Alignment of IL_38807.3 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
3
I

6
3

3
7
3
I

8
3

4
9
4
I

10
5

5
11
5
I

12
5

6
13
5
I

14
5

7
15
6
I

16
7


17
6
I

18
5

8
19
4
I

20
3

9
21
3
I

22
3

10
23
2
I

24
2

11
25
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_38807.3_Instance_1 IL_38807.3_IL_3V2F_039_C1018_G1144CUAAGUGCUUAAG
IL_38807.3_Sequence_1 IL_38807.3_IL_3V2F_039_C_1018_G_1144CUAAGUG*CUUAAGtrue97000.51
IL_38807.3_Instance_2 IL_38807.3_IL_1S72_041_U1115_A1248UUAAGUGCUCAAA
IL_38807.3_Sequence_2 IL_38807.3_IL_1S72_041_U_1115_A_1248UUAAGUG*CUCAAAtrue100000.00
IL_38807.3_Instance_3 IL_38807.3_IL_4IOA_035_C1029_G1155CUCAGUGCUCAAG
IL_38807.3_Sequence_3 IL_38807.3_IL_4IOA_035_C_1029_G_1155CUCAGUG*CUCAAGtrue94001.04
IL_38807.3_Instance_4 IL_38807.3_IL_2QBG_039_U1018_A1144UUAAGUGCUAAA
IL_38807.3_Sequence_4 IL_38807.3_IL_2QBG_039_U_1018_A_1144UUAAGUG*CUAAAtrue98000.37

Conserved interactions between motif group positions in IL_38807.3:
1 2 s35 
1 11 cWW 
2 10 tWH 
2 11 s55 
3 4 s55 
3 9 s53 
3 10 s55 
4 6 s35 
4 9 tHW 
4 10 tWW 
5 6 cSH 
5 7 s35 
5 8 s33 
5 9 s55 
6 7 s35 
7 8 cWW 
10 11 s35 
4 2 2BR
6 5 7BR
3 9 6BR
7 11 2BR
JAR3D SCFG/MRF model for IL_38807.3:
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 [11] // Initial node C1018 - G1144 from junction 
BasepairNode | Deletion Probability [0.0000001215781528] | Pair Probability [[0.009389328,0.018311644,0.010532081,0.196004232,0.000000000],[0.022201629,0.008876226,0.219726245,0.011917651,0.000000000],[0.010613182,0.196724789,0.002110478,0.023262344,0.000000000],[0.219745044,0.011558533,0.027184577,0.011842020,0.000000000],[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 [0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Left Index [1] | Right Index [11] // Basepair C1018 - G1144 cWW 
ClusterNode  | Deletion Probability [0.000000000000056748929858366210000000000000000000000000000000] | Num Left Bases [3] | Num Right Bases [2] | Left Index [2] | Right Index [10] | Norm Constant [0.360205348511261] // Cluster node U1019:A1021 and U1141:A1142A
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.033115265,0.068984957,0.006945048,0.732966383,0.000000000],[0.002457439,0.020402667,0.002457439,0.002457439,0.000000000],[0.012054279,0.016312099,0.028759757,0.030316299,0.000000000],[0.002457439,0.002457439,0.011463236,0.026392811,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1021 - U1141 tHW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.025472342,0.005342148,0.026204408,0.005342148,0.000000000],[0.053063396,0.044352700,0.035460347,0.005342148,0.000000000],[0.005342148,0.005342148,0.062519909,0.024919560,0.000000000],[0.572676343,0.005342148,0.065903626,0.057374481,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1019 - A1142A tWH 
Interaction  | Interacting Bases [3,5] | Pair Probability [[0.633374642,0.055859126,0.005949131,0.028182839,0.000000000],[0.018190876,0.007495204,0.005886151,0.007392232,0.000000000],[0.001934929,0.005882949,0.182786709,0.010588182,0.000000000],[0.009168390,0.007392376,0.010598000,0.009318263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1021 - A1142A tWW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.704545455,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.022727273,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.022727273,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A1020
Insertion    | Location [4] | Length Distribution [0.253667482,0.736552567,0.009321516,0.000458435] | Letter Distribution [0.100000000,0.500000000,0.100000000,0.300000000,0.000000000]// Insertion after nucleotide 9, position 4 in cluster node
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 [5] | Right Index [8] // New Initial node after Cluster
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [5] | Right Index [8] | Norm Constant [1.000000000000000] // Cluster node G1022:G1024 and C1140:C1140
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.004887557,0.009956935,0.005659065,0.092752426,0.000000000],[0.008246692,0.004030138,0.099899013,0.006358532,0.000000000],[0.027939145,0.553701311,0.005152398,0.066088192,0.000000000],[0.092216823,0.006674609,0.011401633,0.005035534,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1024 - C1140 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.106243868,0.109450239,0.005969057,0.004938655,0.000000000],[0.102770254,0.119376597,0.001269566,0.120308197,0.000000000],[0.010380152,0.005676417,0.011603300,0.165418103,0.000000000],[0.009141931,0.106461489,0.001269566,0.119722610,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1022 - U1023 cSH 
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 [8] | Right Index [7] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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_38807.3:
> IL_38807.3 IL_3V2F_039 C 1018 G 1144
CUAAGUG*CUUAAG
> IL_38807.3 IL_1S72_041 U 1115 A 1248
UUAAGUG*CUCAAA
> IL_38807.3 IL_4IOA_035 C 1029 G 1155
CUCAGUG*CUCAAG
> IL_38807.3 IL_2QBG_039 U 1018 A 1144
UUAAGUG*CUAAA