Alignment of HL_22447.1 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
3

3
7
2
I

8
2

4
9
1
I


In
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Full
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Interior
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Alignment
score
deficit
HL_22447.1_Instance_1 HL_22447.1_HL_4TUW_002_U13_A18UUUUCA
HL_22447.1_Sequence_1 HL_22447.1_HL_4TUW_002_U13_A18UUUUCAtrue100000.00
HL_22447.1_Instance_2 HL_22447.1_HL_4QOZ_001_U11_A16UUUUCA
HL_22447.1_Sequence_2 HL_22447.1_HL_4QOZ_001_U11_A16UUUUCAtrue100000.00
HL_22447.1_Instance_3 HL_22447.1_HL_2PJP_001_G22_C25GGUC
HL_22447.1_Sequence_3 HL_22447.1_HL_2PJP_001_G22_C25GGUCtrue97000.30
HL_22447.1_Instance_4 HL_22447.1_HL_2UWM_002_G22_C25GGUC
HL_22447.1_Sequence_4 HL_22447.1_HL_2UWM_002_G22_C25GGUCtrue97000.30
HL_22447.1_Instance_5 HL_22447.1_HL_4ILM_002_U8_A14UACUAUA
HL_22447.1_Sequence_5 HL_22447.1_HL_4ILM_002_U8_A14UACUAUAtrue82001.74
HL_22447.1_Instance_6 HL_22447.1_HL_4ILL_001_U8_A14UACUAUA
HL_22447.1_Sequence_6 HL_22447.1_HL_4ILL_001_U8_A14UACUAUAtrue82001.74

Conserved interactions between motif group positions in HL_22447.1:
1 3 s35 
1 4 cWW 
2 3 s53 
3 4 s55 
JAR3D SCFG/MRF model for HL_22447.1:
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 [4] // Initial node U13 - A18 from junction 
BasepairNode | Deletion Probability [0.0000001163511744] | Pair Probability [[0.008917739,0.017757404,0.009912684,0.190516459,0.000000000],[0.019625506,0.009368672,0.191487360,0.011346314,0.000000000],[0.009885600,0.210630944,0.001981552,0.023370273,0.000000000],[0.232624561,0.011077789,0.041714145,0.009783000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.661815186,0.335026775,0.003020733,0.000137306] | Left Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Right Length Distribution [0.334109270,0.660002739,0.005614131,0.000273860] | Right Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000] | Left Index [1] | Right Index [4] // Basepair U13 - A18 cWW 
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node U14:U16
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.312500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.312500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.312500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U14
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.562500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U16
Insertion    | Location [1] | Length Distribution [0.334109270,0.660002739,0.005614131,0.000273860] | Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_22447.1:
> HL_22447.1 HL_4TUW_002 U   13 A   18
UUUUCA
> HL_22447.1 HL_4QOZ_001 U   11 A   16
UUUUCA
> HL_22447.1 HL_2PJP_001 G   22 C   25
GGUC
> HL_22447.1 HL_2UWM_002 G   22 C   25
GGUC
> HL_22447.1 HL_4ILM_002 U    8 A   14
UACUAUA
> HL_22447.1 HL_4ILL_001 U    8 A   14
UACUAUA