Alignment of HL_32255.1 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
5
I

8
7
I

9
8

4
10
8
I

11
8

5
12
8
I

13
8

6
14
8
I

15
8

7
16
7
I

17
6

8
18
3
I

19
3

9
20
2
I

21
2

10
22
1
I


In
acceptance
region


Cutoff
score

Full
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distance

Interior
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Alignment
score
deficit
HL_32255.1_Instance_1 HL_32255.1_HL_4V88_209_U1055_G1064UUUUUUAAUG
HL_32255.1_Sequence_1 HL_32255.1_HL_4V88_209_U_1055_G_1064UUUUUUAAUGtrue100000.00

Conserved interactions between motif group positions in HL_32255.1:
1 2 s35 
1 10 cWW 
2 9 cWW 
2 10 s55 
3 6 s33 
4 6 cWW 
5 6 perp 
6 7 cSS 
7 8 s53 
8 9 s55 
9 10 s35 
7 6 2BR
JAR3D SCFG/MRF model for HL_32255.1:
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 [10] // Initial node U1055 - G1064 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.011357495,0.014122426,0.014418960,0.037643649,0.000000000],[0.305533580,0.028227484,0.042773463,0.016192886,0.000000000],[0.014734624,0.037492866,0.003338882,0.014817277,0.000000000],[0.087046211,0.014824487,0.343789173,0.013686536,0.000000000],[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 [10] // Basepair U1055 - G1064 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 [9] // Basepair U1056 - U1063 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [2] | Left Index [4] | Right Index [8] // Fixed node on right
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 [4] | Right Index [7] // New Initial node after Fixed node
HairpinNode  | Num Bases [4] | Left Index [4] | Right Index [7] | Norm Constant [0.275565987730353] // Hairpin node U1058:A1061
Interaction  | Interacting Bases [1,3] | 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]] // Hairpin Interaction U1058 - U1060 cWW 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.076146696,0.074822471,0.076666471,0.069121724,0.000000000],[0.078906659,0.079495189,0.003253861,0.064122585,0.000000000],[0.078575452,0.003326749,0.009031637,0.069548293,0.000000000],[0.093178774,0.073057805,0.075892455,0.074853180,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U1060 - A1061 cSS 
Interaction  | Interacting Bases [2,2] | 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 U1059
Sequences of instances from HL_32255.1:
> HL_32255.1 HL_4V88_209 U 1055 G 1064
UUUUUUAAUG