Alignment of IL_54041.2 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
7
I

12
8

6
13
8
I

14
9


15
8
I

16
8

7
17
5
I

18
5

8
19
4
I

20
4

9
21
3
I

22
3

10
23
2
I

24
2

11
25
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_54041.2_Instance_1 IL_54041.2,IL_5J7L_260,G799_C678GAGAUAGCGAAAC
IL_54041.2_Sequence_1 IL_54041.25J7L_G799_C678GAGAUAGC*GAAACtrue100000.00
IL_54041.2_Instance_2 IL_54041.2,IL_9DFE_016,G799_C678GAGAUAGCGAAAC
IL_54041.2_Sequence_2 IL_54041.29DFE_G799_C678GAGAUAGC*GAAACtrue100000.00
IL_54041.2_Instance_3 IL_54041.2,IL_4WF9_021,G844_C723GAGAUAGCGAAAC
IL_54041.2_Sequence_3 IL_54041.24WF9_G844_C723GAGAUAGC*GAAACtrue100000.00
IL_54041.2_Instance_4 IL_54041.2,IL_7A0S_015,G812_C691GAGAUAGCGAAAC
IL_54041.2_Sequence_4 IL_54041.27A0S_G812_C691GAGAUAGC*GAAACtrue100000.00
IL_54041.2_Instance_5 IL_54041.2,IL_8P9A_256,C931_G809CUAGUAGCGAAAG
IL_54041.2_Sequence_5 IL_54041.28P9A_C931_G809CUAGUAGC*GAAAGtrue82003.63
IL_54041.2_Instance_6 IL_54041.2,IL_8CRE_030,C927_G805CUAGUAGCGAAAG
IL_54041.2_Sequence_6 IL_54041.28CRE_C927_G805CUAGUAGC*GAAAGtrue82003.63
IL_54041.2_Instance_7 IL_54041.2,IL_4V9F_024,G892_C769GCAACAGCGAAUC
IL_54041.2_Sequence_7 IL_54041.24V9F_G892_C769GCAACAGC*GAAUCtrue77004.58

Conserved interactions between motif group positions in IL_54041.2:
1 2 s33 
1 11 cWW 
2 3 s55 
2 10 tWW 
3 4 s35 
3 9 tWH 
3 10 s55 
4 5 s35 
4 8 tWH 
5 7 s33 
5 8 s55 
6 7 cWW 
8 9 s33 
9 10 s55 
10 11 s35 
4 3 7BPh
5 8 6BR
JAR3D SCFG/MRF model for IL_54041.2:
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 [11] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009225160,0.018461010,0.010533281,0.191223781,0.000000000],[0.017164362,0.009144562,0.213851238,0.012801243,0.000000000],[0.010482999,0.244299236,0.001991779,0.024615947,0.000000000],[0.190171317,0.013006918,0.023266199,0.009760966,0.000000000],[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 [11] // Basepair G799 - C678 cWW 
BasepairNode | Deletion Probability [0.0000001232089072] | Pair Probability [[0.382418162,0.026612044,0.003450350,0.016493869,0.000000000],[0.025922251,0.012577988,0.010275794,0.043667329,0.000000000],[0.003450350,0.010290577,0.319063553,0.019445836,0.000000000],[0.078634598,0.012584058,0.019025013,0.016088230,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.007039775,0.985568462,0.007039775,0.000351989] | Left Letter Distribution [0.388888889,0.055555556,0.500000000,0.055555556,0.000000000] | 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 [10] // Basepair A800 - A677 tWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.405834395,0.003041302,0.268297449,0.003041302,0.000000000],[0.026031730,0.012906210,0.003041302,0.003041302,0.000000000],[0.076708152,0.007533718,0.111790406,0.032553138,0.000000000],[0.013742791,0.003041302,0.014576957,0.014818546,0.000000000],[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 [9] // Basepair A802 - A676 tWH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009963261,0.001767869,0.019984304,0.001767869,0.000000000],[0.071081112,0.106635815,0.001767869,0.001767869,0.000000000],[0.001767869,0.004772464,0.014122660,0.010194127,0.000000000],[0.616889197,0.006047715,0.034449920,0.097020078,0.000000000],[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 [8] // Basepair U803 - A675 tWH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.959459459,0.013513514,0.013513514,0.013513514,0.000000000] | Position [1] | Left Index [5] | Right Index [7] // Fixed node on left for 5J7L|1|DA|C|678
InitialNode  | Left Length Distribution [0.007039775,0.985568462,0.007039775,0.000351989] | Left Letter Distribution [0.055555556,0.055555556,0.833333333,0.055555556,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009090944,0.016302246,0.010451159,0.189500131,0.000000000],[0.019328903,0.009258863,0.264630806,0.013146218,0.000000000],[0.010568529,0.193583350,0.001992102,0.022369654,0.000000000],[0.191956811,0.012666128,0.025520256,0.009633898,0.000000000],[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 C806 - G674 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_54041.2:
> IL_54041.2  5J7L G  799 C  678
GAGAUAGC*GAAAC
> IL_54041.2  9DFE G  799 C  678
GAGAUAGC*GAAAC
> IL_54041.2  4WF9 G  844 C  723
GAGAUAGC*GAAAC
> IL_54041.2  7A0S G  812 C  691
GAGAUAGC*GAAAC
> IL_54041.2  8P9A C  931 G  809
CUAGUAGC*GAAAG
> IL_54041.2  8CRE C  927 G  805
CUAGUAGC*GAAAG
> IL_54041.2  4V9F G  892 C  769
GCAACAGC*GAAUC