Alignment of HL_92304.3 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
8

3
7
8
I

8
9

4
9
9
I

10
9

5
11
8
I

12
8

6
13
7
I

14
6

7
15
5
I

16
4

8
17
3
I

18
3

9
19
2
I

20
2

10
21
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_92304.3_Instance_1 HL_92304.3_HL_1MMS_001_C1064_G1074CUUAGAAGCAG
HL_92304.3_Sequence_1 HL_92304.3_HL_1MMS_001_C_1064_G_1074CUUAGAAGCAGtrue100000.00
HL_92304.3_Instance_2 HL_92304.3_HL_5D8H_001_C1174_G1184CUUAGAAGCAG
HL_92304.3_Sequence_2 HL_92304.3_HL_5D8H_001_C_1174_G_1184CUUAGAAGCAGtrue100000.00
HL_92304.3_Instance_3 HL_92304.3_HL_6PRV_001_C1064_G1074CUUAGAAGCAG
HL_92304.3_Sequence_3 HL_92304.3_HL_6PRV_001_C_1064_G_1074CUUAGAAGCAGtrue100000.00
HL_92304.3_Instance_4 HL_92304.3_HL_5J7L_161_C1064_G1074CUUAGAAGCAG
HL_92304.3_Sequence_4 HL_92304.3_HL_5J7L_161_C_1064_G_1074CUUAGAAGCAGtrue100000.00
HL_92304.3_Instance_5 HL_92304.3_HL_5TBW_027_C1239_G1249CAUGGAAGUCG
HL_92304.3_Sequence_5 HL_92304.3_HL_5TBW_027_C_1239_G_1249CAUGGAAGUCGtrue76004.90

Conserved interactions between motif group positions in HL_92304.3:
1 2 s35 
1 10 cWW 
2 3 s35 
2 9 cSW 
2 10 s55 
3 5 ---- 
3 6 tSH 
4 5 s35 
5 6 s35 
6 9 s35 
7 8 s35 
9 10 s35 
3 6 6BPh
2 6 6BR
9 6 7BR
JAR3D SCFG/MRF model for HL_92304.3:
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 [10] // Initial node C1064 - G1074 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009264105,0.016612765,0.010650229,0.193109658,0.000000000],[0.019697072,0.009435223,0.250623774,0.013396622,0.000000000],[0.010769834,0.197270651,0.002030047,0.022795742,0.000000000],[0.195613131,0.012907388,0.026006356,0.009817401,0.000000000],[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 [10] // Basepair C1064 - G1074 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.102656694,0.041237119,0.002830084,0.000819767,0.000000000],[0.098451458,0.001578518,0.000218513,0.000859783,0.000000000],[0.101257109,0.000218513,0.017639504,0.000687240,0.000000000],[0.614140626,0.007998128,0.005375012,0.004031932,0.000000000],[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 [2] | Right Index [9] // Basepair U1065 - A1073 cSW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.642857143,0.071428571,0.214285714,0.000000000] | Position [2] | Left Index [3] | Right Index [8] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | 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 [3] | Right Index [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.071428571,0.785714286,0.071428571,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Right Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Left Index [3] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.044038328,0.040224777,0.000489063,0.002405801,0.000000000],[0.044208451,0.041595888,0.000489063,0.000489063,0.000000000],[0.045477317,0.000489063,0.003022650,0.040601316,0.000000000],[0.413191926,0.316430412,0.003423441,0.003423441,0.000000000],[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 [3] | Right Index [6] // Basepair U1066 - A1069 tSH 
HairpinNode  | Num Bases [2] | Left Index [4] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A1067:G1068
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.642857143,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1067
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.785714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1068
Sequences of instances from HL_92304.3:
> HL_92304.3 HL_1MMS_001 C 1064 G 1074
CUUAGAAGCAG
> HL_92304.3 HL_5D8H_001 C 1174 G 1184
CUUAGAAGCAG
> HL_92304.3 HL_6PRV_001 C 1064 G 1074
CUUAGAAGCAG
> HL_92304.3 HL_5J7L_161 C 1064 G 1074
CUUAGAAGCAG
> HL_92304.3 HL_5TBW_027 C 1239 G 1249
CAUGGAAGUCG