Alignment of IL_89021.2 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
8

5
11
8
I

12
9


13
8
I

14
8

6
15
7
I

16
7

7
17
4
I

18
3

8
19
3
I

20
3

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_89021.2_Instance_1 IL_89021.2,IL_4WF9_051,C1388_G1417CUAAGCGAUG
IL_89021.2_Sequence_1 IL_89021.24WF9_C_1388_G_1417CUAAG*CGAUGtrue96000.47
IL_89021.2_Instance_2 IL_89021.2,IL_7A0S_048,C1364_G1393CUAAGCGAUG
IL_89021.2_Sequence_2 IL_89021.27A0S_C_1364_G_1393CUAAG*CGAUGtrue96000.47
IL_89021.2_Instance_3 IL_89021.2,IL_5J7L_292,C1351_G1380CUAAGCGAUG
IL_89021.2_Sequence_3 IL_89021.25J7L_C_1351_G_1380CUAAG*CGAUGtrue96000.47
IL_89021.2_Instance_4 IL_89021.2,IL_9DFE_074,U1851_G1891UCAAGCGAAG
IL_89021.2_Sequence_4 IL_89021.29DFE_U_1851_G_1891UCAAG*CGAAGtrue94000.74
IL_89021.2_Instance_5 IL_89021.2,IL_7A0S_069,U1843_G1874UCAAGUGAAG
IL_89021.2_Sequence_5 IL_89021.27A0S_U_1843_G_1874UCAAG*UGAAGtrue86001.72
IL_89021.2_Instance_6 IL_89021.2,IL_4WF9_073,U1878_G1918UUAAGCGAAG
IL_89021.2_Sequence_6 IL_89021.24WF9_U_1878_G_1918UUAAG*CGAAGtrue100000.00

Conserved interactions between motif group positions in IL_89021.2:
1 2 s35 
1 10 cWW 
2 8 tWH 
2 9 tSH 
2 10 s55 
3 4 s35 
3 7 s33 
3 8 s55 
4 5 s35 
4 7 tHS 
5 6 cWW 
5 7 s55 
6 7 s35 
8 9 s35 
8 10 s35 
9 10 s35 
7 3 6BPh
4 7 6BR
JAR3D SCFG/MRF model for IL_89021.2:
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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009999236,0.014956157,0.012144288,0.113577937,0.000000000],[0.155316435,0.018121105,0.149224604,0.014349655,0.000000000],[0.012353913,0.115566971,0.002596142,0.018349519,0.000000000],[0.138353991,0.013455419,0.200251764,0.011382864,0.000000000],[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 [10] // Basepair C1388 - G1417 cWW 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [2] | Right Index [9] | Norm Constant [0.307468761068205] // Cluster node 4WF9|1|X|U|1389:4WF9|1|X|U|1389 and 4WF9|1|X|A|1415:4WF9|1|X|U|1416
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.019942725,0.003678126,0.036925004,0.003678126,0.000000000],[0.152271055,0.236122282,0.003678126,0.003678126,0.000000000],[0.003678126,0.009716392,0.029112768,0.020281111,0.000000000],[0.354057298,0.003678126,0.020266348,0.099236264,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|U|1389 - 4WF9|1|X|A|1415 tWH 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.131392922,0.044532614,0.001382892,0.006856603,0.000000000],[0.153412219,0.102638929,0.001382892,0.001382892,0.000000000],[0.119589980,0.001382892,0.009300133,0.044937517,0.000000000],[0.138184339,0.126792210,0.001382892,0.115448072,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|U|1389 - 4WF9|1|X|U|1416 tSH 
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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [7] // Initial node 4WF9|1|X|A|1390 - 4WF9|1|X|G|1414 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.812500000,0.062500000,0.062500000,0.062500000,0.000000000] | Position [1] | Left Index [3] | Right Index [7] // Fixed node on left for 4WF9|1|X|A|1390
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 [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.040046680,0.040344198,0.438040994,0.044702790,0.000000000],[0.042394808,0.042296639,0.003365136,0.042068293,0.000000000],[0.000480734,0.000480734,0.016451081,0.000480734,0.000000000],[0.002265699,0.000480734,0.285620012,0.000480734,0.000000000],[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 [4] | Right Index [7] // Basepair A1391 - G1414 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010345669,0.063869632,0.011184400,0.175001619,0.000000000],[0.015911075,0.009705029,0.168647217,0.012962493,0.000000000],[0.011036499,0.221372192,0.002195693,0.082929291,0.000000000],[0.165236712,0.013579500,0.021122074,0.014900906,0.000000000],[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 [5] | Right Index [6] // Basepair G1392 - C1413 cWW 
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_89021.2:
> IL_89021.2  4WF9 C 1388 G 1417
CUAAG*CGAUG
> IL_89021.2  7A0S C 1364 G 1393
CUAAG*CGAUG
> IL_89021.2  5J7L C 1351 G 1380
CUAAG*CGAUG
> IL_89021.2  9DFE U 1851 G 1891
UCAAG*CGAAG
> IL_89021.2  7A0S U 1843 G 1874
UCAAG*UGAAG
> IL_89021.2  4WF9 U 1878 G 1918
UUAAG*CGAAG