Alignment of HL_73266.3 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
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_73266.3_Instance_1 HL_73266.3_HL_4FEN_003_A59_U67ACCGUAAAU
HL_73266.3_Sequence_1 HL_73266.3_HL_4FEN_003_A59_U67ACCGUAAAUtrue99000.16
HL_73266.3_Instance_2 HL_73266.3_HL_1Y27_003_A59_U67ACCGUAAAU
HL_73266.3_Sequence_2 HL_73266.3_HL_1Y27_003_A59_U67ACCGUAAAUtrue99000.16
HL_73266.3_Instance_3 HL_73266.3_HL_4LX6_003_G59_C67GCCUUAAAC
HL_73266.3_Sequence_3 HL_73266.3_HL_4LX6_003_G59_C67GCCUUAAACtrue100000.00
HL_73266.3_Instance_4 HL_73266.3_HL_5SWD_006_G59_C67GCCUUAAAC
HL_73266.3_Sequence_4 HL_73266.3_HL_5SWD_006_G59_C67GCCUUAAACtrue100000.00
HL_73266.3_Instance_5 HL_73266.3_HL_3LA5_003_G59_C67GCCUUAAAC
HL_73266.3_Sequence_5 HL_73266.3_HL_3LA5_003_G59_C67GCCUUAAACtrue100000.00
HL_73266.3_Instance_6 HL_73266.3_HL_5KPY_002_A59_U67ACCGUAAAU
HL_73266.3_Sequence_6 HL_73266.3_HL_5KPY_002_A59_U67ACCGUAAAUtrue99000.16
HL_73266.3_Instance_7 HL_73266.3_HL_3RKF_009_A59_U67ACUGUAAAU
HL_73266.3_Sequence_7 HL_73266.3_HL_3RKF_009_A59_U67ACUGUAAAUtrue98000.24
HL_73266.3_Instance_8 HL_73266.3_HL_4XNR_003_G59_C67GCCUUAAAC
HL_73266.3_Sequence_8 HL_73266.3_HL_4XNR_003_G59_C67GCCUUAAACtrue100000.00
HL_73266.3_Instance_9 HL_73266.3_HL_1Y26_003_G59_C67GCCUUAAAC
HL_73266.3_Sequence_9 HL_73266.3_HL_1Y26_003_G59_C67GCCUUAAACtrue100000.00
HL_73266.3_Instance_10 HL_73266.3_HL_2ZNI_002_A31_U39ACUCUAAAU
HL_73266.3_Sequence_10 HL_73266.3_HL_2ZNI_002_A31_U39ACUCUAAAUtrue96000.54
HL_73266.3_Instance_11 HL_73266.3_HL_3RG5_010_G31_C39GCUUCAAAC
HL_73266.3_Sequence_11 HL_73266.3_HL_3RG5_010_G31_C39GCUUCAAACtrue98000.27
HL_73266.3_Instance_12 HL_73266.3_HL_3RG5_006_G31_C39GCUUCAAAC
HL_73266.3_Sequence_12 HL_73266.3_HL_3RG5_006_G31_C39GCUUCAAACtrue98000.27

Conserved interactions between motif group positions in HL_73266.3:
1 2 s35 
1 9 cWW 
2 3 s35 
2 8 cWW 
3 7 cSW 
4 5 cSH 
5 6 s55 
6 7 s35 
7 8 s35 
8 9 s35 
6 4 2BPh
JAR3D SCFG/MRF model for HL_73266.3:
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 A59 - U67 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008693563,0.019121607,0.009650564,0.229048924,0.000000000],[0.015730564,0.008706074,0.181536954,0.010987935,0.000000000],[0.009577847,0.248127239,0.001884474,0.034411727,0.000000000],[0.179966837,0.011509408,0.021196057,0.009850227,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair A59 - U67 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.010080286,0.013199009,0.012833387,0.027809212,0.000000000],[0.439209153,0.036996213,0.031439147,0.014330603,0.000000000],[0.013141970,0.026516183,0.003240225,0.013705140,0.000000000],[0.034940627,0.013059696,0.296505749,0.012993400,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair C60 - A66 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.173725874,0.016835553,0.016595177,0.006850719,0.000000000],[0.258053928,0.014812852,0.001884678,0.007301182,0.000000000],[0.173299871,0.001884678,0.057094116,0.005818232,0.000000000],[0.236187312,0.014491142,0.008431629,0.006733057,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [7] // Basepair C61 - A65 cSW 
HairpinNode  | Num Bases [3] | Left Index [4] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node G62:A64
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.068584304,0.069343764,0.003849349,0.069093448,0.000000000],[0.060530190,0.077944113,0.000850733,0.088124335,0.000000000],[0.065142913,0.000850733,0.072248020,0.118559606,0.000000000],[0.069829572,0.106326511,0.000850733,0.127871676,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G62 - U63 cSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.982558140,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.005813953,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.005813953,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.005813953,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A64
Sequences of instances from HL_73266.3:
> HL_73266.3 HL_4FEN_003 A   59 U   67
ACCGUAAAU
> HL_73266.3 HL_1Y27_003 A   59 U   67
ACCGUAAAU
> HL_73266.3 HL_4LX6_003 G   59 C   67
GCCUUAAAC
> HL_73266.3 HL_5SWD_006 G   59 C   67
GCCUUAAAC
> HL_73266.3 HL_3LA5_003 G   59 C   67
GCCUUAAAC
> HL_73266.3 HL_5KPY_002 A   59 U   67
ACCGUAAAU
> HL_73266.3 HL_3RKF_009 A   59 U   67
ACUGUAAAU
> HL_73266.3 HL_4XNR_003 G   59 C   67
GCCUUAAAC
> HL_73266.3 HL_1Y26_003 G   59 C   67
GCCUUAAAC
> HL_73266.3 HL_2ZNI_002 A   31 U   39
ACUCUAAAU
> HL_73266.3 HL_3RG5_010 G   31 C   39
GCUUCAAAC
> HL_73266.3 HL_3RG5_006 G   31 C   39
GCUUCAAAC