Alignment of HL_08748.1 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
5
I

10
5

5
11
5
I

12
5

6
13
4
I

14
4

7
15
3
I

16
3

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_08748.1_Instance_1 HL_08748.1_HL_4V9F_032_A1274_U1282ACUCAUACU
HL_08748.1_Sequence_1 HL_08748.1_HL_4V9F_032_A_1274_U_1282ACUCAUACUtrue91001.24
HL_08748.1_Instance_2 HL_08748.1_HL_4WF9_039_A1673_U1681AUGAGAAUU
HL_08748.1_Sequence_2 HL_08748.1_HL_4WF9_039_A_1673_U_1681AUGAGAAUUtrue100000.00

Conserved interactions between motif group positions in HL_08748.1:
1 2 s35 
1 9 cWW 
2 3 s35 
2 8 cWW 
3 5 s33 
3 7 tSH 
4 5 s35 
5 7 s35 
6 8 perp 
6 9 perp 
7 8 s35 
8 9 s35 
3 6 6BPh
JAR3D SCFG/MRF model for HL_08748.1:
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 [9] // Initial node A1274 - U1282 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009282926,0.022010543,0.009914366,0.223723012,0.000000000],[0.017518170,0.009580259,0.194165974,0.010358839,0.000000000],[0.009895067,0.196683142,0.002041152,0.053213779,0.000000000],[0.196023621,0.011028161,0.023012614,0.011548375,0.000000000],[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 A1274 - U1282 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.014025201,0.257239276,0.012522138,0.021870700,0.000000000],[0.015501176,0.115644582,0.018694225,0.013746415,0.000000000],[0.012260594,0.019043745,0.003865601,0.049383789,0.000000000],[0.019105514,0.014887357,0.015845632,0.396364055,0.000000000],[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 [2] | Right Index [8] // Basepair C1275 - C1281 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.045082454,0.044351636,0.000520299,0.002505376,0.000000000],[0.045334528,0.045021438,0.000520299,0.000520299,0.000000000],[0.217394406,0.002093995,0.010570186,0.177251098,0.000000000],[0.214804909,0.189892275,0.002068399,0.002068399,0.000000000],[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 [3] | Right Index [7] // Basepair U1276 - A1280 tSH 
HairpinNode  | Num Bases [3] | Left Index [4] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node C1277:U1279
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C1277
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 A1278
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U1279
Sequences of instances from HL_08748.1:
> HL_08748.1 HL_4V9F_032 A 1274 U 1282
ACUCAUACU
> HL_08748.1 HL_4WF9_039 A 1673 U 1681
AUGAGAAUU