Alignment of HL_46891.2 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
3
I

8
3

4
9
3
I

10
3

5
11
3
I

12
3

6
13
3
I

14
3

7
15
2
I

16
2

8
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
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Alignment
score
deficit
HL_46891.2_Instance_1 HL_46891.2_HL_3R4F_004_A51_U58AUGGUUGU
HL_46891.2_Sequence_1 HL_46891.2_HL_3R4F_004_A51_U58AUGGUUGUtrue98000.25
HL_46891.2_Instance_2 HL_46891.2_HL_3R4F_002_A51_U58AUGGUUGU
HL_46891.2_Sequence_2 HL_46891.2_HL_3R4F_002_A51_U58AUGGUUGUtrue98000.25
HL_46891.2_Instance_3 HL_46891.2_HL_4V9F_055_C2281_G2289CUGGGGCGG
HL_46891.2_Sequence_3 HL_46891.2_HL_4V9F_055_C_2281_G_2289CUGGGGCGGtrue100000.00
HL_46891.2_Instance_4 HL_46891.2_HL_4WF9_049_C2275_G2283CUGGGGCGG
HL_46891.2_Sequence_4 HL_46891.2_HL_4WF9_049_C_2275_G_2283CUGGGGCGGtrue100000.00
HL_46891.2_Instance_5 HL_46891.2_HL_7A0S_052_C2227_G2235CUGGGGCGG
HL_46891.2_Sequence_5 HL_46891.2_HL_7A0S_052_C_2227_G_2235CUGGGGCGGtrue100000.00
HL_46891.2_Instance_6 HL_46891.2_HL_5TBW_054_C2616_G2624CUGGGGCGG
HL_46891.2_Sequence_6 HL_46891.2_HL_5TBW_054_C_2616_G_2624CUGGGGCGGtrue100000.00
HL_46891.2_Instance_7 HL_46891.2_HL_4V84_034_U6185_G6192UUAGGUAG
HL_46891.2_Sequence_7 HL_46891.2_HL_4V84_034_U_6185_G_6192UUAGGUAGtrue71003.43
HL_46891.2_Instance_8 HL_46891.2_HL_6UFG_003_G69_C76GGUUGGCC
HL_46891.2_Sequence_8 HL_46891.2_HL_6UFG_003_G69_C76GGUUGGCCtrue56005.13
HL_46891.2_Instance_9 HL_46891.2_HL_6UFH_001_G13_C20GCGAUCAC
HL_46891.2_Sequence_9 HL_46891.2_HL_6UFH_001_G13_C20GCGAUCACtrue79002.47
HL_46891.2_Instance_10 HL_46891.2_HL_6UFG_001_G13_C20GCGAUCAC
HL_46891.2_Sequence_10 HL_46891.2_HL_6UFG_001_G13_C20GCGAUCACtrue79002.47
HL_46891.2_Instance_11 HL_46891.2_HL_6UFM_006_G80_C87GGUGAGCC
HL_46891.2_Sequence_11 HL_46891.2_HL_6UFM_006_G80_C87GGUGAGCCtrue59004.86

Conserved interactions between motif group positions in HL_46891.2:
1 2 s35 
1 8 cWW 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
JAR3D SCFG/MRF model for HL_46891.2:
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 [8] // Initial node A51 - U58 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008929643,0.017333964,0.010216417,0.188932372,0.000000000],[0.040688900,0.010370554,0.209686185,0.012117231,0.000000000],[0.010239314,0.209669489,0.002013651,0.026901358,0.000000000],[0.173649179,0.012115827,0.057257976,0.009877940,0.000000000],[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 [8] // Basepair A51 - U58 cWW 
HairpinNode  | Num Bases [6] | Left Index [2] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node U52:G57
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.038461538,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.192307692,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.192307692,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.576923077,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U52
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.115384615,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.653846154,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.192307692,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G53
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.192307692,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.653846154,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.115384615,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G54
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.115384615,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.346153846,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U55
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.038461538,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.192307692,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.269230769,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U56
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.269230769,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.192307692,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G57
Insertion    | Location [1] | Length Distribution [0.633943052,0.364188787,0.001786044,0.000082117] | Letter Distribution [0.083333333,0.083333333,0.750000000,0.083333333,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_46891.2:
> HL_46891.2 HL_3R4F_004 A   51 U   58
AUGGUUGU
> HL_46891.2 HL_3R4F_002 A   51 U   58
AUGGUUGU
> HL_46891.2 HL_4V9F_055 C 2281 G 2289
CUGGGGCGG
> HL_46891.2 HL_4WF9_049 C 2275 G 2283
CUGGGGCGG
> HL_46891.2 HL_7A0S_052 C 2227 G 2235
CUGGGGCGG
> HL_46891.2 HL_5TBW_054 C 2616 G 2624
CUGGGGCGG
> HL_46891.2 HL_4V84_034 U 6185 G 6192
UUAGGUAG
> HL_46891.2 HL_6UFG_003 G   69 C   76
GGUUGGCC
> HL_46891.2 HL_6UFH_001 G   13 C   20
GCGAUCAC
> HL_46891.2 HL_6UFG_001 G   13 C   20
GCGAUCAC
> HL_46891.2 HL_6UFM_006 G   80 C   87
GGUGAGCC