Alignment of IL_41791.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_41791.1
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
3
I

12
4

6
13
4
I

14
5


15
4
I

16
4

7
17
3
I

18
2

8
19
2
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
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distance
Alignment
score
deficit
IL_41791.1_Instance_1 IL_41791.1_IL_1S72_036_G958_C1008GCGACCGCAAAC
IL_41791.1_Sequence_1 IL_41791.1_IL_1S72_036_G958_C_1008GCGACCG*CAAAC

Conserved interactions between motif group positions in IL_41791.1:
1 2 s35 
1 3 tSW 
1 11 cWW 
2 4 cSH 
2 5 tSW 
2 7 s33 
2 8 tWH 
4 5 s35 
4 11 cWS 
5 6 s35 
5 8 cWW 
6 7 cWW 
6 8 s55 
8 11 s35 
9 10 s35 
11 9 7BPh
3 1 7BR
JAR3D SCFG/MRF model for IL_41791.1:
Character Definition | A,C,G,U,* // Define characters here
InitialNode  | 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 [1] | Right Index [11] // Initial node G958 - C1008 from junction 
ClusterNode  | Deletion Probability [0.000000000000000000000009533766986221214500000000000000000000] | Num Left Bases [5] | Num Right Bases [4] | Left Index [1] | Right Index [11] | Norm Constant [0.000844173991047] // Cluster node G958:C963 and A1005:C1008
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.020051501,0.002539818,0.142297221,0.002539818,0.000000000],[0.263882817,0.012018367,0.235478309,0.002539818,0.000000000],[0.002539818,0.002539818,0.017348636,0.026230988,0.000000000],[0.025227938,0.002539818,0.012157548,0.230067766,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C959 - A1005 tWH 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.012225429,0.015145471,0.014725930,0.034760566,0.000000000],[0.381707213,0.018478793,0.035925510,0.016513221,0.000000000],[0.015080020,0.029754800,0.003718062,0.015583401,0.000000000],[0.042294737,0.014884503,0.334044557,0.015157789,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C963 - A1005 cWW 
Interaction  | Interacting Bases [1,9] | Pair Probability [[0.003991852,0.056925429,0.004621971,0.075754404,0.000000000],[0.006735384,0.023040960,0.081591292,0.005193253,0.000000000],[0.004563791,0.599043046,0.000841632,0.010795344,0.000000000],[0.075316957,0.038159832,0.009312144,0.004112711,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G958 - C1008 cWW 
Interaction  | Interacting Bases [4,9] | Pair Probability [[0.004137439,0.053445697,0.004255207,0.005369948,0.000000000],[0.078512827,0.601694427,0.079760014,0.081014891,0.000000000],[0.004574068,0.027091682,0.006610222,0.003367509,0.000000000],[0.005608553,0.036412329,0.004031225,0.004113960,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C962 - C1008 cWS 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.028750495,0.242495727,0.002737822,0.013060892,0.000000000],[0.254895959,0.012747598,0.012368699,0.011240183,0.000000000],[0.283683213,0.074611933,0.002737822,0.008899336,0.000000000],[0.016584213,0.011523157,0.015256354,0.008406597,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G958 - A961 tSW 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.111414184,0.110164164,0.006015482,0.005004925,0.000000000],[0.107770754,0.141613670,0.001317127,0.123910582,0.000000000],[0.011483518,0.005613507,0.009660713,0.123848748,0.000000000],[0.007736315,0.106213420,0.001317127,0.126915765,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C959 - C962 cSH 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.199738643,0.010889283,0.002471564,0.013930491,0.000000000],[0.011522819,0.257057341,0.019747221,0.022305949,0.000000000],[0.011507868,0.026066064,0.002471564,0.009842358,0.000000000],[0.165962880,0.222962299,0.013113694,0.010409963,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C959 - C963 tSW 
Interaction  | Interacting Bases [7,7] | 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]] // Right strand conserved insertion A1006
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]] // Right strand conserved insertion A1007
Insertion    | Location [2] | 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 2, position 2 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 [7] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010296034,0.020975088,0.011921277,0.195390483,0.000000000],[0.017372323,0.008489812,0.210445347,0.013394761,0.000000000],[0.011771213,0.226979836,0.002170788,0.027844024,0.000000000],[0.194262192,0.014060602,0.024018461,0.010607760,0.000000000],[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 [6] | Right Index [7] // Basepair G964 - C1004 cWW 
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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_41791.1:
> IL_41791.1 IL_1S72_036 G  958 C 1008
GCGACCG*CAAAC