Alignment of IL_77045.1 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
2

2
5
2
I

6
2

3
7
2
I

8
2

4
9
2
I

10
2

5
11
3
I

12
4

6
13
5
I

14
6

7
15
6
I

16
7


17
6
I

18
6

8
19
3
I

20
2

9
21
2
I

22
2

10
23
2
I

24
2

11
25
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_77045.1_Instance_1 IL_77045.1,IL_3IGI_006,A149_U225AUAUGAGGUAAAU
IL_77045.1_Sequence_1 IL_77045.13IGI_A149_U225AUAUGAGG*UAAAUtrue100000.00

Conserved interactions between motif group positions in IL_77045.1:
1 2 s35 
1 11 cWW 
3 10 s35 
4 10 tSW 
5 6 s35 
5 9 tHW 
5 10 s53 
5 11 tSS 
6 7 s35 
6 9 s55 
7 8 cWW 
9 10 s33 
9 4 7BR
JAR3D SCFG/MRF model for IL_77045.1:
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 [11] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000000009307413805830298684477952266866271607] | Num Left Bases [5] | Num Right Bases [3] | Left Index [1] | Right Index [11] | Norm Constant [0.123060176487766] // Cluster node 3IGI|1|A|A|149:3IGI|1|A|A|154 and 3IGI|1|A|A|222:3IGI|1|A|U|225
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.489593015,0.008211756,0.000959384,0.004335188,0.000000000],[0.004796920,0.004071287,0.002376525,0.000959384,0.000000000],[0.423174558,0.000959384,0.035264484,0.004598327,0.000000000],[0.004796920,0.000959384,0.010268946,0.004674537,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3IGI|1|A|A|154 - 3IGI|1|A|A|222 tHW 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.166586913,0.165788799,0.002070551,0.010011986,0.000000000],[0.193757756,0.009129710,0.002070551,0.008278035,0.000000000],[0.216956090,0.002070551,0.002070551,0.006790033,0.000000000],[0.179185112,0.008998530,0.016291903,0.009942930,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3IGI|1|A|G|153 - 3IGI|1|A|A|224 tSW 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.009374836,0.022228469,0.010012528,0.216037101,0.000000000],[0.017691617,0.009675113,0.196088410,0.010461402,0.000000000],[0.009993038,0.198630499,0.002061361,0.053740648,0.000000000],[0.197964449,0.011137350,0.023240462,0.011662716,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3IGI|1|A|A|149 - 3IGI|1|A|U|225 cWW 
Interaction  | Interacting Bases [5,8] | Pair Probability [[0.205456407,0.209533177,0.206255896,0.233635027,0.000000000],[0.002237340,0.002237340,0.014813093,0.002237340,0.000000000],[0.011136660,0.002237340,0.011489181,0.089781837,0.000000000],[0.002237340,0.002237340,0.002237340,0.002237340,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3IGI|1|A|A|154 - 3IGI|1|A|U|225 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 3IGI|1|A|U|150
Interaction  | Interacting Bases [3,3] | 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 3IGI|1|A|A|151
Insertion    | Location [3] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 3, position 3 in cluster node
Insertion    | Location [6] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 9, position 6 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 [6] | Right Index [8] // Initial node 3IGI|1|A|G|155 - 3IGI|1|A|U|221 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Position [1] | Left Index [6] | Right Index [8] // Fixed node on left for 3IGI|1|A|A|154
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 [7] | Right Index [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.015996656,0.299826436,0.014459392,0.085420251,0.000000000],[0.013858629,0.012916026,0.036792527,0.014547577,0.000000000],[0.014149624,0.041974486,0.003276514,0.337552385,0.000000000],[0.036940494,0.015890415,0.014540501,0.041858086,0.000000000],[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 G156 - U221 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_77045.1:
> IL_77045.1  3IGI A  149 U  225
AUAUGAGG*UAAAU