Alignment of HL_29129.3 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
4

3
7
4
I

8
4

4
9
4
I

10
4

5
11
4
I

12
4

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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distance
Alignment
score
deficit
HL_29129.3_Instance_1 HL_29129.3,HL_5TPY_005,U28_G38UUUGGGGAAAG
HL_29129.3_Sequence_1 HL_29129.35TPY_U28_G38UUUGGGGAAAGtrue100000.00
HL_29129.3_Instance_2 HL_29129.3,HL_7U4A_002,U28_G38UUUGGGGAAAG
HL_29129.3_Sequence_2 HL_29129.37U4A_U28_G38UUUGGGGAAAGtrue100000.00
HL_29129.3_Instance_3 HL_29129.3,HL_8X5V_002,G71_C80GUUGGGGAUC
HL_29129.3_Sequence_3 HL_29129.38X5V_G71_C80GUUGGGGAUCtrue91001.53

Conserved interactions between motif group positions in HL_29129.3:
1 2 s35 
1 8 cWW 
2 6 s33 
2 7 tWH 
2 8 s55 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35
JAR3D SCFG/MRF model for HL_29129.3:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [8] // Initial node
BasepairNode | Deletion Probability [0.0000001200211660] | Pair Probability [[0.010637704,0.015923797,0.013084809,0.091063864,0.000000000],[0.205377759,0.021603649,0.094980442,0.014970651,0.000000000],[0.013250532,0.103185169,0.002872365,0.018521481,0.000000000],[0.122508888,0.014242306,0.245431788,0.012344797,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.500000000,0.100000000,0.100000000,0.300000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair U28 - G38 cWW 
BasepairNode | Deletion Probability [0.0000000035094402] | Pair Probability [[0.018593320,0.004114731,0.019312206,0.004114731,0.000000000],[0.041379046,0.331568716,0.004114731,0.004114731,0.000000000],[0.004114731,0.009863283,0.031292185,0.018300908,0.000000000],[0.440599350,0.004114731,0.023873178,0.040529420,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.005372012,0.333064733,0.650013430,0.011012624,0.000537201] | Left Letter Distribution [0.071428571,0.071428571,0.357142857,0.500000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair U29 - A36 tWH 
HairpinNode  | Num Bases [4] | Left Index [3] | Right Index [6] | Norm Constant [0.999999999999999] // Hairpin node G32:A35
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G32
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G33
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G34
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A35
Sequences of instances from HL_29129.3:
> HL_29129.3  5TPY U   28 G   38
UUUGGGGAAAG
> HL_29129.3  7U4A U   28 G   38
UUUGGGGAAAG
> HL_29129.3  8X5V G   71 C   80
GUUGGGGAUC