Alignment of IL_12211.1 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
5

2
5
5
I

6
5

3
7
5
I

8
5

4
9
5
I

10
5

5
11
5
I

12
5

6
13
6
I

14
7


15
6
I

16
5

7
17
5
I

18
5

8
19
5
I

20
5

9
21
5
I

22
5

10
23
4
I

24
3

11
25
2
I

26
2

12
27
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_12211.1_Instance_1 IL_12211.1_IL_1S72_100_G21_C59GGUUGCCUAUAAGC
IL_12211.1_Sequence_1 IL_12211.1_IL_1S72_100_G21_C59GGUUGCCU*AUAAGCtrue100000.00
IL_12211.1_Instance_2 IL_12211.1_IL_3U5H_144_G21_C58GAAAGCAUUAAGC
IL_12211.1_Sequence_2 IL_12211.1_IL_3U5H_144_G21_C58GAAAGCA*UUAAGCtrue92001.62

Conserved interactions between motif group positions in IL_12211.1:
1 12 cWW 
2 3 s35 
2 4 tSW 
2 5 s35 
2 8 s33 
3 4 s35 
4 5 s35 
5 6 s35 
5 7 bif 
5 8 cWW 
6 7 cWW 
6 10 tSW 
7 8 s35 
7 9 perp 
9 10 s35 
10 11 s35 
11 12 s35 
12 11 7BPh
JAR3D SCFG/MRF model for IL_12211.1:
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 [12] // Initial node G21 - C59 from junction 
BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.003952716,0.056367336,0.004576658,0.075011714,0.000000000],[0.006669351,0.022815069,0.080791377,0.005142338,0.000000000],[0.004519048,0.602973996,0.000833380,0.010689507,0.000000000],[0.074578555,0.037785716,0.009220848,0.004072390,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | 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 [12] // Basepair G21 - C59 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [2] | Left Index [2] | Right Index [11] // 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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [10] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000000000000008487548749722519800000000000000000000] | Num Left Bases [5] | Num Right Bases [4] | Left Index [2] | Right Index [10] | Norm Constant [0.024808460704894] // Cluster node G22:U28 and A54:A57
Interaction  | Interacting Bases [4,6] | Pair Probability [[0.015164621,0.014596964,0.003316707,0.003316707,0.000000000],[0.341474666,0.012192158,0.003316707,0.102247189,0.000000000],[0.003316707,0.003316707,0.204081524,0.003316707,0.000000000],[0.003316707,0.003316707,0.280392512,0.003316707,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C27 - A54 bif 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.009183469,0.022285751,0.009814417,0.220857782,0.000000000],[0.022291510,0.009418174,0.193045342,0.010327057,0.000000000],[0.009814439,0.193043865,0.002150936,0.025717104,0.000000000],[0.220868443,0.010326961,0.025722659,0.015132092,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U28 - A54 cWW 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.018651682,0.015154458,0.043678332,0.018110765,0.000000000],[0.016812716,0.009974951,0.024519362,0.398157400,0.000000000],[0.046462097,0.023358245,0.003785496,0.016914760,0.000000000],[0.018238846,0.314182292,0.018739559,0.013259038,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C27 - U55 cWW 
Interaction  | Interacting Bases [5,9] | Pair Probability [[0.343551684,0.013009703,0.002770506,0.012447068,0.000000000],[0.018196343,0.186036580,0.013571899,0.012534088,0.000000000],[0.016782196,0.026237419,0.002770506,0.009403153,0.000000000],[0.286854562,0.033075011,0.013375361,0.009383920,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U28 - A57 tSW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.182627929,0.026212171,0.101178320,0.072488382,0.000000000],[0.052618857,0.023706576,0.024051089,0.016245789,0.000000000],[0.061258760,0.234587796,0.002247839,0.009558020,0.000000000],[0.021287620,0.013586802,0.148929228,0.009414824,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G22 - C26 tSW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion G25
Interaction  | Interacting Bases [8,8] | 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]] // Right strand conserved insertion A56
Insertion    | Location [1] | Length Distribution [0.481347774,0.024067389,0.481949458,0.012033694,0.000601685] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion after nucleotide 2, position 1 in cluster node
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 [7] | Right Index [6] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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_12211.1:
> IL_12211.1 IL_1S72_100 G   21 C   59
GGUUGCCU*AUAAGC
> IL_12211.1 IL_3U5H_144 G   21 C   58
GAAAGCA*UUAAGC