Alignment of HL_76406.3 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
4
I

6
5

3
7
6
I

8
7

4
9
8
I

10
9

5
11
9
I

12
10

6
13
10
I

14
10

7
15
9
I

16
9

8
17
2
I

18
2

9
19
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_76406.3_Instance_1 HL_76406.3_HL_4V9F_057_G2338_C2346GACAGAGAC
HL_76406.3_Sequence_1 HL_76406.3_HL_4V9F_057_G_2338_C_2346GACAGAGACtrue100000.00
HL_76406.3_Instance_2 HL_76406.3_HL_5TBW_056_A2673_U2681AACAGAAAU
HL_76406.3_Sequence_2 HL_76406.3_HL_5TBW_056_A_2673_U_2681AACAGAAAUtrue100000.06

Conserved interactions between motif group positions in HL_76406.3:
1 9 cWW 
2 3 s35 
3 4 s33 
4 5 s53 
4 8 s53 
5 7 s55 
5 8 cWH 
6 7 s35 
9 8 7BPh
JAR3D SCFG/MRF model for HL_76406.3:
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 [9] // Initial node G2338 - C2346 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.003625340,0.031935851,0.004007138,0.313070369,0.000000000],[0.006591797,0.014892244,0.075717760,0.015993196,0.000000000],[0.003979397,0.333377958,0.000787133,0.074010905,0.000000000],[0.075219462,0.020993034,0.008855864,0.016942552,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair G2338 - C2346 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // Fixed node on left
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [3] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [4] | Right Index [8] // Fixed node on left
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [5] | Right Index [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.002839261,0.002839261,0.245743704,0.235280129,0.000000000],[0.002839261,0.019473421,0.002839261,0.010750004,0.000000000],[0.303533980,0.002839261,0.118056128,0.002839261,0.000000000],[0.010460384,0.002839261,0.009699227,0.027128194,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair G2342 - A2345 cWH 
HairpinNode  | Num Bases [2] | Left Index [6] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node A2343:G2344
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2343
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2344
Sequences of instances from HL_76406.3:
> HL_76406.3 HL_4V9F_057 G 2338 C 2346
GACAGAGAC
> HL_76406.3 HL_5TBW_056 A 2673 U 2681
AACAGAAAU