Alignment of HL_87954.2 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
3
I

6
4

3
7
3
I

8
3

4
9
2
I

10
2

5
11
1
I


In
acceptance
region

Cutoff
score
Full
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distance
Interior
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Alignment
score
deficit
HL_87954.2_Instance_1 HL_87954.2,HL_5J7L_156,U779_G785UGAAAGG
HL_87954.2_Sequence_1 HL_87954.25J7L_U779_G785UGAAAGGtrue100000.00
HL_87954.2_Instance_2 HL_87954.2,HL_9DFE_022,U779_G785UGAAAAG
HL_87954.2_Sequence_2 HL_87954.29DFE_U779_G785UGAAAAGtrue88001.10
HL_87954.2_Instance_3 HL_87954.2,HL_4V9F_025,U872_G878UGAAAGG
HL_87954.2_Sequence_3 HL_87954.24V9F_U872_G878UGAAAGGtrue100000.00
HL_87954.2_Instance_4 HL_87954.2,HL_4WF9_024,A824_U830AGAAAUU
HL_87954.2_Sequence_4 HL_87954.24WF9_A824_U830AGAAAUUtrue86001.37
HL_87954.2_Instance_5 HL_87954.2,HL_5J7L_025,G1134_C1140GUCCGGC
HL_87954.2_Sequence_5 HL_87954.25J7L_G_1134_C_1140GUCCGGCtrue86001.34
HL_87954.2_Instance_6 HL_87954.2,HL_4V9F_005,C136_G142CUUCGCG
HL_87954.2_Sequence_6 HL_87954.24V9F_C136_G142CUUCGCGtrue79001.99
HL_87954.2_Instance_7 HL_87954.2,HL_4LFB_026,G1134_C1140GUUCGGC
HL_87954.2_Sequence_7 HL_87954.24LFB_G_1134_C_1140GUUCGGCtrue91000.83

Conserved interactions between motif group positions in HL_87954.2:
1 2 s35 
1 5 cWW 
2 3 s35 
2 4 tSW 
2 5 s55 
3 4 s53 
4 5 s55
JAR3D SCFG/MRF model for HL_87954.2:
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 [5] // Initial node
BasepairNode | Deletion Probability [0.0000001232089072] | Pair Probability [[0.009808523,0.016560690,0.011695108,0.134274660,0.000000000],[0.133404018,0.016646147,0.136846754,0.013457447,0.000000000],[0.011803419,0.145202608,0.002482305,0.023726420,0.000000000],[0.143461433,0.013063578,0.176277828,0.011289060,0.000000000],[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 [0.007039775,0.985568462,0.007039775,0.000351989] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [1] | Right Index [5] // Basepair U779 - G785 cWW 
BasepairNode | Deletion Probability [0.0000001232089072] | Pair Probability [[0.101015239,0.099760836,0.002736383,0.081505025,0.000000000],[0.115497961,0.012357068,0.002736383,0.015914571,0.000000000],[0.161809078,0.002736383,0.002736383,0.011514963,0.000000000],[0.104682558,0.012646784,0.198780759,0.073569624,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.007039775,0.985568462,0.007039775,0.000351989] | Left Letter Distribution [0.500000000,0.166666667,0.055555556,0.277777778,0.000000000] | 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 [4] // Basepair G780 - A783 tSW 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node A782:A782
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.388888889,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A782
Sequences of instances from HL_87954.2:
> HL_87954.2  5J7L U  779 G  785
UGAAAGG
> HL_87954.2  9DFE U  779 G  785
UGAAAAG
> HL_87954.2  4V9F U  872 G  878
UGAAAGG
> HL_87954.2  4WF9 A  824 U  830
AGAAAUU
> HL_87954.2  5J7L G 1134 C 1140
GUCCGGC
> HL_87954.2  4V9F C  136 G  142
CUUCGCG
> HL_87954.2  4LFB G 1134 C 1140
GUUCGGC