Alignment of IL_79955.2 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
5

4
9
5
I

10
6

5
11
6
I

12
7

6
13
7
I

14
8


15
7
I

16
7

7
17
6
I

18
6

8
19
5
I

20
5

9
21
4
I

22
4

10
23
3
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_79955.2_Instance_1 IL_79955.2_IL_2AW7_037_A673_U717AGAAUUAGGAAU
IL_79955.2_Sequence_1 IL_79955.2_IL_2AW7_037_A673_U717AGAAUU*AGGAAUtrue100000.08
IL_79955.2_Instance_2 IL_79955.2_IL_1FJG_030_G673_C717GGAAUUAGGAAC
IL_79955.2_Sequence_2 IL_79955.2_IL_1FJG_030_G673_C717GGAAUU*AGGAACtrue100000.00
IL_79955.2_Instance_3 IL_79955.2_IL_4A1B_025_G562_C605GGAGUCACGAAAAC
IL_79955.2_Sequence_3 IL_79955.2_IL_4A1B_025_G562_C605GGAGUCAC*GAAAACtrue52007.64

Conserved interactions between motif group positions in IL_79955.2:
1 2 s35 
1 12 cWW 
2 3 s35 
2 11 cWW 
3 4 s35 
3 10 cWW 
4 5 s35 
4 9 cWW 
5 6 s35 
5 8 cSW 
6 7 cWW 
6 8 s55 
7 8 s35 
8 9 s35 
9 10 s35 
10 11 s35 
11 12 s35 
JAR3D SCFG/MRF model for IL_79955.2:
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 A673 - U717 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009784429,0.021777989,0.011031390,0.208347691,0.000000000],[0.017985926,0.008620950,0.201027673,0.012148861,0.000000000],[0.010927772,0.225150163,0.002128171,0.027374013,0.000000000],[0.195241385,0.012608128,0.023487298,0.012358162,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair A673 - U717 cWW 
BasepairNode | Deletion Probability [0.0000006376409404] | Pair Probability [[0.045115996,0.013962508,0.338697479,0.016071795,0.000000000],[0.014298241,0.005731928,0.019359879,0.043268658,0.000000000],[0.381657250,0.019116179,0.003525310,0.015542429,0.000000000],[0.016099227,0.040676227,0.015894192,0.010982702,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.651642683,0.016291067,0.326364377,0.005430356,0.000271518] | Left Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair G674 - A716 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.417333101,0.017239390,0.259255002,0.017136446,0.000000000],[0.013083937,0.003979156,0.018565226,0.019605876,0.000000000],[0.050924196,0.018873109,0.003979156,0.019011132,0.000000000],[0.072782957,0.040416298,0.014682399,0.013132619,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // Basepair A675 - A715 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.183826124,0.011443433,0.301561645,0.012884831,0.000000000],[0.067115556,0.004309900,0.015299415,0.032554752,0.000000000],[0.271072640,0.015494457,0.002821442,0.012720734,0.000000000],[0.012862876,0.034629574,0.012439205,0.008963416,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // Basepair A676 - G714 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.073047508,0.015684070,0.041196808,0.013291818,0.000000000],[0.016590084,0.014569073,0.321651087,0.016400656,0.000000000],[0.014443454,0.014128846,0.018083854,0.010409951,0.000000000],[0.018093766,0.015069156,0.385176707,0.012163162,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair U677 - G713 cSW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009329508,0.018973088,0.010330785,0.200366695,0.000000000],[0.023032249,0.009121783,0.208662517,0.011447685,0.000000000],[0.010390909,0.196046055,0.002131601,0.023465306,0.000000000],[0.225487075,0.011181893,0.027495044,0.012537807,0.000000000],[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 [6] | Right Index [7] // Basepair U678 - A712 cWW 
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_79955.2:
> IL_79955.2 IL_2AW7_037 A  673 U  717
AGAAUU*AGGAAU
> IL_79955.2 IL_1FJG_030 G  673 C  717
GGAAUU*AGGAAC
> IL_79955.2 IL_4A1B_025 G  562 C  605
GGAGUCAC*GAAAAC