Alignment of J4_19572.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for J4_19572.1
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
24

25
55
25
I

56
26


57
25
I

58
24

26
59
24
I

60
24

27
61
24
I

62
24

28
63
24
I

64
24

29
65
4
I

66
3

30
67
2
I

68
2

31
69
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
J4_19572.1_Instance_1 J4_19572.1,J4_1U9S_003,C119_G222CACAGAGAAGAGACGGUGAAACGCGCGGCACG
J4_19572.1_Sequence_1 J4_19572.11U9S_C119_G222CACAGAGAAGAGAC*GGUGAAACG*CGC*GGCACGtrue100000.00

Conserved interactions between motif group positions in J4_19572.1:
1 19 tSS 
1 31 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 31 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 
22 27 cHW 
23 24 s35 
24 25 s35 
24 28 cWW 
25 26 cWW 
26 28 s35 
26 29 cSW 
27 28 s53 
29 30 perp 
3 2 7BPh
19 2 6BPh
5 8 6BPh
17 20 6BPh
30 29 7BPh
18 1 6BR
21 10 6BR
13 12 7BR
3 17 6BR
19 17 7BR
30 28 7BR
JAR3D SCFG/MRF model for J4_19572.1:
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 [31] // 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 [31] // Basepair C119 - G222 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.833333333,0.055555556,0.055555556,0.000000000] | Position [2] | Left Index [2] | Right Index [30] // Fixed node on right for 1U9S|1|A|A|220
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 [29] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [2] | Right Index [29] // Junction node A120 - A220 ID J6557
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 [29] // Initial node 1U9S|1|A|C|175 - 1U9S|1|A|A|220 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 [29] // 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 [29] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [22] | Right Index [29] // Junction node G176 - A220 ID J357
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 [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [24] | Right Index [29] // Initial node 1U9S|1|A|G|195 - 1U9S|1|A|A|220 from node 
ClusterNode  | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [2] | Num Right Bases [4] | Left Index [24] | Right Index [29] | Norm Constant [0.250280977299386] // Cluster node 1U9S|1|A|G|195:1U9S|1|A|C|196 and 1U9S|1|A|G|217:1U9S|1|A|A|220
Interaction  | Interacting Bases [2,3] | 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 1U9S|1|A|C|196 - 1U9S|1|A|G|217 cWW 
Interaction  | Interacting Bases [1,5] | 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]] // Cluster Interaction 1U9S|1|A|G|195 - 1U9S|1|A|C|219 cWW 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.218661090,0.014620617,0.019969329,0.007807710,0.000000000],[0.206663216,0.011999471,0.002249461,0.008266368,0.000000000],[0.234847085,0.002249461,0.027362667,0.006356246,0.000000000],[0.208475927,0.012213416,0.010584145,0.007673792,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|G|217 - 1U9S|1|A|A|220 cSW 
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 1U9S|1|A|G|218
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 [26] | Right Index [25] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [26] | Right Index [26] | 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_19572.1:
> J4_19572.1  1U9S C  119 G  222
CACAGAGAAGAGAC*GGUGAAACG*CGC*GGCACG