Alignment of HL_75091.3 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
11

3
7
11
I

8
12

4
9
11
I

10
11

5
11
10
I

12
9

6
13
8
I

14
7

7
15
6
I

16
5

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_75091.3_Instance_1 HL_75091.3_HL_5X2G_002_G54_C64GUUUGCGGGAC
HL_75091.3_Sequence_1 HL_75091.3_HL_5X2G_002_G54_C64GUUUGCGGGACtrue85002.20
HL_75091.3_Instance_2 HL_75091.3_HL_5J7L_134_U59_G68UGCUAAUCUG
HL_75091.3_Sequence_2 HL_75091.3_HL_5J7L_134_U59_G68UGCUAAUCUGtrue89001.57
HL_75091.3_Instance_3 HL_75091.3_HL_2JLT_001_G5_C14GGUCCCAGAC
HL_75091.3_Sequence_3 HL_75091.3_HL_2JLT_001_G5_C14GGUCCCAGACtrue100000.00

Conserved interactions between motif group positions in HL_75091.3:
1 2 s35 
1 9 cWW 
3 5 cSH 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
JAR3D SCFG/MRF model for HL_75091.3:
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 G54 - C64 from junction 
BasepairNode | Deletion Probability [0.0000038011627649] | Pair Probability [[0.010138447,0.017999390,0.012030637,0.145215023,0.000000000],[0.111154629,0.015527922,0.148017973,0.014062841,0.000000000],[0.012052549,0.169605488,0.002470680,0.022513399,0.000000000],[0.159661783,0.013947978,0.134332446,0.011268815,0.000000000],[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 [0.657073038,0.336682053,0.005973391,0.000271518] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [1] | Right Index [9] // Basepair G54 - C64 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.500000000,0.300000000,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // Fixed node on left
InitialNode  | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.100000000,0.300000000,0.100000000,0.500000000,0.000000000] | 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 [0.300000000,0.100000000,0.300000000,0.300000000,0.000000000] | Position [2] | Left Index [3] | Right Index [8] // 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 [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.300000000,0.500000000,0.100000000,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // 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 [6] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.300000000,0.300000000,0.000000000] | Position [2] | Left Index [3] | Right Index [6] // 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 [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.095660449,0.095928050,0.006544771,0.050788838,0.000000000],[0.095415297,0.149051757,0.001058658,0.010350084,0.000000000],[0.011122316,0.001058658,0.092735258,0.086415640,0.000000000],[0.108354382,0.107776738,0.001058658,0.086680449,0.000000000],[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 [5] // Basepair U57 - C59 cSH 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G58:G58
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[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 G58
Sequences of instances from HL_75091.3:
> HL_75091.3 HL_5X2G_002 G   54 C   64
GUUUGCGGGAC
> HL_75091.3 HL_5J7L_134 U   59 G   68
UGCUAAUCUG
> HL_75091.3 HL_2JLT_001 G    5 C   14
GGUCCCAGAC