Alignment of J4_75852.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for J4_75852.1
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
4
I

6
7

3
7
7
I

8
8


9
7
I

10
7

4
11
6
I

12
12

5
13
12
I

14
13


15
12
I

16
12

6
17
11
I

18
15

7
19
15
I

20
15

8
21
16
I

22
17

9
23
18
I

24
19

10
25
20
I

26
21


27
20
I

28
19

11
29
19
I

30
19

12
31
19
I

32
19

13
33
16
I

34
15

14
35
15
I

36
15

15
37
2
I

38
2

16
39
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
J4_75852.1_Instance_1 J4_75852.1,J4_6DME_001,A4_U99AGUAGUACACGCAAGU
J4_75852.1_Sequence_1 J4_75852.16DME_A4_U99AGU*AG*UACAC*GCAAGUtrue100000.00

Conserved interactions between motif group positions in J4_75852.1:
1 2 s35 
1 16 cWW 
2 7 tSW 
3 4 cWW 
3 5 s55 
4 5 s35 
5 6 cWW 
7 8 s35 
7 15 cSS 
7 16 s55 
8 9 s35 
8 14 cSS 
8 15 cSS 
10 11 cWW 
10 13 s55 
11 12 s35 
11 13 s35 
12 13 cSH 
13 14 s35 
14 15 s35 
7 2 7BR
10 9 7BR
JAR3D SCFG/MRF model for J4_75852.1:
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 [16] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009374836,0.022228469,0.010012528,0.216037101,0.000000000],[0.017691617,0.009675113,0.196088410,0.010461402,0.000000000],[0.009993038,0.198630499,0.002061361,0.053740648,0.000000000],[0.197964449,0.011137350,0.023240462,0.011662716,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [16] // Basepair A4 - U99 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Position [1] | Left Index [2] | Right Index [15] // Fixed node on left for 6DME|1|A|G|5
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [15] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [3] | Right Index [15] // Junction node U6 - G98 ID J1656
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [4] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009123784,0.017718471,0.010008206,0.198264936,0.000000000],[0.022262210,0.009929018,0.198931998,0.011154256,0.000000000],[0.010027726,0.196386049,0.002064490,0.023275738,0.000000000],[0.216349992,0.010477281,0.053822220,0.010203624,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [4] // Basepair U6 - A50 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node type *
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [15] // Initial node 6DME|1|A|G|51 - 6DME|1|A|G|98 from node 
JunctionNode | Branches [2]  | Left Index [5] | Right Index [15] // Junction node G51 - G98 ID J6019
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.015996656,0.299826436,0.014459392,0.085420251,0.000000000],[0.013858629,0.012916026,0.036792527,0.014547577,0.000000000],[0.014149624,0.041974486,0.003276514,0.337552385,0.000000000],[0.036940494,0.015890415,0.014540501,0.041858086,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // Basepair G51 - U68 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node type *
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [7] | Right Index [15] // Initial node
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [2] | Num Right Bases [2] | Left Index [7] | Right Index [15] | Norm Constant [0.048252095780792] // Cluster node 6DME|1|A|A|69:6DME|1|A|C|70 and 6DME|1|A|A|97:6DME|1|A|G|98
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.081591666,0.075904306,0.078139289,0.071822400,0.000000000],[0.095215600,0.083072861,0.003393533,0.041801731,0.000000000],[0.082006787,0.003458357,0.007809038,0.062580800,0.000000000],[0.080836575,0.075094816,0.077291685,0.079980554,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6DME|1|A|C|70 - 6DME|1|A|A|97 cSS 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.173828786,0.180627895,0.197814686,0.177303033,0.000000000],[0.032571318,0.035505529,0.001457077,0.032698461,0.000000000],[0.033345073,0.001425632,0.003230603,0.032957983,0.000000000],[0.030791020,0.004856325,0.025916982,0.035669599,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6DME|1|A|A|69 - 6DME|1|A|G|98 cSS 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.016335130,0.016489982,0.016677901,0.017033014,0.000000000],[0.015784694,0.015949784,0.406733686,0.017273712,0.000000000],[0.015053123,0.370023484,0.014998297,0.014728455,0.000000000],[0.015505195,0.015542350,0.016736198,0.015134995,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6DME|1|A|C|70 - 6DME|1|A|G|98 cSS 
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [13] // Initial node 6DME|1|A|A|71 - 6DME|1|A|A|96 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [9] | Right Index [13] // Fixed node on left for 6DME|1|A|A|71
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [13] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [1] | Num Right Bases [3] | Left Index [10] | Right Index [13] | Norm Constant [1.000000000000000] // Cluster node 6DME|1|A|C|72:6DME|1|A|C|72 and 6DME|1|A|G|94:6DME|1|A|A|96
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.004741436,0.008502533,0.005450864,0.098834917,0.000000000],[0.050405519,0.024145075,0.529397411,0.034282440,0.000000000],[0.005512079,0.100964543,0.001038993,0.011667026,0.000000000],[0.100116212,0.006606094,0.013310241,0.005024617,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6DME|1|A|C|72 - 6DME|1|A|G|94 cWW 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.110380675,0.105269562,0.005717769,0.037273020,0.000000000],[0.130005463,0.104189678,0.001201045,0.010129477,0.000000000],[0.010623361,0.001201045,0.098039136,0.072282348,0.000000000],[0.112884724,0.103241206,0.001201045,0.096360446,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6DME|1|A|C|95 - 6DME|1|A|A|96 cSH 
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [11] | Right Index [10] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [11] | Right Index [11] | Norm Constant [1.000000000000000] // Hairpin node type *
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation
Sequences of instances from J4_75852.1:
> J4_75852.1  6DME A    4 U   99
AGU*AG*UACAC*GCAAGU