Alignment of HL_32346.4 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
2
I

6
2

3
7
1
I


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HL_32346.4_Instance_1 HL_32346.4,HL_9DFE_050,C2205_G2219CGGAUG
HL_32346.4_Sequence_1 HL_32346.49DFE_C_2205_G_2219CGGAUGtrue58004.03
HL_32346.4_Instance_2 HL_32346.4,HL_9C2K_003,C20_G24CAAUG
HL_32346.4_Sequence_2 HL_32346.49C2K_C20_G24CAAUGtrue83001.60
HL_32346.4_Instance_3 HL_32346.4,HL_8P9A_116,C132_G136CUUCG
HL_32346.4_Sequence_3 HL_32346.48P9A_C132_G136CUUCGtrue86001.32
HL_32346.4_Instance_4 HL_32346.4,HL_6U8D_003,C232_G235CGUG
HL_32346.4_Sequence_4 HL_32346.46U8D_C232_G235CGUGtrue100000.00
HL_32346.4_Instance_5 HL_32346.4,HL_6M0X_002,U56_A59UUCA
HL_32346.4_Sequence_5 HL_32346.46M0X_U56_A59UUCAtrue90000.97
HL_32346.4_Instance_6 HL_32346.4,HL_8VM9_005,C34_G38CAUUG
HL_32346.4_Sequence_6 HL_32346.48VM9_C34_G38CAUUGtrue91000.81
HL_32346.4_Instance_7 HL_32346.4,HL_2UWM_002,G22_C25GGUC
HL_32346.4_Sequence_7 HL_32346.42UWM_G22_C25GGUCtrue98000.22
HL_32346.4_Instance_8 HL_32346.4,HL_5CCB_002,U33_A37UUUUA
HL_32346.4_Sequence_8 HL_32346.45CCB_U33_A37UUUUAtrue96000.40
HL_32346.4_Instance_9 HL_32346.4,HL_5J7L_176,C1728_G1731CUCG
HL_32346.4_Sequence_9 HL_32346.45J7L_C_1728_G_1731CUCGtrue92000.79

Conserved interactions between motif group positions in HL_32346.4:
1 2 s35 
1 3 cWW 
2 3 s55
JAR3D SCFG/MRF model for HL_32346.4:
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 [3] // Initial node
BasepairNode | Deletion Probability [0.0000000035612230] | Pair Probability [[0.008840191,0.016424971,0.010052883,0.185773005,0.000000000],[0.019011281,0.009096257,0.247488234,0.012281345,0.000000000],[0.010120914,0.198023599,0.001946038,0.022215152,0.000000000],[0.207146669,0.011880113,0.030223346,0.009476001,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.004882663,0.879489762,0.114742592,0.000854466,0.000030517] | Left Letter Distribution [0.208333333,0.041666667,0.375000000,0.375000000,0.000000000] | Right Length Distribution [0.443574291,0.553091254,0.003181498,0.000152957] | Right Letter Distribution [0.071428571,0.214285714,0.071428571,0.642857143,0.000000000] | Left Index [1] | Right Index [3] // Basepair C2205 - G2219 cWW 
HairpinNode  | Num Bases [1] | Left Index [2] | Right Index [2] | Norm Constant [1.000000000000000] // Hairpin node A2208:A2208
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.227272727,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.227272727,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2208
Sequences of instances from HL_32346.4:
> HL_32346.4  9DFE C 2205 G 2219
CGGAUG
> HL_32346.4  9C2K C   20 G   24
CAAUG
> HL_32346.4  8P9A C  132 G  136
CUUCG
> HL_32346.4  6U8D C  232 G  235
CGUG
> HL_32346.4  6M0X U   56 A   59
UUCA
> HL_32346.4  8VM9 C   34 G   38
CAUUG
> HL_32346.4  2UWM G   22 C   25
GGUC
> HL_32346.4  5CCB U   33 A   37
UUUUA
> HL_32346.4  5J7L C 1728 G 1731
CUCG