Alignment of IL_92634.2 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
7

4
9
7
I

10
7

5
11
8
I

12
9


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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Interior
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Alignment
score
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IL_92634.2_Instance_1 IL_92634.2,IL_8CRE_007,A143_U123AGUUGUAU
IL_92634.2_Sequence_1 IL_92634.28CRE_A143_U123AGUUGU*AUtrue100000.00
IL_92634.2_Instance_2 IL_92634.2,IL_8P9A_236,A144_U124AGUUGUAU
IL_92634.2_Sequence_2 IL_92634.28P9A_A144_U124AGUUGU*AUtrue100000.00
IL_92634.2_Instance_3 IL_92634.2,IL_4V9F_009,C260_G249CAAUGUAG
IL_92634.2_Sequence_3 IL_92634.24V9F_C260_G249CAAUGU*AGtrue84002.26

Conserved interactions between motif group positions in IL_92634.2:
1 2 s35 
1 7 cWW 
4 5 cSH 
5 6 cWW 
5 7 perp 
7 6 7BPh
5 4 7BR
6 7 2BR
JAR3D SCFG/MRF model for IL_92634.2:
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 [0.0000234451146992] | Pair Probability [[0.005410345,0.011009320,0.006035247,0.433252665,0.000000000],[0.010962546,0.005540956,0.126011258,0.022224172,0.000000000],[0.006071186,0.114967509,0.001187272,0.098527510,0.000000000],[0.114243542,0.007073687,0.014445532,0.023037252,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair A143 - U123 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.500000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [6] // Fixed node on left for 8CRE|1|1|U|123
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [0.300000000,0.100000000,0.100000000,0.500000000,0.000000000] | Position [1] | Left Index [3] | Right Index [6] // Fixed node on left for 8CRE|1|1|A|143
InitialNode  | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000] | 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
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [6] | Norm Constant [0.353971872423088] // Cluster node 8CRE|1|1|G|147:8CRE|1|1|U|148 and 8CRE|1|1|A|122:8CRE|1|1|A|122
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.006911121,0.002684292,0.001516211,0.030036507,0.000000000],[0.016863270,0.001504215,0.030137565,0.001689834,0.000000000],[0.007595843,0.029751862,0.000312764,0.003526200,0.000000000],[0.811035385,0.007936374,0.040769476,0.007729083,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|1|U|148 - 8CRE|1|1|A|122 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.078527006,0.080015416,0.004399495,0.078197963,0.000000000],[0.058625540,0.088349717,0.000974123,0.078361895,0.000000000],[0.068609208,0.000974123,0.083691539,0.126538511,0.000000000],[0.079745425,0.079266702,0.000974123,0.092749213,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|1|G|147 - 8CRE|1|1|U|148 cSH 
InitialNode  | Left Length Distribution [0.952380952,0.047619048] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.952380952,0.047619048] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [5] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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_92634.2:
> IL_92634.2  8CRE A  143 U  123
AGUUGU*AU
> IL_92634.2  8P9A A  144 U  124
AGUUGU*AU
> IL_92634.2  4V9F C  260 G  249
CAAUGU*AG