Alignment of HL_13971.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_13971.1
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
2

2
5
2
I

6
2

3
7
2
I

8
2

4
9
3
I

10
4

5
11
4
I

12
4

6
13
4
I

14
4

7
15
5
I

16
6

8
17
6
I

18
6

9
19
5
I

20
4

10
21
4
I

22
4

11
23
4
I

24
4

12
25
4
I

26
4

13
27
3
I

28
2

14
29
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
HL_13971.1_Instance_1 HL_13971.1,HL_8P9A_183,U32_A45UUCCCGUCCGAUCA
HL_13971.1_Sequence_1 HL_13971.18P9A_U32_A45UUCCCGUCCGAUCAtrue100000.00
HL_13971.1_Instance_2 HL_13971.1,HL_8OI5_068,U32_A45UCCCCGUUCGAUCA
HL_13971.1_Sequence_2 HL_13971.18OI5_U32_A45UCCCCGUUCGAUCAtrue100000.00

Conserved interactions between motif group positions in HL_13971.1:
1 10 s33 
1 14 cWW 
2 3 s35 
4 5 s35 
4 14 cWS 
5 10 cWW 
6 7 s35 
6 10 s55 
6 12 tSH 
7 11 tSH 
8 9 s35 
9 11 s35 
10 13 tSW 
10 14 s35 
11 12 s35 
12 13 s35 
7 10 6BPh
2 1 7BR
11 7 6BR
6 10 6BR
JAR3D SCFG/MRF model for HL_13971.1:
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 [14] // Initial node
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [1] | Right Index [14] | Norm Constant [0.247842822744946] // Cluster node 8P9A|1|AS|U|32:8P9A|1|AS|C|35 and 8P9A|1|AS|A|45:8P9A|1|AS|A|45
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.009034335,0.017544761,0.009910087,0.196321162,0.000000000],[0.022043953,0.009831675,0.196981684,0.011044900,0.000000000],[0.009929415,0.194460696,0.002044250,0.023047545,0.000000000],[0.224032836,0.010374563,0.053294552,0.010103588,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AS|U|32 - 8P9A|1|AS|A|45 cWW 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.019131699,0.023254427,0.016919571,0.023247238,0.000000000],[0.279924596,0.244907340,0.002603168,0.248178480,0.000000000],[0.029116086,0.002603168,0.029305409,0.011062145,0.000000000],[0.016861330,0.025287480,0.012107149,0.015490714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AS|C|35 - 8P9A|1|AS|A|45 cWS 
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],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.458333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8P9A|1|AS|U|33
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.625000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8P9A|1|AS|C|34
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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [13] // Initial node 8P9A|1|AS|C|36 - 8P9A|1|AS|C|44 from node 
ClusterNode  | Deletion Probability [0.000000000000000078125000000000012233710187403301545271878291] | Num Left Bases [3] | Num Right Bases [4] | Left Index [5] | Right Index [13] | Norm Constant [0.262985860300064] // Cluster node 8P9A|1|AS|C|36:8P9A|1|AS|U|38 and 8P9A|1|AS|G|41:8P9A|1|AS|C|44
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AS|C|36 - 8P9A|1|AS|G|41 cWW 
Interaction  | Interacting Bases [3,5] | Pair Probability [[0.046466913,0.042443055,0.000516033,0.002538474,0.000000000],[0.046646417,0.043889779,0.000516033,0.000516033,0.000000000],[0.047985257,0.000516033,0.003189341,0.042840359,0.000000000],[0.380831186,0.333880619,0.003612233,0.003612233,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AS|U|38 - 8P9A|1|AS|A|42 tSH 
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.018231098,0.023015437,0.000835306,0.005069496,0.000000000],[0.010574938,0.010398335,0.000835306,0.000835306,0.000000000],[0.354488164,0.004176531,0.029925467,0.437260948,0.000000000],[0.069345941,0.033337114,0.000835306,0.000835306,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AS|G|37 - 8P9A|1|AS|U|43 tSH 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.007408683,0.007408683,0.007408683,0.007408683,0.000000000],[0.007408683,0.007408683,0.135802279,0.007408683,0.000000000],[0.007408683,0.760476157,0.007408683,0.007408683,0.000000000],[0.007408683,0.007408683,0.007408683,0.007408683,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AS|G|41 - 8P9A|1|AS|C|44 tSW 
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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [9] // New Initial node after Cluster
HairpinNode  | Num Bases [2] | Left Index [8] | Right Index [9] | Norm Constant [1.000000000000000] // Hairpin node C39:C40
Interaction  | Interacting Bases [1,1] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C39
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.625000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C40
Sequences of instances from HL_13971.1:
> HL_13971.1  8P9A U   32 A   45
UUCCCGUCCGAUCA
> HL_13971.1  8OI5 U   32 A   45
UCCCCGUUCGAUCA