Alignment of IL_50521.1 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
3
I

6
4

3
7
4
I

8
4

4
9
4
I

10
4

5
11
5
I

12
6

6
13
7
I

14
8

7
15
8
I

16
9


17
8
I

18
8

8
19
5
I

20
4

9
21
4
I

22
4

10
23
4
I

24
4

11
25
4
I

26
4

12
27
3
I

28
3

13
29
2
I

30
2

14
31
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_50521.1_Instance_1 IL_50521.1_IL_1FJG_017_G409_C433GGAAGAAGUGUAAAC
IL_50521.1_Sequence_1 IL_50521.1_IL_1FJG_017_G409_C433GGAAGAAG*UGUAAACtrue98000.37
IL_50521.1_Instance_2 IL_50521.1_IL_2AW7_020_U409_G433UGAAGAAGUGUAAAG
IL_50521.1_Sequence_2 IL_50521.1_IL_2AW7_020_U409_G433UGAAGAAG*UGUAAAGtrue100000.00

Conserved interactions between motif group positions in IL_50521.1:
1 2 s35 
1 14 cWW 
2 10 s33 
2 13 tSH 
3 4 s35 
3 9 s35 
3 10 s55 
3 11 tWH 
4 9 tSS 
5 6 s35 
5 11 tHW 
5 12 s55 
6 7 s35 
7 8 cWW 
8 9 s33 
9 11 s55 
10 12 cWH 
11 12 s35 
12 13 s35 
13 14 s35 
9 5 6BPh
2 12 6BPh
13 2 6BR
JAR3D SCFG/MRF model for IL_50521.1:
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 [14] // Initial node G409 - C433 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.011606602,0.017778352,0.013679584,0.116107298,0.000000000],[0.167090224,0.012234263,0.126818052,0.015364421,0.000000000],[0.013781309,0.136797428,0.002838808,0.021529953,0.000000000],[0.118996443,0.014843715,0.198100860,0.012432686,0.000000000],[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 [14] // Basepair G409 - C433 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.043716223,0.050956855,0.000526725,0.002508196,0.000000000],[0.044105167,0.046228647,0.000526725,0.000526725,0.000000000],[0.388315159,0.003687073,0.017863095,0.306690455,0.000000000],[0.047517987,0.045777520,0.000526725,0.000526725,0.000000000],[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 [2] | Right Index [13] // Basepair G410 - A432 tSH 
ClusterNode  | Deletion Probability [0.000000000000000000385733987058166880000000000000000000000000] | Num Left Bases [3] | Num Right Bases [4] | Left Index [3] | Right Index [12] | Norm Constant [0.409673001779593] // Cluster node A411:A414 and G428:A431
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.004207186,0.005280481,0.062750142,0.005167681,0.000000000],[0.000917983,0.000917983,0.006425879,0.000917983,0.000000000],[0.082535231,0.085064800,0.662195716,0.074439110,0.000000000],[0.000917983,0.000917983,0.006425879,0.000917983,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G413 - G428 tSS 
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.418144609,0.003985368,0.341751342,0.003985368,0.000000000],[0.031463906,0.014640658,0.022813077,0.003985368,0.000000000],[0.003985368,0.003985368,0.049366656,0.035560217,0.000000000],[0.019002964,0.003985368,0.023593614,0.019750751,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A411 - A430 tWH 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.418144609,0.031463906,0.003985368,0.019002964,0.000000000],[0.003985368,0.014640658,0.003985368,0.003985368,0.000000000],[0.341751342,0.022813077,0.049366656,0.023593614,0.000000000],[0.003985368,0.003985368,0.035560217,0.019750751,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A414 - A430 tHW 
Interaction  | Interacting Bases [5,7] | Pair Probability [[0.003460772,0.003460772,0.017164318,0.012348510,0.000000000],[0.003460772,0.037017516,0.016981393,0.188883971,0.000000000],[0.015181754,0.003460772,0.013849500,0.003460772,0.000000000],[0.365685069,0.003460772,0.277303821,0.034819514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U429 - A431 cWH 
Insertion    | Location [1] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 3, position 1 in cluster node
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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [8] // Initial node A415 - U427 from junction 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [6] | Right Index [8] // 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 [7] | Right Index [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.016500430,0.310288742,0.015571103,0.044672112,0.000000000],[0.014475176,0.011549597,0.038212544,0.015431970,0.000000000],[0.015226490,0.044298882,0.003453650,0.364972803,0.000000000],[0.037922120,0.017096803,0.015161977,0.035165601,0.000000000],[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 [7] | Right Index [8] // Basepair G416 - U427 cWW 
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_50521.1:
> IL_50521.1 IL_1FJG_017 G  409 C  433
GGAAGAAG*UGUAAAC
> IL_50521.1 IL_2AW7_020 U  409 G  433
UGAAGAAG*UGUAAAG