Alignment of HL_13529.1 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
5

2
5
5
I

6
6

3
7
6
I

8
6

4
9
5
I

10
5

5
11
4
I

12
3

6
13
2
I

14
2

7
15
1
I


In
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Cutoff
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Full
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Interior
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Alignment
score
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HL_13529.1_Instance_1 HL_13529.1,HL_5J7L_153,U641_G647UUAACUG
HL_13529.1_Sequence_1 HL_13529.15J7L_U641_G647UUAACUGtrue100000.00
HL_13529.1_Instance_2 HL_13529.1,HL_5U3G_003,G68_C76GAAAAAAGC
HL_13529.1_Sequence_2 HL_13529.15U3G_G68_C76GAAAAAAGCtrue99000.16

Conserved interactions between motif group positions in HL_13529.1:
1 2 s35 
1 7 cWW 
2 4 s53 
2 5 tHH 
3 4 s35 
4 5 s35 
5 7 s35 
2 5 6BPh
JAR3D SCFG/MRF model for HL_13529.1:
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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.010489920,0.017127883,0.012680838,0.119297674,0.000000000],[0.159817824,0.018747803,0.122690376,0.014659067,0.000000000],[0.012775575,0.132830577,0.002697714,0.020718591,0.000000000],[0.142468525,0.014233330,0.186841746,0.011922559,0.000000000],[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 [7] // Basepair U641 - G647 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000] | Position [2] | Left Index [2] | Right Index [6] // Fixed node on right for 5J7L|1|DA|U|646
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 [2] | Right Index [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000001040770180] | Pair Probability [[0.384591231,0.301091426,0.017968935,0.018332598,0.000000000],[0.047102901,0.000535410,0.045644127,0.005087517,0.000000000],[0.002669408,0.045060800,0.001336384,0.000535410,0.000000000],[0.003636545,0.125336486,0.000535410,0.000535410,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.481347774,0.024067389,0.481949458,0.012033694,0.000601685] | Left Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | 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 [5] // Basepair U642 - C645 tHH 
HairpinNode  | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A643:A644
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A643
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A644
Sequences of instances from HL_13529.1:
> HL_13529.1  5J7L U  641 G  647
UUAACUG
> HL_13529.1  5U3G G   68 C   76
GAAAAAAGC