Alignment of HL_86769.2 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
5

3
7
5
I

8
6

4
9
6
I

10
6

5
11
5
I

12
5

6
13
2
I

14
2

7
15
1
I


In
acceptance
region


Cutoff
score

Full
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distance

Interior
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Alignment
score
deficit
HL_86769.2_Instance_1 HL_86769.2_HL_4P5J_004_A69_U76AGGGUCAU
HL_86769.2_Sequence_1 HL_86769.2_HL_4P5J_004_A69_U76AGGGUCAUtrue100000.00
HL_86769.2_Instance_2 HL_86769.2_HL_6MJ0_010_A89_U96AGGGUCAU
HL_86769.2_Sequence_2 HL_86769.2_HL_6MJ0_010_A89_U96AGGGUCAUtrue100000.00
HL_86769.2_Instance_3 HL_86769.2_HL_1ET4_001_C219_G226CACCUCAG
HL_86769.2_Sequence_3 HL_86769.2_HL_1ET4_001_C219_G226CACCUCAGtrue99000.14
HL_86769.2_Instance_4 HL_86769.2_HL_4WF9_001_G67_U74GACGAUAU
HL_86769.2_Sequence_4 HL_86769.2_HL_4WF9_001_G67_U74GACGAUAUtrue88001.34

Conserved interactions between motif group positions in HL_86769.2:
1 2 s35 
1 7 cWW 
2 3 s35 
2 7 s55 
3 4 s35 
3 6 cSS 
4 5 cSH 
5 6 s55 
JAR3D SCFG/MRF model for HL_86769.2:
Character Definition | A,C,G,U,* // Define characters here
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Initial node A69 - U76 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.010774303,0.087781157,0.011060585,0.188806380,0.000000000],[0.016926973,0.010215360,0.165003366,0.011993158,0.000000000],[0.011006102,0.156433179,0.002308841,0.121014314,0.000000000],[0.154469200,0.012523924,0.021379402,0.018303756,0.000000000],[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 A69 - U76 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.083333333,0.416666667,0.083333333,0.000000000] | Position [1] | Left Index [2] | Right Index [6] // Fixed node on left
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
BasepairNode | Deletion Probability [0.0000001215781528] | Pair Probability [[0.073566642,0.073006261,0.070917251,0.073552522,0.000000000],[0.098049710,0.074615088,0.003437300,0.066716418,0.000000000],[0.098025574,0.003379657,0.007155805,0.078088272,0.000000000],[0.072563539,0.069769429,0.068875151,0.068281382,0.000000000],[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 [0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.083333333,0.583333333,0.083333333,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair G71 - A75 cSS 
HairpinNode  | Num Bases [2] | Left Index [4] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node G72:U73
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.044818056,0.046685522,0.006141431,0.110298723,0.000000000],[0.036275831,0.103785704,0.001320968,0.129898382,0.000000000],[0.125066668,0.001320968,0.051530555,0.130731861,0.000000000],[0.046579044,0.049284262,0.001320968,0.114941055,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G72 - U73 cSH 
Sequences of instances from HL_86769.2:
> HL_86769.2 HL_4P5J_004 A   69 U   76
AGGGUCAU
> HL_86769.2 HL_6MJ0_010 A   89 U   96
AGGGUCAU
> HL_86769.2 HL_1ET4_001 C  219 G  226
CACCUCAG
> HL_86769.2 HL_4WF9_001 G   67 U   74
GACGAUAU