Alignment of IL_97296.1 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
5

3
7
5
I

8
6

4
9
6
I

10
7


11
6
I

12
6

5
13
5
I

14
5

6
15
2
I

16
2

7
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_97296.1_Instance_1 IL_97296.1_IL_2O3V_003_C30_G19CGCUAAAAG
IL_97296.1_Sequence_1 IL_97296.1_IL_2O3V_003_C30_G19CGCU*AAAAGtrue100000.00
IL_97296.1_Instance_2 IL_97296.1_IL_3MEI_004_C7_G17CGCCGCCUG
IL_97296.1_Sequence_2 IL_97296.1_IL_3MEI_004_C7_G17CGCC*GCCUGtrue95000.49
IL_97296.1_Instance_3 IL_97296.1_IL_3V2F_105_G2843_C2874GGGGCCGAC
IL_97296.1_Sequence_3 IL_97296.1_IL_3V2F_105_G_2843_C_2874GGGG*CCGACtrue85001.45
IL_97296.1_Instance_4 IL_97296.1_IL_3U5F_017_C270_G285CAUGUGG
IL_97296.1_Sequence_4 IL_97296.1_IL_3U5F_017_C270_G285CAUG*UGGtrue88001.12

Conserved interactions between motif group positions in IL_97296.1:
1 2 s35 
1 7 cWW 
2 3 s35 
2 7 s55 
3 4 s35 
3 6 cWS 
4 5 cWW 
5 6 s35 
JAR3D SCFG/MRF model for IL_97296.1:
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 [7] // Initial node C30 - G19 from junction 
BasepairNode | Deletion Probability [0.0000001177014991] | Pair Probability [[0.009878188,0.017748468,0.011469828,0.188961043,0.000000000],[0.019498419,0.008363241,0.238084568,0.013495422,0.000000000],[0.011542717,0.215631747,0.002108490,0.024257963,0.000000000],[0.189509081,0.013172006,0.026116132,0.010162687,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.250611247,0.495110024,0.250764059,0.003361858,0.000152812] | Right Letter Distribution [0.416666667,0.083333333,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair C30 - G19 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.250000000,0.083333333,0.583333333,0.083333333,0.000000000] | Position [1] | Left Index [2] | Right Index [6] // Fixed node on left
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000016375373120] | Pair Probability [[0.012055565,0.018331342,0.011355527,0.017534010,0.000000000],[0.145009686,0.144826619,0.129873228,0.134137228,0.000000000],[0.085274723,0.108121990,0.019701983,0.086598223,0.000000000],[0.012763005,0.014039013,0.050235073,0.010142786,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Right Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair C32 - A17 cWS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.011240200,0.090328744,0.011978303,0.156393929,0.000000000],[0.018867816,0.009331214,0.170326246,0.012994719,0.000000000],[0.011897924,0.171543763,0.002429090,0.112687596,0.000000000],[0.166335353,0.013385023,0.023141294,0.017118787,0.000000000],[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 U33 - A15 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_97296.1:
> IL_97296.1 IL_2O3V_003 C   30 G   19
CGCU*AAAAG
> IL_97296.1 IL_3MEI_004 C    7 G   17
CGCC*GCCUG
> IL_97296.1 IL_3V2F_105 G 2843 C 2874
GGGG*CCGAC
> IL_97296.1 IL_3U5F_017 C  270 G  285
CAUG*UGG