Alignment of HL_67407.5 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_67407.5
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
3

3
7
3
I

8
3

4
9
3
I

10
3

5
11
3
I

12
3

6
13
3
I

14
3

7
15
3
I

16
3

8
17
3
I

18
3

9
19
2
I

20
2

10
21
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
HL_67407.5_Instance_1 HL_67407.5,HL_9BZC_003,C77_G87CGACCGUCUGG
HL_67407.5_Sequence_1 HL_67407.59BZC_C77_G87CGACCGUCUGGtrue97000.62
HL_67407.5_Instance_2 HL_67407.5,HL_4XWF_002,C50_G60CGCCCGCCUGG
HL_67407.5_Sequence_2 HL_67407.54XWF_C50_G60CGCCCGCCUGGtrue94001.10
HL_67407.5_Instance_3 HL_67407.5,HL_4ZNP_002,C58_G68CGACCGCCUGG
HL_67407.5_Sequence_3 HL_67407.54ZNP_C58_G68CGACCGCCUGGtrue100000.00
HL_67407.5_Instance_4 HL_67407.5,HL_8VVJ_002,C50_G60CGCCCGCCUGG
HL_67407.5_Sequence_4 HL_67407.58VVJ_C50_G60CGCCCGCCUGGtrue94001.10
HL_67407.5_Instance_5 HL_67407.5,HL_4PJO_001,G17_C27GAGGUGCACAC
HL_67407.5_Sequence_5 HL_67407.54PJO_G17_C27GAGGUGCACACtrue75004.92
HL_67407.5_Instance_6 HL_67407.5,HL_7JRT_003,G35_C45GAAGCUCGCAC
HL_67407.5_Sequence_6 HL_67407.57JRT_G35_C45GAAGCUCGCACtrue92001.57
HL_67407.5_Instance_7 HL_67407.5,HL_5BTP_004,C62_G72CGACCGUCUGG
HL_67407.5_Sequence_7 HL_67407.55BTP_C62_G72CGACCGUCUGGtrue97000.62
HL_67407.5_Instance_8 HL_67407.5,HL_7JRS_002,G63_C73GAAGCAGGCAC
HL_67407.5_Sequence_8 HL_67407.57JRS_G63_C73GAAGCAGGCACtrue82003.55
HL_67407.5_Instance_9 HL_67407.5,HL_7JRT_002,G102_C112GAAGCCUCCAC
HL_67407.5_Sequence_9 HL_67407.57JRT_G102_C112GAAGCCUCCACtrue89002.09
HL_67407.5_Instance_10 HL_67407.5,HL_7JRT_001,G35_C45GAAGCUCGCAC
HL_67407.5_Sequence_10 HL_67407.57JRT_G35_C45GAAGCUCGCACtrue92001.57

Conserved interactions between motif group positions in HL_67407.5:
1 2 s33 
1 10 cWW 
2 10 s35 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
9 10 s35
JAR3D SCFG/MRF model for HL_67407.5:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [10] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008934398,0.017327562,0.010222045,0.185505595,0.000000000],[0.017327896,0.008928520,0.236473696,0.012552788,0.000000000],[0.010222058,0.236473075,0.001937552,0.023289094,0.000000000],[0.185505866,0.012552735,0.023289441,0.009457677,0.000000000],[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 [10] // Basepair C77 - G87 cWW 
HairpinNode  | Num Bases [8] | Left Index [2] | Right Index [9] | Norm Constant [0.999999999999999] // Hairpin node G78:G86
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.458333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.458333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G78
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.041666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.458333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.458333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C80
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.041666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.791666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[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 C81
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.541666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.208333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G82
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.041666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.541666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.291666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U83
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.541666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.291666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C84
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.041666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.458333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.458333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U85
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.458333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.458333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G86
Insertion    | Location [1] | Length Distribution [0.004949270,0.989853997,0.004949270,0.000247463] | Letter Distribution [0.625000000,0.208333333,0.125000000,0.041666667,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_67407.5:
> HL_67407.5  9BZC C   77 G   87
CGACCGUCUGG
> HL_67407.5  4XWF C   50 G   60
CGCCCGCCUGG
> HL_67407.5  4ZNP C   58 G   68
CGACCGCCUGG
> HL_67407.5  8VVJ C   50 G   60
CGCCCGCCUGG
> HL_67407.5  4PJO G   17 C   27
GAGGUGCACAC
> HL_67407.5  7JRT G   35 C   45
GAAGCUCGCAC
> HL_67407.5  5BTP C   62 G   72
CGACCGUCUGG
> HL_67407.5  7JRS G   63 C   73
GAAGCAGGCAC
> HL_67407.5  7JRT G  102 C  112
GAAGCCUCCAC
> HL_67407.5  7JRT G   35 C   45
GAAGCUCGCAC