Alignment of IL_06691.1 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
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
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_06691.1_Instance_1 IL_06691.1,IL_5J7L_051,G1144_C1128GAACUCGUUGC
IL_06691.1_Sequence_1 IL_06691.15J7L_G_1144_C_1128GAACUC*GUUGCtrue95001.07
IL_06691.1_Instance_2 IL_06691.1,IL_4V9F_035,G958_C1008GCGACCGCAAAC
IL_06691.1_Sequence_2 IL_06691.14V9F_G958_C_1008GCGACCG*CAAACtrue100000.00

Conserved interactions between motif group positions in IL_06691.1:
1 2 s35 
1 3 tSW 
1 10 cWW 
2 3 perp 
2 4 cSH 
2 5 tSW 
2 7 s33 
2 8 tWH 
2 9 cWW 
3 4 s35 
4 5 s35 
4 10 cWS 
5 6 s35 
5 8 cWW 
6 7 cWW 
6 8 s55 
7 8 cSH 
7 9 s35 
8 9 s35 
8 10 s35 
9 10 s35
JAR3D SCFG/MRF model for IL_06691.1:
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 [10] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000000122368629759416866559708989908376050276] | Num Left Bases [5] | Num Right Bases [3] | Left Index [1] | Right Index [10] | Norm Constant [0.000067041245439] // Cluster node 5J7L|1|AA|G|1144:5J7L|1|AA|U|1148 and 5J7L|1|AA|U|1125:5J7L|1|AA|C|1128
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.027924827,0.003262473,0.093329234,0.102192954,0.000000000],[0.336051234,0.023769222,0.003262473,0.003262473,0.000000000],[0.003262473,0.011390225,0.029337962,0.030072816,0.000000000],[0.032808466,0.003262473,0.014668147,0.282142548,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|AA|A|1145 - 5J7L|1|AA|U|1125 tWH 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.010153793,0.013295259,0.012926971,0.028012001,0.000000000],[0.336189288,0.037265996,0.031668407,0.014435104,0.000000000],[0.013237803,0.026709543,0.003263854,0.013805080,0.000000000],[0.035195420,0.013154930,0.298667921,0.112018631,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|AA|U|1148 - 5J7L|1|AA|U|1125 cWW 
Interaction  | Interacting Bases [2,7] | Pair Probability [[0.027077160,0.013263515,0.336823218,0.015884116,0.000000000],[0.111882560,0.008821255,0.017156401,0.038551963,0.000000000],[0.314186837,0.017349072,0.003270193,0.014431498,0.000000000],[0.015853196,0.040733305,0.014122327,0.010593386,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|AA|A|1145 - 5J7L|1|AA|G|1127 cWW 
Interaction  | Interacting Bases [1,8] | 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]] // Cluster Interaction 5J7L|1|AA|G|1144 - 5J7L|1|AA|C|1128 cWW 
Interaction  | Interacting Bases [4,8] | Pair Probability [[0.015946486,0.021094317,0.014190945,0.019217607,0.000000000],[0.250280716,0.285636061,0.002660282,0.256139873,0.000000000],[0.023389228,0.002660282,0.028048170,0.010653057,0.000000000],[0.016345983,0.026420949,0.012444452,0.014871593,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|AA|C|1147 - 5J7L|1|AA|C|1128 cWS 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.149957916,0.149239472,0.001863865,0.009012572,0.000000000],[0.174416518,0.008218366,0.001863865,0.007451707,0.000000000],[0.295120901,0.001863865,0.001863865,0.006112240,0.000000000],[0.161298541,0.008100281,0.014665616,0.008950410,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|AA|G|1144 - 5J7L|1|AA|A|1146 tSW 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.073487471,0.172991129,0.004089809,0.072451280,0.000000000],[0.074228657,0.095370878,0.000855670,0.059533332,0.000000000],[0.062984968,0.000855670,0.075123456,0.077606387,0.000000000],[0.075261748,0.075253413,0.000855670,0.079050462,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|AA|A|1145 - 5J7L|1|AA|C|1147 cSH 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.030266179,0.014471746,0.003677806,0.117213399,0.000000000],[0.016804021,0.377584550,0.003677806,0.024981981,0.000000000],[0.016216603,0.003677806,0.003677806,0.014957526,0.000000000],[0.017608979,0.316224142,0.016878549,0.022081100,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|AA|A|1145 - 5J7L|1|AA|U|1148 tSW 
Insertion    | Location [2] | Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node
Insertion    | Location [6] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000]// Insertion after nucleotide 8, position 6 in cluster node
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 [6] | Right Index [7] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009635135,0.018686586,0.011023774,0.200055053,0.000000000],[0.018686946,0.009628796,0.215804967,0.013537321,0.000000000],[0.011023788,0.215804297,0.002089517,0.025115689,0.000000000],[0.200055346,0.013537264,0.025116064,0.010199456,0.000000000],[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 C1149 - G1124 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_06691.1:
> IL_06691.1  5J7L G 1144 C 1128
GAACUC*GUUGC
> IL_06691.1  4V9F G  958 C 1008
GCGACCG*CAAAC