Alignment of HL_41464.2 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
7
I

8
8

4
9
7
I

10
7

5
11
6
I

12
5

6
13
2
I

14
2

7
15
1
I


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Alignment
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HL_41464.2_Instance_1 HL_41464.2,HL_8P9A_127,G686_C694GUGUAAAAC
HL_41464.2_Sequence_1 HL_41464.28P9A_G686_C694GUGUAAAACtrue100000.00
HL_41464.2_Instance_2 HL_41464.2,HL_8CRE_014,G684_C692GUGUAAAAC
HL_41464.2_Sequence_2 HL_41464.28CRE_G684_C692GUGUAAAACtrue100000.00
HL_41464.2_Instance_3 HL_41464.2,HL_3IGI_010,C305_G314CUGUUCGCAG
HL_41464.2_Sequence_3 HL_41464.23IGI_C305_G314CUGUUCGCAGtrue53005.11
HL_41464.2_Instance_4 HL_41464.2,HL_6DB9_002,G36_C45GGUGAAUGAC
HL_41464.2_Sequence_4 HL_41464.26DB9_G36_C45GGUGAAUGACtrue55004.95

Conserved interactions between motif group positions in HL_41464.2:
1 2 s35 
1 7 cWW 
2 3 s35 
2 7 s55 
3 4 s35 
3 5 tSH 
5 6 s35 
6 7 s35
JAR3D SCFG/MRF model for HL_41464.2:
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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009498175,0.019104591,0.010841350,0.196828520,0.000000000],[0.017548139,0.009402467,0.210196267,0.013152764,0.000000000],[0.010780994,0.232320656,0.002049218,0.025441577,0.000000000],[0.195565178,0.013399649,0.023821386,0.010049069,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair G686 - C694 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.083333333,0.250000000,0.583333333,0.000000000] | Position [1] | Left Index [2] | Right Index [6] // Fixed node on left for 8P9A|1|AR|U|687
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [3] | Right Index [6] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [2] | Left Index [3] | Right Index [6] // Fixed node on right for 8P9A|1|AR|A|691
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.741082411,0.255227552,0.003536285,0.000153752] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [3] | Right Index [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000000001562551] | Pair Probability [[0.100525084,0.106419350,0.001206737,0.005687353,0.000000000],[0.101271913,0.106172926,0.001206737,0.001206737,0.000000000],[0.139904431,0.054528415,0.005899352,0.102423242,0.000000000],[0.112212840,0.105599732,0.001206737,0.054528415,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Left Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Right Length Distribution [0.006093845,0.490554540,0.252894576,0.247105424,0.003199269,0.000152346] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [3] | Right Index [5] // Basepair G688 - A692 tSH 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A690:A690
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.416666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A690
Sequences of instances from HL_41464.2:
> HL_41464.2  8P9A G  686 C  694
GUGUAAAAC
> HL_41464.2  8CRE G  684 C  692
GUGUAAAAC
> HL_41464.2  3IGI C  305 G  314
CUGUUCGCAG
> HL_41464.2  6DB9 G   36 C   45
GGUGAAUGAC