Alignment of J4_12209.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for J4_12209.1
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
7

2
5
7
I

6
7

3
7
7
I

8
7

4
9
7
I

10
7

5
11
7
I

12
7

6
13
7
I

14
7

7
15
7
I

16
7

8
17
7
I

18
7

9
19
7
I

20
7

10
21
8
I

22
9

11
23
10
I

24
13

12
25
13
I

26
13

13
27
14
I

28
15


29
14
I

30
13

14
31
12
I

32
11

15
33
8
I

34
7

16
35
7
I

36
7

17
37
7
I

38
7

18
39
7
I

40
7

19
41
7
I

42
7

20
43
6
I

44
17

21
45
18
I

46
21

22
47
21
I

48
22


49
21
I

50
21

23
51
20
I

52
24

24
53
24
I

54
25


55
24
I

56
24

25
57
4
I

58
3

26
59
2
I

60
2

27
61
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
J4_12209.1_Instance_1 J4_12209.1,J4_1U9S_002,C119_G222CACAGAGAAGAGACGGUGAAACGCGCACG
J4_12209.1_Sequence_1 J4_12209.11U9S_C119_G222CACAGAGAAGAGAC*GGUGAAACG*CG*CACGtrue100000.00

Conserved interactions between motif group positions in J4_12209.1:
1 19 tSS 
1 27 cWW 
2 3 s35 
2 18 tHH 
3 4 s35 
4 5 s35 
4 8 tWH 
4 16 cSS 
5 20 tSW 
6 7 s35 
6 13 s55 
7 10 cSS 
7 20 s33 
8 17 tWS 
8 19 s33 
8 20 s55 
9 21 s55 
9 27 s35 
10 11 s35 
10 20 tSS 
10 21 s53 
12 13 cSH 
13 14 cWW 
14 15 s35 
15 16 s35 
16 17 s35 
16 20 tWH 
17 19 s33 
17 20 s55 
18 19 s35 
22 23 cWW 
22 24 s55 
23 24 s35 
24 25 cWW 
3 2 7BPh
19 2 6BPh
5 8 6BPh
17 20 6BPh
18 1 6BR
21 10 6BR
13 12 7BR
3 17 6BR
19 17 7BR
26 25 7BR
JAR3D SCFG/MRF model for J4_12209.1:
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 [27] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | 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]] | 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 [27] // Basepair C119 - G222 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.785714286,0.071428571,0.071428571,0.000000000] | Position [2] | Left Index [2] | Right Index [26] // Fixed node on right for 1U9S|1|A|C|219
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [2] | Right Index [25] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [2] | Right Index [25] // Junction node A120 - C219 ID J4217
InitialNode  | Left Length Distribution [1.000000000] | 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 [20] // Initial node 1U9S|1|A|A|120 - 1U9S|1|A|A|174 from node 
ClusterNode  | Deletion Probability [0.000000000000000000000000000000000029793021831941294771334241] | Num Left Bases [9] | Num Right Bases [5] | Left Index [2] | Right Index [20] | Norm Constant [0.001190246544109] // Cluster node 1U9S|1|A|A|120:1U9S|1|A|A|129 and 1U9S|1|A|U|170:1U9S|1|A|A|174
Interaction  | Interacting Bases [3,10] | Pair Probability [[0.076146696,0.078906659,0.078575452,0.093178774,0.000000000],[0.074822471,0.079495189,0.003326749,0.073057805,0.000000000],[0.076666471,0.003253861,0.009031637,0.075892455,0.000000000],[0.069121724,0.064122585,0.069548293,0.074853180,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|A|122 - 1U9S|1|A|U|170 cSS 
Interaction  | Interacting Bases [7,11] | Pair Probability [[0.071773872,0.083480414,0.634367958,0.077201799,0.000000000],[0.071430006,0.003933530,0.006244670,0.003877011,0.000000000],[0.000892096,0.000892096,0.006244670,0.007019357,0.000000000],[0.004313658,0.003566586,0.020478373,0.004283906,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|A|126 - 1U9S|1|A|G|171 tWS 
Interaction  | Interacting Bases [1,12] | Pair Probability [[0.383941828,0.060098347,0.003586629,0.003659217,0.000000000],[0.329063595,0.000748082,0.063774503,0.007108337,0.000000000],[0.018648642,0.062959472,0.001867211,0.000748082,0.000000000],[0.025405115,0.036894776,0.000748082,0.000748082,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|A|120 - 1U9S|1|A|A|172 tHH 
Interaction  | Interacting Bases [4,14] | Pair Probability [[0.071773872,0.071430006,0.000892096,0.004313658,0.000000000],[0.083480414,0.003933530,0.000892096,0.003566586,0.000000000],[0.634367958,0.006244670,0.006244670,0.020478373,0.000000000],[0.077201799,0.003877011,0.007019357,0.004283906,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|G|123 - 1U9S|1|A|A|174 tSW 
Interaction  | Interacting Bases [9,14] | Pair Probability [[0.207494268,0.188108213,0.192542081,0.181451180,0.000000000],[0.001975933,0.001975933,0.020316853,0.001975933,0.000000000],[0.016360862,0.001975933,0.016877025,0.161042056,0.000000000],[0.001975933,0.001975933,0.001975933,0.001975933,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|A|129 - 1U9S|1|A|A|174 tSS 
