Alignment of IL_65851.3 sequences from 3D to the JAR3D model

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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
4

3
7
4
I

8
4

4
9
5
I

10
6

5
11
6
I

12
7

6
13
7
I

14
8

7
15
8
I

16
9


17
8
I

18
8

8
19
7
I

20
7

9
21
6
I

22
6

10
23
5
I

24
4

11
25
4
I

26
4

12
27
3
I

28
3

13
29
2
I

30
2

14
31
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_65851.3_Instance_1 IL_65851.3,IL_3KTW_004,G201_C222GCCAGGCGAGCAAC
IL_65851.3_Sequence_1 IL_65851.33KTW_G201_C222GCCAGGC*GAGCAACtrue100000.00
IL_65851.3_Instance_2 IL_65851.3,IL_3NDB_008,G200_C221GCCAGGCGAGCAAC
IL_65851.3_Sequence_2 IL_65851.33NDB_G200_C221GCCAGGC*GAGCAACtrue100000.00

Conserved interactions between motif group positions in IL_65851.3:
1 2 s35 
1 14 cWW 
2 3 s35 
2 13 cWW 
3 10 s33 
3 11 tWH 
3 12 tSH 
4 5 s35 
4 11 tHW 
4 12 s55 
5 6 s35 
5 10 tHS 
6 7 s35 
6 9 cWW 
7 8 cWW 
8 9 s35 
9 10 s35 
10 11 s35 
11 12 s35 
12 13 s35 
13 14 s35 
10 4 6BPh
3 11 6BPh
12 3 6BR
JAR3D SCFG/MRF model for IL_65851.3:
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 [14] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Basepair G201 - C222 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.010153793,0.013295259,0.012926971,0.028012001,0.000000000],[0.435119769,0.037265996,0.031668407,0.014435104,0.000000000],[0.013237803,0.026709543,0.003263854,0.013805080,0.000000000],[0.035195420,0.013154930,0.298667921,0.013088150,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [13] // Basepair C202 - A221 cWW 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [2] | Num Right Bases [2] | Left Index [3] | Right Index [12] | Norm Constant [0.257276798587684] // Cluster node 3KTW|1|C|C|203:3KTW|1|C|A|204 and 3KTW|1|C|C|219:3KTW|1|C|A|220
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.004692036,0.001105661,0.005021001,0.001105661,0.000000000],[0.056388190,0.793570728,0.007739629,0.007739629,0.000000000],[0.001105661,0.001610391,0.006784273,0.005207273,0.000000000],[0.089095169,0.001105661,0.004826812,0.012902223,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3KTW|1|C|C|203 - 3KTW|1|C|C|219 tWH 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.030717309,0.378479886,0.003588720,0.036089313,0.000000000],[0.003588720,0.026146144,0.012529247,0.003588720,0.000000000],[0.102662158,0.003588720,0.032271758,0.016134962,0.000000000],[0.003588720,0.003588720,0.033080098,0.310356803,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3KTW|1|C|A|204 - 3KTW|1|C|C|219 tHW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.059133653,0.007656442,0.000609857,0.003033099,0.000000000],[0.446508052,0.298693334,0.004269002,0.004269002,0.000000000],[0.051180538,0.000609857,0.004231774,0.007720767,0.000000000],[0.055127570,0.055737339,0.000609857,0.000609857,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3KTW|1|C|C|203 - 3KTW|1|C|A|220 tSH 
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009233717,0.007375870,0.036375504,0.006569651,0.000000000],[0.004568870,0.004667945,0.007440758,0.005516210,0.000000000],[0.001062965,0.001062965,0.763683665,0.001062965,0.000000000],[0.095938841,0.001062965,0.053314141,0.001062965,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // Basepair G205 - G218 tHS 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.022937090,0.014347847,0.348044880,0.017561601,0.000000000],[0.014692845,0.010155161,0.019218678,0.045122890,0.000000000],[0.381868061,0.019005244,0.003622602,0.015644206,0.000000000],[0.017595852,0.042706478,0.015986694,0.011489870,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair G206 - A217 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // Basepair C207 - G216 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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 IL_65851.3:
> IL_65851.3  3KTW G  201 C  222
GCCAGGC*GAGCAAC
> IL_65851.3  3NDB G  200 C  221
GCCAGGC*GAGCAAC