Alignment of IL_22732.1 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
5
I

8
6

4
9
6
I

10
7


11
6
I

12
6

5
13
5
I

14
5

6
15
4
I

16
3

7
17
3
I

18
3

8
19
2
I

20
2

9
21
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_22732.1_Instance_1 IL_22732.1_IL_1FJG_061_C1466_G1435CGAGCGAAG
IL_22732.1_Sequence_1 IL_22732.1_IL_1FJG_061_C_1466_G_1435CGAG*CGAAGtrue89001.20
IL_22732.1_Instance_2 IL_22732.1_IL_2QBG_061_C1526_G1546CGAGUGAAG
IL_22732.1_Sequence_2 IL_22732.1_IL_2QBG_061_C_1526_G_1546CGAG*UGAAGtrue84001.74
IL_22732.1_Instance_3 IL_22732.1_IL_2QBG_075_U1864_G1878UUAGCGAAG
IL_22732.1_Sequence_3 IL_22732.1_IL_2QBG_075_U_1864_G_1878UUAG*CGAAGtrue100000.00
IL_22732.1_Instance_4 IL_22732.1_IL_2ZY6_001_A7_U29AUAGCGAGU
IL_22732.1_Sequence_4 IL_22732.1_IL_2ZY6_001_A7_U29AUAG*CGAGUtrue93000.72

Conserved interactions between motif group positions in IL_22732.1:
1 2 s35 
1 9 cWW 
2 6 s33 
2 7 tWH 
2 8 tSH 
3 4 s35 
3 6 tHS 
3 7 s55 
4 5 cWW 
4 6 s55 
5 6 s35 
7 8 s35 
8 9 s35 
6 3 6BPh
JAR3D SCFG/MRF model for IL_22732.1:
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 [9] // Initial node C1466 - G1435 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.010379139,0.018054448,0.011936187,0.166132001,0.000000000],[0.092831895,0.010420694,0.182890129,0.013631115,0.000000000],[0.012091289,0.159186893,0.002446059,0.022275606,0.000000000],[0.156779526,0.012908548,0.115428336,0.012608136,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair C1466 - G1435 cWW 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [2] | Right Index [8] | Norm Constant [0.287323481329397] // Cluster node G1467:G1467 and A1433:A1434
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.023156674,0.004856498,0.023822189,0.004856498,0.000000000],[0.048239451,0.040320637,0.032236679,0.004856498,0.000000000],[0.111499855,0.004856498,0.056836281,0.022654145,0.000000000],[0.504880592,0.004856498,0.059912387,0.052158619,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1467 - A1433 tWH 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.099771965,0.116296998,0.001202125,0.005724366,0.000000000],[0.100659637,0.105505979,0.001202125,0.001202125,0.000000000],[0.139443264,0.001202125,0.005824043,0.099992658,0.000000000],[0.161770273,0.104476389,0.054523803,0.001202125,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1467 - A1434 tSH 
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [0.0000239574126029] | Pair Probability [[0.059593935,0.060124143,0.342732568,0.064776498,0.000000000],[0.069464361,0.063018870,0.003042710,0.062403894,0.000000000],[0.000718031,0.000718031,0.014741292,0.000718031,0.000000000],[0.003419172,0.000718031,0.253092402,0.000718031,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair A1468 - G1432 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.011545053,0.091357941,0.012500960,0.153268922,0.000000000],[0.016202600,0.009015557,0.162650528,0.013540081,0.000000000],[0.012307163,0.197820616,0.002427935,0.114576839,0.000000000],[0.150792068,0.014433261,0.021211816,0.016348660,0.000000000],[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 G1469 - C1431 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_22732.1:
> IL_22732.1 IL_1FJG_061 C 1466 G 1435
CGAG*CGAAG
> IL_22732.1 IL_2QBG_061 C 1526 G 1546
CGAG*UGAAG
> IL_22732.1 IL_2QBG_075 U 1864 G 1878
UUAG*CGAAG
> IL_22732.1 IL_2ZY6_001 A    7 U   29
AUAG*CGAGU