Interaction  | Interacting Bases [3,7] | Pair Probability [[0.375057930,0.003651569,0.322134033,0.003651569,0.000000000],[0.031255259,0.015495970,0.003651569,0.003651569,0.000000000],[0.003651569,0.009045434,0.134222277,0.039085253,0.000000000],[0.016500420,0.003651569,0.017501970,0.017792036,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|A|122 - 1U9S|1|A|A|126 tWH 
Interaction  | Interacting Bases [6,9] | Pair Probability [[0.083071528,0.077827995,0.079676854,0.073574035,0.000000000],[0.086320773,0.084839186,0.003406498,0.011604013,0.000000000],[0.099703595,0.003481632,0.007719409,0.061927698,0.000000000],[0.084731846,0.078131797,0.078751916,0.085231224,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|G|125 - 1U9S|1|A|A|129 cSS 
Interaction  | Interacting Bases [10,14] | Pair Probability [[0.018961504,0.004196211,0.019694625,0.004196211,0.000000000],[0.042198433,0.338134433,0.004196211,0.004196211,0.000000000],[0.004196211,0.010058595,0.031911832,0.018663303,0.000000000],[0.429522110,0.004196211,0.024345914,0.041331983,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|U|170 - 1U9S|1|A|A|174 tWH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.013513514,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.959459459,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.013513514,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.013513514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 1U9S|1|A|C|121
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 1U9S|1|A|A|124
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 1U9S|1|A|A|127
Interaction  | Interacting Bases [13,13] | Pair Probability [[0.959459459,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.013513514,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.013513514,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.013513514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 1U9S|1|A|A|173
Insertion    | Location [8] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000]// Insertion after nucleotide 9, position 8 in cluster node
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 [15] // Initial node 1U9S|1|A|G|130 - 1U9S|1|A|G|169 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Position [1] | Left Index [11] | Right Index [15] // Fixed node on left for 1U9S|1|A|A|129
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 [12] | Right Index [15] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Position [2] | Left Index [12] | Right Index [15] // Fixed node on right for 1U9S|1|A|G|168
InitialNode  | Left Length Distribution [1.000000000] | 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 [12] | Right Index [14] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [12] | Right Index [14] | Norm Constant [0.290489050332303] // Cluster node 1U9S|1|A|A|131:1U9S|1|A|C|132 and 1U9S|1|A|G|168:1U9S|1|A|G|168
Interaction  | Interacting Bases [2,3] | 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 1U9S|1|A|C|132 - 1U9S|1|A|G|168 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.104166825,0.124612443,0.005621093,0.043860124,0.000000000],[0.100542670,0.099286043,0.001147115,0.009317734,0.000000000],[0.010004306,0.001147115,0.104180479,0.094225112,0.000000000],[0.104547355,0.103291070,0.001147115,0.092903402,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|A|131 - 1U9S|1|A|C|132 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 [14] | Right Index [13] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [14] | Right Index [14] | 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 [21] | Right Index [25] // Initial node 1U9S|1|A|C|175 - 1U9S|1|A|C|219 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.785714286,0.071428571,0.071428571,0.000000000] | Position [1] | Left Index [21] | Right Index [25] // Fixed node on left for 1U9S|1|A|A|174
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 [22] | Right Index [25] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [22] | Right Index [25] // Junction node G176 - C219 ID J9157
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 [22] | Right Index [23] // Initial node
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 [22] | Right Index [23] // Basepair G176 - C194 cWW 
HairpinNode  | Num Bases [1] | Left Index [23] | Right Index [23] | 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 [24] | Right Index [25] // Initial node
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 [24] | Right Index [25] // Basepair G195 - C219 cWW 
HairpinNode  | Num Bases [1] | Left Index [25] | Right Index [25] | 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_12209.1:
> J4_12209.1  1U9S C  119 G  222
CACAGAGAAGAGAC*GGUGAAACG*CG*CACG