Alignment of J3_79305.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for J3_79305.1
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
2

2
5
2
I

6
2

3
7
2
I

8
2

4
9
2
I

10
2

5
11
2
I

12
2

6
13
2
I

14
2

7
15
2
I

16
2

8
17
3
I

18
6

9
19
6
I

20
7


21
6
I

22
6

10
23
5
I

24
9

11
25
10
I

26
11

12
27
11
I

28
12


29
11
I

30
11

13
31
3
I

32
2

14
33
2
I

34
2

15
35
2
I

36
2

16
37
2
I

38
2

17
39
2
I

40
2

18
41
2
I

42
2

19
43
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
J3_79305.1_Instance_1 J3_79305.1,J3_6CZR_025,G1157_C1144GAGGAAGGAGCGCGGACUGC
J3_79305.1_Sequence_1 J3_79305.16CZR_G_1157_C_1144GAGGAAGGAG*CGC*GGACUGCtrue100000.00

Conserved interactions between motif group positions in J3_79305.1:
1 2 s35 
1 19 cWW 
2 3 s35 
2 18 cWW 
3 4 s35 
3 7 tWH 
4 15 tSW 
5 6 s35 
5 12 s55 
5 14 tWS 
6 15 s33 
7 8 s35 
7 15 s55 
7 18 s35 
8 17 s35 
8 18 cWH 
9 10 cWW 
9 11 s55 
10 11 s35 
12 13 cWW 
13 14 s35 
16 18 s35 
17 19 cSH 
18 19 s35 
4 7 6BPh
6 4 7BR
17 8 7BR
5 11 2BR
JAR3D SCFG/MRF model for J3_79305.1:
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 [19] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000000000000000006103515625000001877100676877] | Num Left Bases [8] | Num Right Bases [6] | Left Index [1] | Right Index [19] | Norm Constant [0.088576807035806] // Cluster node 6CZR|1|1a|G|1157:6CZR|1|1a|G|1164 and 6CZR|1|1a|G|1139:6CZR|1|1a|C|1144
Interaction  | Interacting Bases [5,9] | Pair Probability [[0.207393546,0.241220078,0.267675690,0.223077762,0.000000000],[0.041279986,0.002273219,0.000515549,0.002240557,0.000000000],[0.000515549,0.000515549,0.000515549,0.004056544,0.000000000],[0.002492898,0.002061159,0.001690660,0.002475704,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6CZR|1|1a|A|1161 - 6CZR|1|1a|G|1139 tWS 
Interaction  | Interacting Bases [4,10] | 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 6CZR|1|1a|G|1160 - 6CZR|1|1a|A|1140 tSW 
Interaction  | Interacting Bases [2,13] | Pair Probability [[0.030079776,0.014734320,0.373183812,0.017645523,0.000000000],[0.014388349,0.009799453,0.019058893,0.042827032,0.000000000],[0.349027357,0.019272929,0.003632828,0.016031822,0.000000000],[0.017611175,0.045250265,0.015688367,0.011768099,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6CZR|1|1a|A|1158 - 6CZR|1|1a|G|1143 cWW 
Interaction  | Interacting Bases [8,13] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6CZR|1|1a|G|1164 - 6CZR|1|1a|G|1143 cWH 
Interaction  | Interacting Bases [1,14] | 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 6CZR|1|1a|G|1157 - 6CZR|1|1a|C|1144 cWW 
Interaction  | Interacting Bases [3,7] | Pair Probability [[0.172874286,0.004703112,0.090279950,0.004703112,0.000000000],[0.042292986,0.028858025,0.004703112,0.004703112,0.000000000],[0.004703112,0.007289268,0.480212228,0.047363501,0.000000000],[0.035766773,0.004703112,0.036599675,0.030244634,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6CZR|1|1a|G|1159 - 6CZR|1|1a|G|1163 tWH 
Interaction  | Interacting Bases [12,14] | Pair Probability [[0.041984485,0.044993566,0.003911611,0.042848727,0.000000000],[0.042952486,0.043945512,0.000499683,0.005642555,0.000000000],[0.006313110,0.000499683,0.045580696,0.040660379,0.000000000],[0.214399399,0.259742401,0.002498414,0.203527293,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6CZR|1|1a|U|1142 - 6CZR|1|1a|C|1144 cSH 
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.785714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 6CZR|1|1a|A|1162
Interaction  | Interacting Bases [11,11] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 6CZR|1|1a|C|1141
InitialNode  | Left Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | 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 6CZR|1|1a|G|1166 - 6CZR|1|1a|G|1138 from node 
JunctionNode | Branches [2]  | Left Index [9] | Right Index [13] // Junction node G1166 - G1138 ID J2550
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 [9] | Right Index [10] // 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 [9] | Right Index [10] // Basepair G1166 - C1099 cWW 
HairpinNode  | Num Bases [1] | Left Index [10] | Right Index [10] | 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 [11] | Right Index [13] // Initial node 6CZR|1|1a|G|1100 - 6CZR|1|1a|G|1138 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 [13] // Fixed node on left for 6CZR|1|1a|G|1157
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 [13] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224863733088] | 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 [0.990049834,0.009900498,0.000049502,0.000000165] | 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 [12] | Right Index [13] // Basepair C1101 - G1138 cWW 
HairpinNode  | Num Bases [1] | Left Index [13] | Right Index [13] | 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_79305.1:
> J3_79305.1  6CZR G 1157 C 1144
GAGGAAGGAG*CGC*GGACUGC