Alignment of HL_56131.2 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
3

3
7
2
I

8
2

4
9
1
I


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HL_56131.2_Instance_1 HL_56131.2,HL_1F7U_002,G931_C939GCUGCGAAC
HL_56131.2_Sequence_1 HL_56131.21F7U_G931_C939GCUGCGAACtrue66003.23
HL_56131.2_Instance_2 HL_56131.2,HL_2ZUE_002,C931_G939CCUCCUAAG
HL_56131.2_Sequence_2 HL_56131.22ZUE_C931_G939CCUCCUAAGtrue70002.83
HL_56131.2_Instance_3 HL_56131.2,HL_4ILL_001,U8_A14UACUAUA
HL_56131.2_Sequence_3 HL_56131.24ILL_U8_A14UACUAUAtrue100000.00
HL_56131.2_Instance_4 HL_56131.2,HL_4ILM_005,U8_A14UACUAUA
HL_56131.2_Sequence_4 HL_56131.24ILM_U8_A14UACUAUAtrue100000.00
HL_56131.2_Instance_5 HL_56131.2,HL_2PJP_001,G22_C25GGUC
HL_56131.2_Sequence_5 HL_56131.22PJP_G22_C25GGUCtrue88001.11
HL_56131.2_Instance_6 HL_56131.2,HL_3WQY_004,U1633_G1637UUGCG
HL_56131.2_Sequence_6 HL_56131.23WQY_U_1633_G_1637UUGCGtrue78002.06

Conserved interactions between motif group positions in HL_56131.2:
1 3 s35 
1 4 cWW 
2 3 s53 
3 4 s55
JAR3D SCFG/MRF model for HL_56131.2:
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 [4] // Initial node
BasepairNode | Deletion Probability [0.0000001163511744] | Pair Probability [[0.009353012,0.017115225,0.010782073,0.165404832,0.000000000],[0.064326949,0.012255484,0.178046090,0.012586828,0.000000000],[0.010818665,0.186779082,0.002191230,0.022094170,0.000000000],[0.194304352,0.012235239,0.091370254,0.010336514,0.000000000],[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 [0.416666667,0.083333333,0.083333333,0.416666667,0.000000000] | Left Index [1] | Right Index [4] // Basepair G931 - C939 cWW 
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node C932:A937
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.562500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.187500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.187500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C932
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.562500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.187500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A937
Insertion    | Location [1] | Length Distribution [0.168193628,0.493641460,0.004170655,0.002939970,0.328182688,0.002734856,0.000136743] | Letter Distribution [0.038461538,0.269230769,0.269230769,0.423076923,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_56131.2:
> HL_56131.2  1F7U G  931 C  939
GCUGCGAAC
> HL_56131.2  2ZUE C  931 G  939
CCUCCUAAG
> HL_56131.2  4ILL U    8 A   14
UACUAUA
> HL_56131.2  4ILM U    8 A   14
UACUAUA
> HL_56131.2  2PJP G   22 C   25
GGUC
> HL_56131.2  3WQY U 1633 G 1637
UUGCG