Alignment of HL_37369.2 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
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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Interior
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Alignment
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HL_37369.2_Instance_1 HL_37369.2,HL_9DFE_007,C246_G252CGGCGAG
HL_37369.2_Sequence_1 HL_37369.29DFE_C246_G252CGGCGAGtrue100000.00
HL_37369.2_Instance_2 HL_37369.2,HL_7A0S_008,C223_G229CGGCGAG
HL_37369.2_Sequence_2 HL_37369.27A0S_C223_G229CGGCGAGtrue100000.00
HL_37369.2_Instance_3 HL_37369.2,HL_8P9A_115,C90_G96CGGCGAG
HL_37369.2_Sequence_3 HL_37369.28P9A_C90_G96CGGCGAGtrue100000.00
HL_37369.2_Instance_4 HL_37369.2,HL_8CRE_003,C89_G95CGGCGAG
HL_37369.2_Sequence_4 HL_37369.28CRE_C89_G95CGGCGAGtrue100000.00
HL_37369.2_Instance_5 HL_37369.2,HL_5J7L_141,C246_G252CGGCGAG
HL_37369.2_Sequence_5 HL_37369.25J7L_C246_G252CGGCGAGtrue100000.00
HL_37369.2_Instance_6 HL_37369.2,HL_4WF9_008,C249_G255CGGCGAG
HL_37369.2_Sequence_6 HL_37369.24WF9_C249_G255CGGCGAGtrue100000.00
HL_37369.2_Instance_7 HL_37369.2,HL_4V9F_008,C217_G223CCGCGAG
HL_37369.2_Sequence_7 HL_37369.24V9F_C217_G223CCGCGAGtrue88001.54
HL_37369.2_Instance_8 HL_37369.2,HL_8P9A_220,U1396_G1402UUUCAAG
HL_37369.2_Sequence_8 HL_37369.28P9A_U_1396_G_1402UUUCAAGtrue68004.20
HL_37369.2_Instance_9 HL_37369.2,HL_8CRE_221,U1382_G1388UUUCAAG
HL_37369.2_Sequence_9 HL_37369.28CRE_U_1382_G_1388UUUCAAGtrue68004.20

Conserved interactions between motif group positions in HL_37369.2:
1 2 s35 
1 7 cWW 
2 4 s35 
2 6 tSH 
2 7 s55 
3 5 s55 
5 6 s35 
6 7 s35 
4 1 6BPh
4 2 7BPh
2 6 6BPh
JAR3D SCFG/MRF model for HL_37369.2:
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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009279644,0.015354855,0.010948571,0.152435898,0.000000000],[0.077670878,0.012881591,0.225126109,0.013371540,0.000000000],[0.011103183,0.155522414,0.002208500,0.020130439,0.000000000],[0.164484185,0.012723218,0.106585204,0.010173772,0.000000000],[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 [1] | Right Index [7] // Basepair C246 - G252 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.063273048,0.047240103,0.000714791,0.003451896,0.000000000],[0.073323537,0.058893068,0.000714791,0.000714791,0.000000000],[0.340447017,0.002896469,0.014762774,0.231348278,0.000000000],[0.096714976,0.064074881,0.000714791,0.000714791,0.000000000],[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 G247 - A251 tSH 
HairpinNode  | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node G248:G250
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.045454545,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.681818182,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.227272727,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G248
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.001128668,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.996613995,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.001128668,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.001128668,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C249
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.227272727,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.681818182,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.045454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G250
Sequences of instances from HL_37369.2:
> HL_37369.2  9DFE C  246 G  252
CGGCGAG
> HL_37369.2  7A0S C  223 G  229
CGGCGAG
> HL_37369.2  8P9A C   90 G   96
CGGCGAG
> HL_37369.2  8CRE C   89 G   95
CGGCGAG
> HL_37369.2  5J7L C  246 G  252
CGGCGAG
> HL_37369.2  4WF9 C  249 G  255
CGGCGAG
> HL_37369.2  4V9F C  217 G  223
CCGCGAG
> HL_37369.2  8P9A U 1396 G 1402
UUUCAAG
> HL_37369.2  8CRE U 1382 G 1388
UUUCAAG