Alignment of IL_31066.3 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
5

2
5
5
I

6
6


7
5
I

8
5

3
9
4
I

10
3

4
11
2
I

12
2

5
13
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_31066.3_Instance_1 IL_31066.3_IL_2AW7_060_C1399_G1504CCGCAAG
IL_31066.3_Sequence_1 IL_31066.3_IL_2AW7_060_C_1399_G_1504CCG*CAAGtrue100000.00
IL_31066.3_Instance_2 IL_31066.3_IL_3U5F_080_C1636_G1767CCGCAAG
IL_31066.3_Sequence_2 IL_31066.3_IL_3U5F_080_C_1636_G_1767CCG*CAAGtrue100000.00
IL_31066.3_Instance_3 IL_31066.3_IL_4BPP_080_C1608_G1720CCGCAAG
IL_31066.3_Sequence_3 IL_31066.3_IL_4BPP_080_C_1608_G_1720CCG*CAAGtrue100000.00
IL_31066.3_Instance_4 IL_31066.3_IL_1FJG_054_C1399_G1504CCGCAAG
IL_31066.3_Sequence_4 IL_31066.3_IL_1FJG_054_C_1399_G_1504CCG*CAAGtrue100000.00

Conserved interactions between motif group positions in IL_31066.3:
1 2 s55 
1 4 s35 
1 5 cWW 
2 3 cWW 
3 5 s33 
4 5 s55 
4 1 6BR
3 5 7BR
JAR3D SCFG/MRF model for IL_31066.3:
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 [5] // Initial node C1399 - G1504 from junction 
BasepairNode | Deletion Probability [0.0000000006169801] | Pair Probability [[0.009837906,0.016874612,0.011433973,0.188696651,0.000000000],[0.020374159,0.008402684,0.249321155,0.013657771,0.000000000],[0.011579737,0.204416164,0.002108596,0.023330341,0.000000000],[0.189792617,0.013011006,0.027046303,0.010116326,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Left Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | 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 [5] // Basepair C1399 - G1504 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.931818182,0.022727273,0.022727273,0.022727273,0.000000000] | Position [2] | Left Index [2] | Right Index [4] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | 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 [2] | Right Index [3] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.006152877,0.042303194,0.007124117,0.116764735,0.000000000],[0.010381645,0.017122510,0.125761474,0.008004667,0.000000000],[0.007034440,0.476272743,0.001297256,0.016639501,0.000000000],[0.116090472,0.028357850,0.014353356,0.006339164,0.000000000],[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 [2] | Right Index [3] // Basepair G1401 - C1501 cWW 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | 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_31066.3:
> IL_31066.3 IL_2AW7_060 C 1399 G 1504
CCG*CAAG
> IL_31066.3 IL_3U5F_080 C 1636 G 1767
CCG*CAAG
> IL_31066.3 IL_4BPP_080 C 1608 G 1720
CCG*CAAG
> IL_31066.3 IL_1FJG_054 C 1399 G 1504
CCG*CAAG