Alignment of IL_06136.2 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_06136.2_Instance_1 IL_06136.2,IL_3FTF_001,G1515_C1520GGGAACGGGAAC
IL_06136.2_Sequence_1 IL_06136.23FTF_G_1515_C_1520GGGAAC*GGGAACtrue100000.00
IL_06136.2_Instance_2 IL_06136.2,IL_3FTE_001,G1515_C1520GGGAACGGGAAC
IL_06136.2_Sequence_2 IL_06136.23FTE_G_1515_C_1520GGGAAC*GGGAACtrue100000.00
IL_06136.2_Instance_3 IL_06136.2,IL_3R9W_001,G1515_C1520GGGAACGGGAAC
IL_06136.2_Sequence_3 IL_06136.23R9W_G_1515_C_1520GGGAAC*GGGAACtrue100000.00
IL_06136.2_Instance_4 IL_06136.2,IL_5LR4_002,C3_G8CGGAUGCGGAUG
IL_06136.2_Sequence_4 IL_06136.25LR4_C3_G8CGGAUG*CGGAUGtrue98000.29
IL_06136.2_Instance_5 IL_06136.2,IL_5LR3_002,C3_G8CGGAUGCGGAUG
IL_06136.2_Sequence_5 IL_06136.25LR3_C3_G8CGGAUG*CGGAUGtrue98000.29
IL_06136.2_Instance_6 IL_06136.2,IL_7A0S_018,G736_C721GCGGAGUGAAAC
IL_06136.2_Sequence_6 IL_06136.27A0S_G736_C721GCGGAG*UGAAACtrue78003.23

Conserved interactions between motif group positions in IL_06136.2:
1 2 s35 
1 12 cWW 
2 3 s35 
2 11 tSH 
2 12 s55 
3 9 s33 
3 10 tSH 
4 5 s35 
4 8 s33 
4 9 tHS 
4 10 s55 
5 6 s35 
5 8 tHS 
6 7 cWW 
6 8 s55 
7 8 s35 
8 9 s35 
10 11 s35 
11 12 s35
JAR3D SCFG/MRF model for IL_06136.2:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [12] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009303158,0.018489895,0.010627125,0.192911785,0.000000000],[0.017471954,0.009238523,0.216141290,0.012945225,0.000000000],[0.010587651,0.236901681,0.002010592,0.024697007,0.000000000],[0.192085542,0.013106691,0.023637380,0.009844500,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair G1515 - C1520 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.083928127,0.092947454,0.001687479,0.009202510,0.000000000],[0.103889074,0.078873753,0.001687479,0.001687479,0.000000000],[0.183115013,0.001687479,0.010347045,0.176029550,0.000000000],[0.147730183,0.103812416,0.001687479,0.001687479,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair G1516 - A1519 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.103324974,0.109383411,0.001240347,0.005845761,0.000000000],[0.104092605,0.109130123,0.001240347,0.001240347,0.000000000],[0.225562147,0.001240347,0.006063665,0.105276001,0.000000000],[0.115338265,0.108540964,0.001240347,0.001240347,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // Basepair G1517 - A1518 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.103324974,0.104092605,0.193666370,0.115338265,0.000000000],[0.109383411,0.109130123,0.001240347,0.108540964,0.000000000],[0.033136125,0.001240347,0.006063665,0.001240347,0.000000000],[0.005845761,0.001240347,0.105276001,0.001240347,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // Basepair A1518 - G1517 tHS 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.089420779,0.082779780,0.191033087,0.145754852,0.000000000],[0.098147433,0.086140462,0.001651418,0.107235222,0.000000000],[0.001651418,0.001651418,0.009856129,0.001651418,0.000000000],[0.008845142,0.001651418,0.170878606,0.001651418,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair A1519 - G1516 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010250831,0.062344241,0.011126372,0.173783681,0.000000000],[0.017440548,0.009785795,0.199811270,0.013206254,0.000000000],[0.011096934,0.190253136,0.002195921,0.081342052,0.000000000],[0.166498348,0.013338697,0.022714799,0.014811119,0.000000000],[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 C1520 - G1515 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_06136.2:
> IL_06136.2  3FTF G 1515 C 1520
GGGAAC*GGGAAC
> IL_06136.2  3FTE G 1515 C 1520
GGGAAC*GGGAAC
> IL_06136.2  3R9W G 1515 C 1520
GGGAAC*GGGAAC
> IL_06136.2  5LR4 C    3 G    8
CGGAUG*CGGAUG
> IL_06136.2  5LR3 C    3 G    8
CGGAUG*CGGAUG
> IL_06136.2  7A0S G  736 C  721
GCGGAG*UGAAAC