Alignment of HL_02733.4 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
2
I

12
2

6
13
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
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distance

Alignment
score
deficit
HL_02733.4_Instance_1 HL_02733.4_HL_5J7L_203_C38_G44CAUGCCG
HL_02733.4_Sequence_1 HL_02733.4_HL_5J7L_203_C38_G44CAUGCCGtrue100000.00
HL_02733.4_Instance_2 HL_02733.4_HL_5FDV_069_C38_G44CAUUCCG
HL_02733.4_Sequence_2 HL_02733.4_HL_5FDV_069_C38_G44CAUUCCGtrue92001.10
HL_02733.4_Instance_3 HL_02733.4_HL_1MJI_002_C38_G44CAUGCCG
HL_02733.4_Sequence_3 HL_02733.4_HL_1MJI_002_C38_G44CAUGCCGtrue100000.00
HL_02733.4_Instance_4 HL_02733.4_HL_4V9F_071_C37_G43CAUCCCG
HL_02733.4_Sequence_4 HL_02733.4_HL_4V9F_071_C37_G43CAUCCCGtrue92001.10
HL_02733.4_Instance_5 HL_02733.4_HL_4WF9_066_C36_G42CAUGCCG
HL_02733.4_Sequence_5 HL_02733.4_HL_4WF9_066_C36_G42CAUGCCGtrue100000.00
HL_02733.4_Instance_6 HL_02733.4_HL_5TBW_185_C36_G41CGUCCG
HL_02733.4_Sequence_6 HL_02733.4_HL_5TBW_185_C36_G41CGUCCGtrue80002.89
HL_02733.4_Instance_7 HL_02733.4_HL_7A0S_069_C40_G46CAUGCCG
HL_02733.4_Sequence_7 HL_02733.4_HL_7A0S_069_C40_G46CAUGCCGtrue100000.00

Conserved interactions between motif group positions in HL_02733.4:
1 2 s35 
1 6 cWW 
2 3 s35 
2 6 s55 
4 5 s35 
3 6 6BPh
5 3 7BR
2 6 6BR
JAR3D SCFG/MRF model for HL_02733.4:
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 [6] // Initial node C38 - G44 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009090944,0.016302246,0.010451159,0.189500131,0.000000000],[0.019328903,0.009258863,0.264630806,0.013146218,0.000000000],[0.010568529,0.193583350,0.001992102,0.022369654,0.000000000],[0.191956811,0.012666128,0.025520256,0.009633898,0.000000000],[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 [6] // Basepair C38 - G44 cWW 
HairpinNode  | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A39:C43
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.824324324,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.013513514,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.148648649,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.013513514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A39
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.009803922,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.009803922,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.009803922,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.970588235,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U40
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.833333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C42
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.013513514,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.959459459,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.013513514,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.013513514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C43
Insertion    | Location [2] | Length Distribution [0.146977400,0.846630090,0.006090502,0.000302008] | Letter Distribution [0.062500000,0.187500000,0.562500000,0.187500000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2
Sequences of instances from HL_02733.4:
> HL_02733.4 HL_5J7L_203 C   38 G   44
CAUGCCG
> HL_02733.4 HL_5FDV_069 C   38 G   44
CAUUCCG
> HL_02733.4 HL_1MJI_002 C   38 G   44
CAUGCCG
> HL_02733.4 HL_4V9F_071 C   37 G   43
CAUCCCG
> HL_02733.4 HL_4WF9_066 C   36 G   42
CAUGCCG
> HL_02733.4 HL_5TBW_185 C   36 G   41
CGUCCG
> HL_02733.4 HL_7A0S_069 C   40 G   46
CAUGCCG