Alignment of IL_90351.1 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
3
I

6
4

3
7
4
I

8
5

4
9
5
I

10
6


11
5
I

12
5

5
13
4
I

14
4

6
15
3
I

16
2

7
17
1
I


In
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Cutoff
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Full
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Interior
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Alignment
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IL_90351.1_Instance_1 IL_90351.1,IL_2QEK_002,G7_C17GAAGCAC
IL_90351.1_Sequence_1 IL_90351.12QEK_G7_C17GAAG*CACtrue99000.07
IL_90351.1_Instance_2 IL_90351.1,IL_5J7L_364,G1491_C1409GAAGCAC
IL_90351.1_Sequence_2 IL_90351.15J7L_G_1491_C_1409GAAG*CACtrue99000.07
IL_90351.1_Instance_3 IL_90351.1,IL_5J7L_006,C99_G69CGAGCGG
IL_90351.1_Sequence_3 IL_90351.15J7L_C99_G69CGAG*CGGtrue100000.00
IL_90351.1_Instance_4 IL_90351.1,IL_8CRE_092,G2184_C2215GAAUGCGC
IL_90351.1_Sequence_4 IL_90351.18CRE_G_2184_C_2215GAAUG*CGCtrue65003.30
IL_90351.1_Instance_5 IL_90351.1,IL_4WF9_003,U480_A44UCUCGAA
IL_90351.1_Sequence_5 IL_90351.14WF9_U480_A44UCUC*GAAtrue79001.96
IL_90351.1_Instance_6 IL_90351.1,IL_8P9A_400,U533_A518UAACGUA
IL_90351.1_Sequence_6 IL_90351.18P9A_U533_A518UAAC*GUAtrue83001.65
IL_90351.1_Instance_7 IL_90351.1,IL_9DFE_030,A899_U877AAACGCU
IL_90351.1_Sequence_7 IL_90351.19DFE_A899_U877AAAC*GCUtrue88001.15
IL_90351.1_Instance_8 IL_90351.1,IL_3MXH_001,G94_C13GAUGGCAC
IL_90351.1_Sequence_8 IL_90351.13MXH_G94_C13GAUGG*CACtrue81001.84

Conserved interactions between motif group positions in IL_90351.1:
1 7 cWW 
2 3 s35 
2 7 tHS 
3 4 s35 
3 6 cWW 
4 5 cWW 
4 6 s55 
5 6 s35 
6 7 s35
JAR3D SCFG/MRF model for IL_90351.1:
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
ClusterNode  | Deletion Probability [0.0000000622013889] | Num Left Bases [2] | Num Right Bases [1] | Left Index [1] | Right Index [7] | Norm Constant [0.250699937715072] // Cluster node 2QEK|1|B|G|7:2QEK|1|B|A|8 and 2QEK|1|A|C|17:2QEK|1|A|C|17
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.008951320,0.018332685,0.010038774,0.198246118,0.000000000],[0.017740498,0.009106308,0.199235598,0.011731804,0.000000000],[0.009997466,0.228805224,0.001956951,0.027133389,0.000000000],[0.207551081,0.011830860,0.029539446,0.009802478,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 2QEK|1|B|G|7 - 2QEK|1|A|C|17 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.098902659,0.229281229,0.078616169,0.095024619,0.000000000],[0.075619268,0.054407566,0.001922404,0.081869324,0.000000000],[0.001922404,0.001922404,0.124060402,0.001922404,0.000000000],[0.102545196,0.001922404,0.048139149,0.001922404,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 2QEK|1|B|A|8 - 2QEK|1|A|C|17 tHS 
Insertion    | Location [1] | Length Distribution [0.869396619,0.129517605,0.001046999,0.000038778] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 1, position 1 in cluster node
InitialNode  | Left Length Distribution [0.869396619,0.129517605,0.001046999,0.000038778] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.089384739,0.097324691,0.203498886,0.053822351,0.000000000],[0.011078492,0.008491859,0.016846217,0.026853964,0.000000000],[0.203449339,0.018065177,0.002750772,0.081946322,0.000000000],[0.052056042,0.027164183,0.047614634,0.059652332,0.000000000],[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 [3] | Right Index [6] // Basepair A9 - A16 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008984793,0.017610738,0.010272725,0.186448108,0.000000000],[0.017188779,0.008954615,0.219198431,0.012571477,0.000000000],[0.010256362,0.251542629,0.001945607,0.023605698,0.000000000],[0.186105612,0.012638408,0.023166459,0.009509558,0.000000000],[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 G10 - C15 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_90351.1:
> IL_90351.1  2QEK G    7 C   17
GAAG*CAC
> IL_90351.1  5J7L G 1491 C 1409
GAAG*CAC
> IL_90351.1  5J7L C   99 G   69
CGAG*CGG
> IL_90351.1  8CRE G 2184 C 2215
GAAUG*CGC
> IL_90351.1  4WF9 U  480 A   44
UCUC*GAA
> IL_90351.1  8P9A U  533 A  518
UAAC*GUA
> IL_90351.1  9DFE A  899 U  877
AAAC*GCU
> IL_90351.1  3MXH G   94 C   13
GAUGG*CAC