Alignment of HL_46465.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_46465.1
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
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
3
I

20
3

10
21
3
I

22
3


23
4
I

24
5

11
25
4
I

26
3

12
27
3
I

28
3

13
29
3
I

30
3

14
31
3
I

32
3

15
33
3
I

34
3

16
35
3
I

36
3

17
37
3
I

38
3

18
39
3
I

40
3

19
41
3
I

42
3

20
43
3
I

44
3

21
45
2
I

46
2

22
47
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_46465.1_Instance_1 HL_46465.1_HL_6E8S_001_A8_U31AGGAAGGAUUGGUAUGUGGUAUAU
HL_46465.1_Sequence_1 HL_46465.1_HL_6E8S_001_A8_U31AGGAAGGAUUGGUAUGUGGUAUAUtrue96000.98
HL_46465.1_Instance_2 HL_46465.1_HL_6E8T_001_A7_U30AGGAAGGUUUGGUAUGUGGUAUAU
HL_46465.1_Sequence_2 HL_46465.1_HL_6E8T_001_A7_U30AGGAAGGUUUGGUAUGUGGUAUAUtrue100000.00

Conserved interactions between motif group positions in HL_46465.1:
1 15 s33 
1 22 cWW 
2 3 s35 
2 4 s53 
2 5 cWH 
2 14 s35 
2 15 s55 
2 16 cHW 
3 5 s53 
3 6 cWH 
3 14 cHW 
4 5 s35 
5 6 s35 
5 9 cWH 
6 8 perp 
6 9 s53 
6 10 cWH 
7 8 perp 
7 13 tWW 
9 10 s35 
9 16 cWH 
9 21 s55 
10 14 cWH 
11 12 s35 
11 18 tWW 
11 19 s35 
12 17 s35 
12 18 s53 
12 19 tHH 
14 16 s53 
15 16 s55 
15 21 tSW 
16 17 s33 
16 21 s55 
17 20 cSH 
19 20 s35 
21 22 s35 
12 19 6BPh
6 8 2BR
16 15 2BR
21 16 7BR
JAR3D SCFG/MRF model for HL_46465.1:
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 [22] // Initial node A8 - U31 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 [22] // Basepair A8 - U31 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000000000000000000000000000000000002324854825] | Num Left Bases [10] | Num Right Bases [10] | Left Index [2] | Right Index [21] | Norm Constant [0.021746083431234] // Cluster node G9:U20 and A21:A30
Interaction  | Interacting Bases [6,12] | Pair Probability [[0.021092272,0.036425574,0.004478161,0.208014926,0.000000000],[0.031991796,0.034671284,0.016991909,0.034459906,0.000000000],[0.004478161,0.017978475,0.021445131,0.163657287,0.000000000],[0.043876651,0.031832799,0.038700931,0.289904738,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A15 - U22 tWW 
Interaction  | Interacting Bases [2,13] | Pair Probability [[0.004917740,0.004917740,0.204479002,0.016996810,0.000000000],[0.004917740,0.052126028,0.004917740,0.004917740,0.000000000],[0.050576271,0.004917740,0.511381834,0.015383823,0.000000000],[0.041662297,0.017736492,0.004917740,0.055233263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G10 - G23 cHW 
Interaction  | Interacting Bases [9,13] | Pair Probability [[0.004917740,0.004917740,0.050576271,0.041662297,0.000000000],[0.004917740,0.052126028,0.004917740,0.017736492,0.000000000],[0.204479002,0.004917740,0.511381834,0.004917740,0.000000000],[0.016996810,0.004917740,0.015383823,0.055233263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G19 - G23 cWH 
Interaction  | Interacting Bases [1,15] | Pair Probability [[0.001267184,0.001267184,0.263446768,0.004379672,0.000000000],[0.001267184,0.013431632,0.006335920,0.001267184,0.000000000],[0.013032297,0.001267184,0.653199885,0.003964044,0.000000000],[0.010735378,0.004570270,0.006335920,0.014232292,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G9 - G25 cHW 
Interaction  | Interacting Bases [8,15] | Pair Probability [[0.001492205,0.001492205,0.076732572,0.012641719,0.000000000],[0.001492205,0.015816762,0.007461025,0.005381839,0.000000000],[0.062045696,0.001492205,0.765710357,0.001492205,0.000000000],[0.005157395,0.001492205,0.023339805,0.016759600,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G18 - G25 cWH 
