183821034,0.001910391,0.046659830,0.000000000],[0.193482797,0.010251972,0.024683320,0.010656514,0.000000000],[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 [10] // Basepair A30 - U40 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.014436950,0.264791255,0.012889761,0.022512775,0.000000000],[0.015956256,0.017204790,0.019243046,0.014149980,0.000000000],[0.012620538,0.019602827,0.003979087,0.050833588,0.000000000],[0.019666410,0.015324417,0.016310825,0.480477495,0.000000000],[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 [9] // Basepair U31 - U39 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.227272727,0.045454545,0.681818182,0.045454545,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left for 4LX6|1|A|G|32
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.045454545,0.045454545,0.863636364,0.045454545,0.000000000] | Position [2] | Left Index [4] | Right Index [8] // Fixed node on right for 4LX6|1|A|G|37
InitialNode  | Left Length Distribution [1.000000000] | 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 [4] | Right Index [7] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [7] | Norm Constant [0.254903752478470] // Cluster node 4LX6|1|A|A|33:4LX6|1|A|U|34 and 4LX6|1|A|G|37:4LX6|1|A|G|37
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.073792229,0.076245171,0.177564044,0.075112783,0.000000000],[0.080050626,0.075296342,0.003143338,0.069039891,0.000000000],[0.071753000,0.003078342,0.006839640,0.071214051,0.000000000],[0.066559058,0.018358256,0.057161984,0.074791246,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LX6|1|A|A|33 - 4LX6|1|A|G|37 cSS 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.069829061,0.072864383,0.073175033,0.067175553,0.000000000],[0.079179257,0.070983057,0.003192756,0.062386608,0.000000000],[0.067697012,0.003241272,0.007248810,0.063576568,0.000000000],[0.069848860,0.064138152,0.160061465,0.065402151,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LX6|1|A|U|34 - 4LX6|1|A|G|37 cSS 
InitialNode  | 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 [0.005492996,0.988739357,0.005492996,0.000274650] | Right Letter Distribution [0.045454545,0.045454545,0.045454545,0.863636364,0.000000000] | Left Index [6] | Right Index [6] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node A35:A35
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.772727273,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.136363636,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.045454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A35
Sequences of instances from HL_04171.7:
> HL_04171.7  4LX6 A   30 U   40
AUGAUAUGGUU
> HL_04171.7  4XNR A   30 U   40
AUGAUAUGGUU
> HL_04171.7  1Y26 A   30 U   40
AUGAUAUGGUU
> HL_04171.7  8KEB A   18 U   28
AUGAUAUGGUU
> HL_04171.7  3LA5 A   30 U   40
AUGAUAUGGUU
> HL_04171.7  5SWD A   30 U   40
AUGAUAUGGUU
> HL_04171.7  3IVN A   21 U   31
AUGAUAUGGUU
> HL_04171.7  7KVT A   23 U   33
AUAAUAUGGUU
> HL_04171.7  4ATO U   15 A   25
UUACCGUAGUA