Alignment of J3_72575.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for J3_72575.1
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
6

3
7
6
I

8
7

4
9
7
I

10
8


11
7
I

12
7

5
13
6
I

14
6

6
15
5
I

16
10

7
17
10
I

18
10

8
19
10
I

20
10

9
21
10
I

22
10

10
23
11
I

24
12


25
11
I

26
10

11
27
3
I

28
3

12
29
2
I

30
2

13
31
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
J3_72575.1_Instance_1 J3_72575.1,J3_3NDB_001,G145_C233GGUGCUUUACGAC
J3_72575.1_Sequence_1 J3_72575.13NDB_G145_C233GGUG*CUUUAC*GACtrue100000.00

Conserved interactions between motif group positions in J3_72575.1:
1 2 s35 
1 8 tSW 
1 13 cWW 
2 10 s35 
2 12 cWW 
3 4 s35 
3 6 cWW 
3 7 s55 
4 5 cWW 
4 6 s55 
5 6 s35 
6 7 s35 
7 9 tSS 
8 9 s33 
8 13 cSS 
10 11 cWW 
11 12 s35 
12 13 s35 
3 10 7BPh
7 10 6BPh
JAR3D SCFG/MRF model for J3_72575.1:
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 [13] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009830065,0.020472507,0.011193821,0.203314028,0.000000000],[0.017266777,0.009639366,0.205036802,0.013415526,0.000000000],[0.011069507,0.220897605,0.002109966,0.027030175,0.000000000],[0.200711998,0.013924020,0.023693165,0.010394672,0.000000000],[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 [13] // Basepair G145 - C233 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.023164190,0.014489905,0.351490869,0.017735478,0.000000000],[0.014838319,0.010255708,0.019408962,0.045569652,0.000000000],[0.375747942,0.019193415,0.003658470,0.015799099,0.000000000],[0.017770069,0.043129315,0.016144978,0.011603631,0.000000000],[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 [2] | Right Index [12] // Basepair G146 - A232 cWW 
JunctionNode | Branches [2]  | Left Index [3] | Right Index [11] // Junction node U147 - G231 ID J5852
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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.003956608,0.072569007,0.003532583,0.006169878,0.000000000],[0.004372991,0.004715165,0.005273772,0.003877960,0.000000000],[0.003458800,0.005372374,0.001090513,0.013931514,0.000000000],[0.037728597,0.029398796,0.031291148,0.773260294,0.000000000],[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 [3] | Right Index [6] // Basepair U147 - U183 cWW 
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009830065,0.020472507,0.011193821,0.203314028,0.000000000],[0.017266777,0.009639366,0.205036802,0.013415526,0.000000000],[0.011069507,0.220897605,0.002109966,0.027030175,0.000000000],[0.200711998,0.013924020,0.023693165,0.010394672,0.000000000],[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 [4] | Right Index [5] // Basepair G148 - C182 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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 [7] | Right Index [11] // Initial node 3NDB|1|M|U|184 - 3NDB|1|M|G|231 from node 
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [7] | Right Index [11] | Norm Constant [1.000000000000000] // Cluster node 3NDB|1|M|U|184:3NDB|1|M|C|187 and 3NDB|1|M|G|231:3NDB|1|M|G|231
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3NDB|1|M|C|187 - 3NDB|1|M|G|231 cWW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.024752475,0.024752475,0.024752475,0.024752475,0.000000000],[0.024752475,0.024752475,0.024752475,0.024752475,0.000000000],[0.024752475,0.024752475,0.024752475,0.024752475,0.000000000],[0.183168317,0.173267327,0.173267327,0.173267327,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3NDB|1|M|U|184 - 3NDB|1|M|A|186 tSS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3NDB|1|M|U|185
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 J3_72575.1:
> J3_72575.1  3NDB G  145 C  233
GGUG*CUUUAC*GAC