Alignment of IL_46301.1 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
3

2
5
4
I

6
9

3
7
9
I

8
10

4
9
10
I

10
11


11
10
I

12
10

5
13
9
I

14
9

6
15
8
I

16
7

7
17
6
I

18
5

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_46301.1_Instance_1 IL_46301.1_IL_1NUV_002_G43_C27GGAGCCGAGC
IL_46301.1_Sequence_1 IL_46301.1_IL_1NUV_002_G43_C27GGAG*CCGAGCtrue94000.69
IL_46301.1_Instance_2 IL_46301.1_IL_1NUV_003_G43_C27GGAGCCGAGC
IL_46301.1_Sequence_2 IL_46301.1_IL_1NUV_003_G43_C27GGAG*CCGAGCtrue94000.69
IL_46301.1_Instance_3 IL_46301.1_IL_429D_002_G143_C127GGAGCCGAGC
IL_46301.1_Sequence_3 IL_46301.1_IL_429D_002_G143_C127GGAG*CCGAGCtrue94000.69
IL_46301.1_Instance_4 IL_46301.1_IL_2AW7_010_G227_C136GAUGCUGCC
IL_46301.1_Sequence_4 IL_46301.1_IL_2AW7_010_G227_C136GAUG*CUGCCtrue85001.72
IL_46301.1_Instance_5 IL_46301.1_IL_2QBG_108_G2843_C2874GGUGCUAAC
IL_46301.1_Sequence_5 IL_46301.1_IL_2QBG_108_G_2843_C_2874GGUG*CUAACtrue100000.00
IL_46301.1_Instance_6 IL_46301.1_IL_1FJG_008_G227_C136GAUGCUACC
IL_46301.1_Sequence_6 IL_46301.1_IL_1FJG_008_G227_C136GAUG*CUACCtrue98000.25
IL_46301.1_Instance_7 IL_46301.1_IL_3BNQ_002_C7_G19CACCGCAAG
IL_46301.1_Sequence_7 IL_46301.1_IL_3BNQ_002_C7_G19CACC*GCAAGtrue68003.76

Conserved interactions between motif group positions in IL_46301.1:
1 2 s35 
1 9 cWW 
2 3 s35 
2 9 s55 
3 4 s35 
3 6 cWW 
4 5 cWW 
4 6 s55 
5 6 s35 
7 8 s35 
8 9 s35 
9 8 7BPh
JAR3D SCFG/MRF model for IL_46301.1:
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 [9] // Initial node G43 - C27 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.006295927,0.038704674,0.007295738,0.119757154,0.000000000],[0.011147152,0.015884338,0.139388841,0.008310045,0.000000000],[0.007244124,0.460777835,0.001332193,0.016571652,0.000000000],[0.119369086,0.026181520,0.015255875,0.006483846,0.000000000],[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 G43 - C27 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.388888889,0.055555556,0.500000000,0.055555556,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // Fixed node on left
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 [3] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.277777778,0.277777778,0.388888889,0.055555556,0.000000000] | Position [2] | Left Index [3] | Right Index [8] // 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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.722222222,0.055555556,0.166666667,0.055555556,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // 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 [0.568485889,0.428131469,0.003231181,0.000151462] | Right Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Left Index [3] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.013993991,0.258807327,0.013386597,0.033410534,0.000000000],[0.016349387,0.047220491,0.021592336,0.014415690,0.000000000],[0.013115176,0.023100305,0.004010946,0.099227971,0.000000000],[0.027907040,0.015718289,0.016415483,0.381328436,0.000000000],[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 [6] // Basepair A45 - C23 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009696313,0.019313569,0.011232880,0.184287162,0.000000000],[0.016884566,0.008035654,0.208890895,0.012733823,0.000000000],[0.011131706,0.260092205,0.002049121,0.025767468,0.000000000],[0.183526462,0.013182737,0.023188255,0.009987184,0.000000000],[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 G46 - C22 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_46301.1:
> IL_46301.1 IL_1NUV_002 G   43 C   27
GGAG*CCGAGC
> IL_46301.1 IL_1NUV_003 G   43 C   27
GGAG*CCGAGC
> IL_46301.1 IL_429D_002 G  143 C  127
GGAG*CCGAGC
> IL_46301.1 IL_2AW7_010 G  227 C  136
GAUG*CUGCC
> IL_46301.1 IL_2QBG_108 G 2843 C 2874
GGUG*CUAAC
> IL_46301.1 IL_1FJG_008 G  227 C  136
GAUG*CUACC
> IL_46301.1 IL_3BNQ_002 C    7 G   19
CACC*GCAAG