Alignment of IL_02809.3 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


11
5
I

12
5

5
13
4
I

14
4

6
15
3
I

16
3

7
17
2
I

18
2

8
19
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_02809.3_Instance_1 IL_02809.3_IL_4B5R_004_G82_C69GAAAUCCUGC
IL_02809.3_Sequence_1 IL_02809.3_IL_4B5R_004_G82_C69GAAA*UCCUGCtrue90001.25
IL_02809.3_Instance_2 IL_02809.3_IL_3GX5_004_G82_C69GAAAUCCUGC
IL_02809.3_Sequence_2 IL_02809.3_IL_3GX5_004_G82_C69GAAA*UCCUGCtrue90001.25
IL_02809.3_Instance_3 IL_02809.3_IL_4AOB_004_G82_C69GAAAUCCUGC
IL_02809.3_Sequence_3 IL_02809.3_IL_4AOB_004_G82_C69GAAA*UCCUGCtrue90001.25
IL_02809.3_Instance_4 IL_02809.3_IL_4KQY_006_G106_C90GGAAUCCAGC
IL_02809.3_Sequence_4 IL_02809.3_IL_4KQY_006_G106_C90GGAA*UCCAGCtrue70003.89
IL_02809.3_Instance_5 IL_02809.3_IL_3V7E_009_G314_C301GAAAUCCUGC
IL_02809.3_Sequence_5 IL_02809.3_IL_3V7E_009_G314_C301GAAA*UCCUGCtrue90001.25
IL_02809.3_Instance_6 IL_02809.3_IL_4ERD_002_U127_G142UUCGUUCG
IL_02809.3_Sequence_6 IL_02809.3_IL_4ERD_002_U127_G142UUCG*UUCGtrue100000.00
IL_02809.3_Instance_7 IL_02809.3_IL_165D_001_U3_G15UUCGUUCG
IL_02809.3_Sequence_7 IL_02809.3_IL_165D_001_U3_G15UUCG*UUCGtrue100000.00
IL_02809.3_Instance_8 IL_02809.3_IL_422D_001_U7_G22UUCGUUCG
IL_02809.3_Sequence_8 IL_02809.3_IL_422D_001_U7_G22UUCG*UUCGtrue100000.00
IL_02809.3_Instance_9 IL_02809.3_IL_1QBP_002_U22_G10UUCGUUCG
IL_02809.3_Sequence_9 IL_02809.3_IL_1QBP_002_U22_G10UUCG*UUCGtrue100000.00

Conserved interactions between motif group positions in IL_02809.3:
1 2 s35 
1 8 cWW 
2 3 s35 
2 7 cWW 
2 8 s55 
3 4 s35 
3 6 cWW 
4 5 cWW 
4 6 s55 
6 7 s35 
7 8 s35 
8 7 7BPh
JAR3D SCFG/MRF model for IL_02809.3:
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 [8] // Initial node G82 - C69 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.007469190,0.035454171,0.008848563,0.055108842,0.000000000],[0.135299260,0.018541243,0.060822847,0.009937285,0.000000000],[0.008965028,0.365385918,0.001900604,0.011999087,0.000000000],[0.057751514,0.026200513,0.188225765,0.008090169,0.000000000],[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 [8] // Basepair G82 - C69 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.031367251,0.013715955,0.156150857,0.014879404,0.000000000],[0.012363135,0.006744102,0.019055853,0.256312561,0.000000000],[0.035633151,0.020003102,0.032649911,0.015287890,0.000000000],[0.014774915,0.345521165,0.013799204,0.011741543,0.000000000],[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 [7] // Basepair A83 - G68 cWW 
BasepairNode | Deletion Probability [0.0000000665942263] | Pair Probability [[0.045076221,0.012605543,0.036331824,0.133311299,0.000000000],[0.013984889,0.008297207,0.020395310,0.351576389,0.000000000],[0.038647371,0.019429488,0.003148791,0.014069770,0.000000000],[0.015171150,0.261338176,0.015587646,0.011028925,0.000000000],[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 [0.440515158,0.005506439,0.550766313,0.003059133,0.000152957] | Right Letter Distribution [0.041666667,0.875000000,0.041666667,0.041666667,0.000000000] | Left Index [3] | Right Index [6] // Basepair A84 - U67 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.011671890,0.141753274,0.011575960,0.176125399,0.000000000],[0.016460837,0.009640055,0.115829431,0.011760984,0.000000000],[0.011423945,0.118941193,0.002553126,0.194780112,0.000000000],[0.123257240,0.012491177,0.018568110,0.023167266,0.000000000],[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 [4] | Right Index [5] // Basepair A85 - U64 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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_02809.3:
> IL_02809.3 IL_4B5R_004 G   82 C   69
GAAA*UCCUGC
> IL_02809.3 IL_3GX5_004 G   82 C   69
GAAA*UCCUGC
> IL_02809.3 IL_4AOB_004 G   82 C   69
GAAA*UCCUGC
> IL_02809.3 IL_4KQY_006 G  106 C   90
GGAA*UCCAGC
> IL_02809.3 IL_3V7E_009 G  314 C  301
GAAA*UCCUGC
> IL_02809.3 IL_4ERD_002 U  127 G  142
UUCG*UUCG
> IL_02809.3 IL_165D_001 U    3 G   15
UUCG*UUCG
> IL_02809.3 IL_422D_001 U    7 G   22
UUCG*UUCG
> IL_02809.3 IL_1QBP_002 U   22 G   10
UUCG*UUCG