Alignment of HL_81205.2 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
8

3
7
8
I

8
11

4
9
11
I

10
12

5
11
12
I

12
12

6
13
12
I

14
12

7
15
11
I

16
11

8
17
10
I

18
9

9
19
8
I

20
8

10
21
7
I

22
6

11
23
5
I

24
4

12
25
3
I

26
3

13
27
2
I

28
2

14
29
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_81205.2_Instance_1 HL_81205.2_HL_4LFB_008_C320_G333CACUGAGACACGGG
HL_81205.2_Sequence_1 HL_81205.2_HL_4LFB_008_C320_G333CACUGAGACACGGGtrue100000.00
HL_81205.2_Instance_2 HL_81205.2_HL_5J7L_008_A320_U333AACUGAGACACGGU
HL_81205.2_Sequence_2 HL_81205.2_HL_5J7L_008_A320_U333AACUGAGACACGGUtrue97000.53
HL_81205.2_Instance_3 HL_81205.2_HL_6CZR_079_C316_G329CACUGAGACACGGG
HL_81205.2_Sequence_3 HL_81205.2_HL_6CZR_079_C316_G329CACUGAGACACGGGtrue100000.00

Conserved interactions between motif group positions in HL_81205.2:
1 2 s35 
1 14 cWW 
2 3 s35 
2 9 s35 
2 13 cWW 
2 14 s55 
3 4 s35 
3 10 tWH 
4 5 s35 
4 8 tWH 
5 8 s55 
6 7 s35 
8 10 s35 
10 13 s35 
13 14 s35 
5 8 6BPh
1 10 7BPh
2 10 7BPh
JAR3D SCFG/MRF model for HL_81205.2:
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 [14] // Initial node C320 - G333 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.011047284,0.024765524,0.012000462,0.249792715,0.000000000],[0.039103953,0.018888315,0.424233191,0.026390557,0.000000000],[0.004179666,0.078595762,0.000811066,0.013105297,0.000000000],[0.078066430,0.004899587,0.009976494,0.004143697,0.000000000],[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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Basepair C320 - G333 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.057673175,0.028250710,0.725663104,0.033832476,0.000000000],[0.003941052,0.002684127,0.005220341,0.011730572,0.000000000],[0.095600616,0.005278967,0.000995053,0.004391209,0.000000000],[0.004823803,0.012394310,0.004297135,0.003223350,0.000000000],[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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [13] // Basepair A321 - G332 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [2] | Left Index [3] | Right Index [12] // 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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [11] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [3] | Right Index [11] // 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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.030419083,0.003553878,0.101665438,0.003553878,0.000000000],[0.384514062,0.025892298,0.003553878,0.003553878,0.000000000],[0.003553878,0.012407604,0.031958440,0.032758932,0.000000000],[0.035738931,0.003553878,0.015978312,0.307343630,0.000000000],[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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // Basepair C322 - A329 tWH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [4] | Right Index [9] // 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 [0.993970181,0.005999820,0.000029999] | 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
BasepairNode | Deletion Probability [0.0000234451146992] | 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 [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [8] // Basepair U323 - A327 tWH 
HairpinNode  | Num Bases [3] | Left Index [5] | Right Index [7] | Norm Constant [0.999999999999999] // Hairpin node G324:G326
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.021739130,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.934782609,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.021739130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G324
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[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 A325
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 G326
Sequences of instances from HL_81205.2:
> HL_81205.2 HL_4LFB_008 C  320 G  333
CACUGAGACACGGG
> HL_81205.2 HL_5J7L_008 A  320 U  333
AACUGAGACACGGU
> HL_81205.2 HL_6CZR_079 C  316 G  329
CACUGAGACACGGG