Alignment of HL_34135.1 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
4

3
7
4
I

8
5

4
9
4
I

10
4

5
11
3
I

12
3

6
13
2
I

14
2

7
15
1
I


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Alignment
score
deficit
HL_34135.1_Instance_1 HL_34135.1_HL_4JXZ_002_U931_A939UUUUUGAUA
HL_34135.1_Sequence_1 HL_34135.1_HL_4JXZ_002_U931_A939UUUUUGAUAtrue100000.00

Conserved interactions between motif group positions in HL_34135.1:
1 2 s35 
1 7 cWW 
2 3 s35 
2 6 cWW 
2 7 s55 
3 5 tSH 
4 5 s35 
5 6 s35 
6 7 s35 
JAR3D SCFG/MRF model for HL_34135.1:
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 [7] // Initial node U931 - A939 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009123784,0.017718471,0.010008206,0.198264936,0.000000000],[0.022262210,0.009929018,0.198931998,0.011154256,0.000000000],[0.010027726,0.196386049,0.002064490,0.023275738,0.000000000],[0.216349992,0.010477281,0.053822220,0.010203624,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair U931 - A939 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.015580470,0.285764820,0.013910732,0.024295965,0.000000000],[0.017220118,0.018567546,0.020767248,0.015270770,0.000000000],[0.013620185,0.021155527,0.004294262,0.054860011,0.000000000],[0.021224145,0.016538232,0.017602771,0.439327198,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [6] // Basepair U932 - U938 cWW 
BasepairNode | Deletion Probability [0.0000000005956745] | Pair Probability [[0.121583738,0.111055049,0.001350235,0.006642085,0.000000000],[0.122053423,0.114840499,0.001350235,0.001350235,0.000000000],[0.125556588,0.001350235,0.008345120,0.112094623,0.000000000],[0.144924515,0.124802948,0.001350235,0.001350235,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [3] | Right Index [5] // Basepair U933 - A937 tSH 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node U935:U935
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U935
Sequences of instances from HL_34135.1:
> HL_34135.1 HL_4JXZ_002 U  931 A  939
UUUUUGAUA