Interaction  | Interacting Bases [10,17] | Pair Probability [[0.024978059,0.030331969,0.005356900,0.036479807,0.000000000],[0.047086784,0.030567281,0.018993974,0.027347187,0.000000000],[0.005356900,0.018115093,0.025662695,0.038984076,0.000000000],[0.046635242,0.029148575,0.059657587,0.555297871,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U20 - U27 tWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.004917740,0.004917740,0.050576271,0.041662297,0.000000000],[0.004917740,0.052126028,0.004917740,0.017736492,0.000000000],[0.204479002,0.004917740,0.511381834,0.004917740,0.000000000],[0.016996810,0.004917740,0.015383823,0.055233263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G9 - G13 cWH 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.001492205,0.001492205,0.076732572,0.012641719,0.000000000],[0.001492205,0.015816762,0.007461025,0.005381839,0.000000000],[0.062045696,0.001492205,0.765710357,0.001492205,0.000000000],[0.005157395,0.001492205,0.023339805,0.016759600,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G10 - G14 cWH 
Interaction  | Interacting Bases [4,8] | Pair Probability [[0.004917740,0.004917740,0.050576271,0.041662297,0.000000000],[0.004917740,0.052126028,0.004917740,0.017736492,0.000000000],[0.204479002,0.004917740,0.511381834,0.004917740,0.000000000],[0.016996810,0.004917740,0.015383823,0.055233263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G13 - G18 cWH 
Interaction  | Interacting Bases [5,9] | Pair Probability [[0.001267184,0.001267184,0.013032297,0.010735378,0.000000000],[0.001267184,0.013431632,0.001267184,0.004570270,0.000000000],[0.263446768,0.006335920,0.653199885,0.006335920,0.000000000],[0.004379672,0.001267184,0.003964044,0.014232292,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G14 - G19 cWH 
Interaction  | Interacting Bases [11,18] | Pair Probability [[0.431873884,0.331200569,0.019765828,0.020165858,0.000000000],[0.051813191,0.000588951,0.050208540,0.005596268,0.000000000],[0.002936349,0.049566880,0.001470022,0.000588951,0.000000000],[0.004000200,0.029046605,0.000588951,0.000588951,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A21 - A28 tHH 
Interaction  | Interacting Bases [16,19] | Pair Probability [[0.079296878,0.080799881,0.004442628,0.078964610,0.000000000],[0.059200300,0.089215891,0.000983673,0.079130149,0.000000000],[0.069281848,0.000983673,0.084512044,0.117975163,0.000000000],[0.080527243,0.080043827,0.000983673,0.093658519,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G26 - U29 cSH 
Interaction  | Interacting Bases [14,20] | Pair Probability [[0.233349860,0.004938038,0.000525442,0.002449099,0.000000000],[0.233744771,0.002515764,0.000525442,0.002092228,0.000000000],[0.227358206,0.000525442,0.000525442,0.001662399,0.000000000],[0.282328755,0.002403502,0.002606074,0.002449536,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U24 - A30 tSW 
Interaction  | Interacting Bases [3,3] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A12
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion U17
Insertion    | Location [2] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 3, position 2 in cluster node
Insertion    | Location [6] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion after nucleotide 7, position 6 in cluster node
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 [12] | Right Index [11] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [11] | Right Index [11] | Norm Constant [1.000000000000000] // Hairpin node U20:U20
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U20
Sequences of instances from HL_46465.1:
> HL_46465.1 HL_6E8S_001 A    8 U   31
AGGAAGGAUUGGUAUGUGGUAUAU
> HL_46465.1 HL_6E8T_001 A    7 U   30
AGGAAGGUUUGGUAUGUGGUAUAU