Alignment of HL_01609.3 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
4
I

8
4

4
9
4
I

10
4

5
11
3
I

12
3

6
13
2
I

14
2

7
15
1
I


In
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Full
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Alignment
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HL_01609.3_Instance_1 HL_01609.3,HL_5J7L_142,C305_G312CUGGAAAG
HL_01609.3_Sequence_1 HL_01609.35J7L_C305_G312CUGGAAAGtrue90001.27
HL_01609.3_Instance_2 HL_01609.3,HL_7A0S_010,C316_G323CUGGAAAG
HL_01609.3_Sequence_2 HL_01609.37A0S_C316_G323CUGGAAAGtrue90001.27
HL_01609.3_Instance_3 HL_01609.3,HL_5DH6_002,C27_G34CUGGGAUG
HL_01609.3_Sequence_3 HL_01609.35DH6_C27_G34CUGGGAUGtrue91001.08
HL_01609.3_Instance_4 HL_01609.3,HL_3F2X_001,G17_C25GUGAAAUUC
HL_01609.3_Sequence_4 HL_01609.33F2X_G17_C25GUGAAAUUCtrue93000.91
HL_01609.3_Instance_5 HL_01609.3,HL_6DN2_001,G17_C25GUGAAAUUC
HL_01609.3_Sequence_5 HL_01609.36DN2_G17_C25GUGAAAUUCtrue93000.91
HL_01609.3_Instance_6 HL_01609.3,HL_4V9F_010,U312_A319UUGGAAUA
HL_01609.3_Sequence_6 HL_01609.34V9F_U312_A319UUGGAAUAtrue100000.00
HL_01609.3_Instance_7 HL_01609.3,HL_9DFE_009,U305_G312UUGGGAAG
HL_01609.3_Sequence_7 HL_01609.39DFE_U305_G312UUGGGAAGtrue69003.90
HL_01609.3_Instance_8 HL_01609.3,HL_4FRN_005,G28_C36GUGUAAUUC
HL_01609.3_Sequence_8 HL_01609.34FRN_G28_C36GUGUAAUUCtrue85001.87
HL_01609.3_Instance_9 HL_01609.3,HL_6DN2_003,G68_C76GUGAAAUUC
HL_01609.3_Sequence_9 HL_01609.36DN2_G68_C76GUGAAAUUCtrue93000.91
HL_01609.3_Instance_10 HL_01609.3,HL_4WF9_010,C348_G355CUGGAAAG
HL_01609.3_Sequence_10 HL_01609.34WF9_C348_G355CUGGAAAGtrue90001.27
HL_01609.3_Instance_11 HL_01609.3,HL_3F2X_004,G68_C76GUGAAAUUC
HL_01609.3_Sequence_11 HL_01609.33F2X_G68_C76GUGAAAUUCtrue93000.91
HL_01609.3_Instance_12 HL_01609.3,HL_4FRG_001,G28_C36GUGAAAUUC
HL_01609.3_Sequence_12 HL_01609.34FRG_G28_C36GUGAAAUUCtrue93000.91
HL_01609.3_Instance_13 HL_01609.3,HL_8P9A_117,U194_A201UUGGAACA
HL_01609.3_Sequence_13 HL_01609.38P9A_U194_A201UUGGAACAtrue87001.61
HL_01609.3_Instance_14 HL_01609.3,HL_8CRE_005,U193_A200UUGGAACA
HL_01609.3_Sequence_14 HL_01609.38CRE_U193_A200UUGGAACAtrue87001.61
HL_01609.3_Instance_15 HL_01609.3,HL_2A64_002,C69_G76CUGAGAUG
HL_01609.3_Sequence_15 HL_01609.32A64_C69_G76CUGAGAUGtrue89001.34
HL_01609.3_Instance_16 HL_01609.3,HL_3VJR_001,G13_C21GUUCGAUCC
HL_01609.3_Sequence_16 HL_01609.33VJR_G13_C21GUUCGAUCCtrue47006.62
HL_01609.3_Instance_17 HL_01609.3,HL_8CRE_224,G1581_C1589GUCAUCAGC
HL_01609.3_Sequence_17 HL_01609.38CRE_G_1581_C_1589GUCAUCAGCtrue110011.09
HL_01609.3_Instance_18 HL_01609.3,HL_5X2G_003,G73_C81GUUACAAUC
HL_01609.3_Sequence_18 HL_01609.35X2G_G73_C81GUUACAAUCtrue56005.50

Conserved interactions between motif group positions in HL_01609.3:
1 2 s35 
1 7 cWW 
2 3 s35 
2 6 tWH 
2 7 s55 
3 6 s55 
4 5 s35 
6 7 s35 
3 6 6BPh
5 3 7BR
JAR3D SCFG/MRF model for HL_01609.3:
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 [0.0000000157319090] | Pair Probability [[0.008338417,0.016066983,0.009536419,0.164816999,0.000000000],[0.029962714,0.009216170,0.210712076,0.011413917,0.000000000],[0.009530576,0.245129363,0.001858052,0.021227536,0.000000000],[0.193262625,0.011348965,0.048597582,0.008981606,0.000000000],[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 [0.001687919,0.608725007,0.388374841,0.001158526,0.000053707] | Right Letter Distribution [0.166666667,0.129629630,0.055555556,0.648148148,0.000000000] | Left Index [1] | Right Index [7] // Basepair C305 - G312 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.016229762,0.003591672,0.016857264,0.003591672,0.000000000],[0.036118998,0.289420151,0.003591672,0.003591672,0.000000000],[0.003591672,0.008609476,0.027314365,0.015974522,0.000000000],[0.511709602,0.003591672,0.020838452,0.035377375,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [6] // Basepair U306 - A310 tWH 
HairpinNode  | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node G307:A309
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.003906250,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.058593750,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.824218750,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.113281250,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G307
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.325000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.425000000,0.000000000,0.000000000],[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 G308
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.711956522,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.059782609,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.222826087,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.005434783,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A309
Insertion    | Location [1] | Length Distribution [0.886338815,0.113215093,0.000430710,0.000015382] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 1
Sequences of instances from HL_01609.3:
> HL_01609.3  5J7L C  305 G  312
CUGGAAAG
> HL_01609.3  7A0S C  316 G  323
CUGGAAAG
> HL_01609.3  5DH6 C   27 G   34
CUGGGAUG
> HL_01609.3  3F2X G   17 C   25
GUGAAAUUC
> HL_01609.3  6DN2 G   17 C   25
GUGAAAUUC
> HL_01609.3  4V9F U  312 A  319
UUGGAAUA
> HL_01609.3  9DFE U  305 G  312
UUGGGAAG
> HL_01609.3  4FRN G   28 C   36
GUGUAAUUC
> HL_01609.3  6DN2 G   68 C   76
GUGAAAUUC
> HL_01609.3  4WF9 C  348 G  355
CUGGAAAG
> HL_01609.3  3F2X G   68 C   76
GUGAAAUUC
> HL_01609.3  4FRG G   28 C   36
GUGAAAUUC
> HL_01609.3  8P9A U  194 A  201
UUGGAACA
> HL_01609.3  8CRE U  193 A  200
UUGGAACA
> HL_01609.3  2A64 C   69 G   76
CUGAGAUG
> HL_01609.3  3VJR G   13 C   21
GUUCGAUCC
> HL_01609.3  8CRE G 1581 C 1589
GUCAUCAGC
> HL_01609.3  5X2G G   73 C   81
GUUACAAUC