Alignment of HL_17926.4 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
3
I

6
3

3
7
3
I

8
3

4
9
3
I

10
3

5
11
3
I

12
3

6
13
3
I

14
3

7
15
3
I

16
3

8
17
2
I

18
2

9
19
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_17926.4_Instance_1 HL_17926.4_HL_4WF9_002_U87_A95UGUAAGUAA
HL_17926.4_Sequence_1 HL_17926.4_HL_4WF9_002_U87_A95UGUAAGUAAtrue90001.14
HL_17926.4_Instance_2 HL_17926.4_HL_4Y4O_104_C87_G95CGGUAGCGG
HL_17926.4_Sequence_2 HL_17926.4_HL_4Y4O_104_C87_G95CGGUAGCGGtrue85001.74
HL_17926.4_Instance_3 HL_17926.4_HL_4QLM_002_U72_G81UACUCCUUCG
HL_17926.4_Sequence_3 HL_17926.4_HL_4QLM_002_U72_G81UACUCCUUCGtrue57004.92
HL_17926.4_Instance_4 HL_17926.4_HL_5J7L_135_U87_A95UGAUAUGAA
HL_17926.4_Sequence_4 HL_17926.4_HL_5J7L_135_U87_A95UGAUAUGAAtrue82001.99
HL_17926.4_Instance_5 HL_17926.4_HL_6UFJ_004_G33_C41GCUCAAAGC
HL_17926.4_Sequence_5 HL_17926.4_HL_6UFJ_004_G33_C41GCUCAAAGCtrue100000.00
HL_17926.4_Instance_6 HL_17926.4_HL_5K7D_002_G33_C41GCCCUAAGC
HL_17926.4_Sequence_6 HL_17926.4_HL_5K7D_002_G33_C41GCCCUAAGCtrue83001.95

Conserved interactions between motif group positions in HL_17926.4:
1 9 cWW 
2 3 s35 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
JAR3D SCFG/MRF model for HL_17926.4:
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 [9] // Initial node U87 - A95 from junction 
BasepairNode | Deletion Probability [0.0000097596267952] | 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 [0.826344012,0.171868555,0.001718686,0.000068747] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | 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 [9] // Basepair U87 - A95 cWW 
HairpinNode  | Num Bases [7] | Left Index [2] | Right Index [8] | Norm Constant [1.000000000000000] // Hairpin node G88:A94
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.437500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.437500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G88
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.187500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.187500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.437500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U89
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.187500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.437500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.312500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A90
Interaction  | Interacting Bases [4,4] | 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 A91
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.312500000,0.000000000,0.000000000],[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 G92
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.187500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.312500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U93
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.437500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A94
Sequences of instances from HL_17926.4:
> HL_17926.4 HL_4WF9_002 U   87 A   95
UGUAAGUAA
> HL_17926.4 HL_4Y4O_104 C   87 G   95
CGGUAGCGG
> HL_17926.4 HL_4QLM_002 U   72 G   81
UACUCCUUCG
> HL_17926.4 HL_5J7L_135 U   87 A   95
UGAUAUGAA
> HL_17926.4 HL_6UFJ_004 G   33 C   41
GCUCAAAGC
> HL_17926.4 HL_5K7D_002 G   33 C   41
GCCCUAAGC