Alignment of IL_77691.5 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
6
I

10
7

5
11
7
I

12
8


13
7
I

14
7

6
15
4
I

16
4

7
17
3
I

18
3

8
19
2
I

20
2

9
21
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_77691.5_Instance_1 IL_77691.5,IL_5J7L_317,C1874_G1867CGAAGUUAG
IL_77691.5_Sequence_1 IL_77691.55J7L_C_1874_G_1867CGAAG*UUAGtrue100000.00
IL_77691.5_Instance_2 IL_77691.5,IL_4WF9_075,C1901_G1894CGAAGUUAG
IL_77691.5_Sequence_2 IL_77691.54WF9_C_1901_G_1894CGAAG*UUAGtrue100000.00
IL_77691.5_Instance_3 IL_77691.5,IL_3FS0_001,C-1_G49CGGAAUGAG
IL_77691.5_Sequence_3 IL_77691.53FS0_C-1_G49CGGAA*UGAGtrue95000.47
IL_77691.5_Instance_4 IL_77691.5,IL_4LFB_062,C1431_G1469CGAAGCGAG
IL_77691.5_Sequence_4 IL_77691.54LFB_C_1431_G_1469CGAAG*CGAGtrue92000.74
IL_77691.5_Instance_5 IL_77691.5,IL_2R8S_002,G112_C208GAAAGUAAC
IL_77691.5_Sequence_5 IL_77691.52R8S_G112_C208GAAAG*UAACtrue93000.69
IL_77691.5_Instance_6 IL_77691.5,IL_3FTM_002,C-1_G49CGGAAUGAG
IL_77691.5_Sequence_6 IL_77691.53FTM_C-1_G49CGGAA*UGAGtrue95000.47
IL_77691.5_Instance_7 IL_77691.5,IL_3IGI_009,C190_G175CAAAGUGAG
IL_77691.5_Sequence_7 IL_77691.53IGI_C190_G175CAAAG*UGAGtrue97000.25

Conserved interactions between motif group positions in IL_77691.5:
1 2 s35 
1 9 cWW 
2 7 s33 
2 8 tSH 
2 9 s55 
3 4 s35 
3 7 tHS 
3 8 s55 
4 5 s35 
5 6 cWW 
6 7 s35 
8 9 s35 
8 2 6BR
JAR3D SCFG/MRF model for IL_77691.5:
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 [9] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009117787,0.016733999,0.010467584,0.189844861,0.000000000],[0.018895995,0.009236003,0.254474892,0.013077223,0.000000000],[0.010551423,0.203726527,0.001992038,0.022818912,0.000000000],[0.191599712,0.012734286,0.025069445,0.009659312,0.000000000],[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 [9] // Basepair C1874 - G1867 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.143645405,0.086894129,0.001403410,0.007281600,0.000000000],[0.124060837,0.100221149,0.001403410,0.001403410,0.000000000],[0.179024738,0.001403410,0.008690899,0.088735625,0.000000000],[0.129083474,0.123941684,0.001403410,0.001403410,0.000000000],[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 [8] // Basepair G1875 - A1866 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.107987991,0.096183028,0.135018428,0.138788209,0.000000000],[0.059244635,0.071098115,0.001879416,0.093517091,0.000000000],[0.001879416,0.001879416,0.136208906,0.001879416,0.000000000],[0.085661198,0.001879416,0.065015903,0.001879416,0.000000000],[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 [7] // Basepair A1876 - U1865 tHS 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.833333333,0.055555556,0.055555556,0.055555556,0.000000000] | Position [1] | Left Index [4] | Right Index [6] // Fixed node on left for 5J7L|1|DA|G|1867
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.012482246,0.170477642,0.012008947,0.147775691,0.000000000],[0.014574816,0.010875866,0.100377512,0.012477159,0.000000000],[0.011819843,0.114007625,0.002607761,0.232252099,0.000000000],[0.100380093,0.013452335,0.017305668,0.027124696,0.000000000],[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 [5] | Right Index [6] // Basepair G1878 - U1864 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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_77691.5:
> IL_77691.5  5J7L C 1874 G 1867
CGAAG*UUAG
> IL_77691.5  4WF9 C 1901 G 1894
CGAAG*UUAG
> IL_77691.5  3FS0 C   -1 G   49
CGGAA*UGAG
> IL_77691.5  4LFB C 1431 G 1469
CGAAG*CGAG
> IL_77691.5  2R8S G  112 C  208
GAAAG*UAAC
> IL_77691.5  3FTM C   -1 G   49
CGGAA*UGAG
> IL_77691.5  3IGI C  190 G  175
CAAAG*UGAG