Alignment of IL_99358.1 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
3

2
5
4
I

6
5

3
7
6
I

8
9

4
9
9
I

10
10


11
9
I

12
9

5
13
8
I

14
7

6
15
2
I

16
2

7
17
1
I


In
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Full
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Alignment
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IL_99358.1_Instance_1 IL_99358.1,IL_4N0T_004,G78_C68GAUGCCC
IL_99358.1_Sequence_1 IL_99358.14N0T_G78_C68GAUG*CCCtrue99000.10
IL_99358.1_Instance_2 IL_99358.1,IL_8CRE_417,G495_C487GGUCGGC
IL_99358.1_Sequence_2 IL_99358.18CRE_G495_C487GGUC*GGCtrue99000.06
IL_99358.1_Instance_3 IL_99358.1,IL_7KJT_002,C39_G30CCAGCUG
IL_99358.1_Sequence_3 IL_99358.17KJT_C39_G30CCAG*CUGtrue100000.00
IL_99358.1_Instance_4 IL_99358.1,IL_4QIK_001,U11_G12UGUGCUG
IL_99358.1_Sequence_4 IL_99358.14QIK_U11_G12UGUG*CUGtrue99000.11
IL_99358.1_Instance_5 IL_99358.1,IL_6ZDU_001,A1283_U1270AUAGCUU
IL_99358.1_Sequence_5 IL_99358.16ZDU_A_1283_U_1270AUAG*CUUtrue94000.52
IL_99358.1_Instance_6 IL_99358.1,IL_6VMY_001,U219_G232UCCGCAG
IL_99358.1_Sequence_6 IL_99358.16VMY_U219_G232UCCG*CAGtrue84001.54
IL_99358.1_Instance_7 IL_99358.1,IL_4PHY_003,G17_C34GAUCGAAC
IL_99358.1_Sequence_7 IL_99358.14PHY_G17_C34GAUC*GAACtrue81001.78
IL_99358.1_Instance_8 IL_99358.1,IL_7MLW_007,G89_C76GAAAUCGC
IL_99358.1_Sequence_8 IL_99358.17MLW_G89_C76GAAA*UCGCtrue78002.09

Conserved interactions between motif group positions in IL_99358.1:
1 2 s35 
1 7 cWW 
2 3 s35 
2 7 s55 
3 4 s35 
4 5 cWW 
4 6 s55 
5 6 s35 
6 7 s35
JAR3D SCFG/MRF model for IL_99358.1:
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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009473553,0.017491943,0.011069992,0.160693456,0.000000000],[0.083968295,0.013384422,0.162726311,0.012909818,0.000000000],[0.011097922,0.191656586,0.002254899,0.025155832,0.000000000],[0.161116632,0.012847221,0.113536349,0.010616770,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair G78 - C68 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.350000000,0.250000000,0.250000000,0.150000000,0.000000000] | Position [1] | Left Index [2] | Right Index [6] // Fixed node on left for 4N0T|1|B|C|67
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [3] | Right Index [6] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.350000000,0.150000000,0.050000000,0.450000000,0.000000000] | Position [1] | Left Index [3] | Right Index [6] // Fixed node on left for 4N0T|1|B|C|68
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [4] | Right Index [6] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.250000000,0.150000000,0.250000000,0.350000000,0.000000000] | Position [2] | Left Index [4] | Right Index [6] // Fixed node on right for 4N0T|1|B|U|80
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.745505270,0.252634842,0.001782393,0.000077495] | Right Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009093175,0.018602282,0.010301728,0.199127731,0.000000000],[0.016947871,0.009058406,0.210624429,0.012320293,0.000000000],[0.010255860,0.240789130,0.001967639,0.027621701,0.000000000],[0.188000840,0.012577609,0.022886192,0.009825113,0.000000000],[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 [4] | Right Index [5] // Basepair G81 - C66 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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_99358.1:
> IL_99358.1  4N0T G   78 C   68
GAUG*CCC
> IL_99358.1  8CRE G  495 C  487
GGUC*GGC
> IL_99358.1  7KJT C   39 G   30
CCAG*CUG
> IL_99358.1  4QIK U   11 G   12
UGUG*CUG
> IL_99358.1  6ZDU A 1283 U 1270
AUAG*CUU
> IL_99358.1  6VMY U  219 G  232
UCCG*CAG
> IL_99358.1  4PHY G   17 C   34
GAUC*GAAC
> IL_99358.1  7MLW G   89 C   76
GAAA*UCGC