Alignment of HL_53504.3 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
6

4
9
6
I

10
6

5
11
6
I

12
6

6
13
7
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
acceptance
region

Cutoff
score
Full
edit
distance
Interior
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distance
Alignment
score
deficit
HL_53504.3_Instance_1 HL_53504.3,HL_1NBS_004,C96_G107CGAAGUCAUAAG
HL_53504.3_Sequence_1 HL_53504.31NBS_C96_G107CGAAGUCAUAAGtrue95000.65
HL_53504.3_Instance_2 HL_53504.3,HL_2A64_005,G288_C297GGAAAUGAAC
HL_53504.3_Sequence_2 HL_53504.32A64_G288_C297GGAAAUGAACtrue100000.00

Conserved interactions between motif group positions in HL_53504.3:
1 2 s35 
1 10 cWW 
2 9 tSH 
3 4 s33 
3 8 s33 
3 9 s55 
4 6 tSW 
4 8 tHW 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
9 10 s35 
9 2 6BR
JAR3D SCFG/MRF model for HL_53504.3:
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 [0.0000229437914523] | Pair Probability [[0.009635135,0.018686586,0.011023774,0.200055053,0.000000000],[0.018686946,0.009628796,0.215804967,0.013537321,0.000000000],[0.011023788,0.215804297,0.002089517,0.025115689,0.000000000],[0.200055346,0.013537264,0.025116064,0.010199456,0.000000000],[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 [10] // Basepair C96 - G107 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.112745781,0.119356604,0.001353438,0.006378757,0.000000000],[0.113583401,0.119080223,0.001353438,0.001353438,0.000000000],[0.154951637,0.001353438,0.006616528,0.114874695,0.000000000],[0.125854401,0.118437346,0.001353438,0.001353438,0.000000000],[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 [2] | Right Index [9] // Basepair G97 - A106 tSH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left for 1NBS|1|B|A|98
InitialNode  | Left Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | 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
ClusterNode  | Deletion Probability [0.0000000000396545] | Num Left Bases [3] | Num Right Bases [1] | Left Index [4] | Right Index [8] | Norm Constant [0.282976330497376] // Cluster node 1NBS|1|B|G|100:1NBS|1|B|A|103 and 1NBS|1|B|A|105:1NBS|1|B|A|105
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.338510258,0.028135304,0.003287063,0.014853320,0.000000000],[0.003287063,0.013949136,0.008142503,0.003287063,0.000000000],[0.388908532,0.003287063,0.120823975,0.015754893,0.000000000],[0.003287063,0.003287063,0.035183695,0.016016004,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|G|100 - 1NBS|1|B|A|105 tHW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.149957916,0.149239472,0.001863865,0.107943053,0.000000000],[0.174416518,0.008218366,0.001863865,0.007451707,0.000000000],[0.196190420,0.001863865,0.001863865,0.006112240,0.000000000],[0.161298541,0.008100281,0.014665616,0.008950410,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1NBS|1|B|G|100 - 1NBS|1|B|A|103 tSW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 1NBS|1|B|C|102
Insertion    | Location [1] | Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 4, position 1 in cluster node
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 [7] | Right Index [7] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node U104:U104
Interaction  | Interacting Bases [1,1] | 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 U104
Sequences of instances from HL_53504.3:
> HL_53504.3  1NBS C   96 G  107
CGAAGUCAUAAG
> HL_53504.3  2A64 G  288 C  297
GGAAAUGAAC