Alignment of IL_70401.1 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
6
I

8
7

4
9
7
I

10
7

5
11
7
I

12
7

6
13
7
I

14
7

7
15
7
I

16
7

8
17
7
I

18
7

9
19
8
I

20
9


21
8
I

22
7

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_70401.1_Instance_1 IL_70401.1_IL_4M4O_003_U15_A45UAAAGAGUGCA
IL_70401.1_Sequence_1 IL_70401.1_IL_4M4O_003_U15_A45UAAAGAGUG*CAtrue100000.00
IL_70401.1_Instance_2 IL_70401.1_IL_4M6D_012_U15_A45UAAAGAGUGCA
IL_70401.1_Sequence_2 IL_70401.1_IL_4M6D_012_U15_A45UAAAGAGUG*CAtrue100000.00

Conserved interactions between motif group positions in IL_70401.1:
1 9 s35 
1 11 cWW 
2 3 s35 
3 4 s35 
4 5 s35 
4 8 tWW 
5 7 s33 
6 7 s35 
9 10 cWW 
9 11 s55 
10 11 s35 
5 8 6BPh
JAR3D SCFG/MRF model for IL_70401.1:
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 [11] // Initial node U15 - A45 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009116058,0.020135905,0.009819016,0.207298319,0.000000000],[0.024500257,0.009533097,0.193859401,0.010377090,0.000000000],[0.009835776,0.192739951,0.002153778,0.023649137,0.000000000],[0.234985657,0.010304218,0.027858593,0.013833748,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [11] // Basepair U15 - A45 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [2] | Right Index [10] // Fixed node on left
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [3] | Right Index [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [10] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000000078125000000000012000000000000000000000000000] | Num Left Bases [6] | Num Right Bases [1] | Left Index [4] | Right Index [10] | Norm Constant [1.000000000000000] // Cluster node A18:G23 and C44:C44
Interaction  | Interacting Bases [6,7] | Pair Probability [[0.010195092,0.020769450,0.011804402,0.193474890,0.000000000],[0.017202006,0.008406578,0.208382157,0.013263440,0.000000000],[0.011655809,0.234558465,0.002149506,0.027571043,0.000000000],[0.192357660,0.013922753,0.023782986,0.010503762,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G23 - C44 cWW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.022062116,0.052061168,0.004657104,0.485318270,0.000000000],[0.021929599,0.060153984,0.019602286,0.060262558,0.000000000],[0.004657104,0.026684972,0.023169287,0.051844976,0.000000000],[0.048915432,0.051457529,0.021223473,0.046000141,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A18 - U22 tWW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.031250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.031250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.906250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion G19
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A20
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion G21
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 [10] | Right Index [9] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [10] | Right Index [10] | 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_70401.1:
> IL_70401.1 IL_4M4O_003 U   15 A   45
UAAAGAGUG*CA
> IL_70401.1 IL_4M6D_012 U   15 A   45
UAAAGAGUG*CA