Alignment of IL_30381.1 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
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_30381.1_Instance_1 IL_30381.1_IL_2QBG_046_G1202_C1243GUAAGUAUC
IL_30381.1_Sequence_1 IL_30381.1_IL_2QBG_046_G_1202_C_1243GUAAG*UAUCtrue84001.93
IL_30381.1_Instance_2 IL_30381.1_IL_255D_001_U5_G8UUCGUUCG
IL_30381.1_Sequence_2 IL_30381.1_IL_255D_001_U5_G8UUCG*UUCGtrue100000.00

Conserved interactions between motif group positions in IL_30381.1:
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 
JAR3D SCFG/MRF model for IL_30381.1:
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 [8] // Initial node G1202 - C1243 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.011606602,0.017778352,0.013679584,0.116107298,0.000000000],[0.167090224,0.012234263,0.126818052,0.015364421,0.000000000],[0.013781309,0.136797428,0.002838808,0.021529953,0.000000000],[0.118996443,0.014843715,0.198100860,0.012432686,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair G1202 - C1243 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.026988300,0.093954263,0.030613407,0.027793783,0.000000000],[0.017478333,0.014280225,0.023277829,0.162701978,0.000000000],[0.029096715,0.024066390,0.004320739,0.034282392,0.000000000],[0.024710051,0.204808540,0.018326347,0.263300708,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair U1203 - U1242 cWW 
BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.115886556,0.013776780,0.039707575,0.016464332,0.000000000],[0.015284287,0.009068137,0.022290329,0.353939882,0.000000000],[0.042238270,0.021234768,0.003441360,0.015377055,0.000000000],[0.016580769,0.285620266,0.017035963,0.012053671,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair A1204 - A1241 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.016500430,0.310288742,0.015571103,0.044672112,0.000000000],[0.014475176,0.011549597,0.038212544,0.015431970,0.000000000],[0.015226490,0.044298882,0.003453650,0.364972803,0.000000000],[0.037922120,0.017096803,0.015161977,0.035165601,0.000000000],[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 G1206 - U1240 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_30381.1:
> IL_30381.1 IL_2QBG_046 G 1202 C 1243
GUAAG*UAUC
> IL_30381.1 IL_255D_001 U    5 G    8
UUCG*UUCG