Alignment of IL_47758.2 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


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_47758.2_Instance_1 IL_47758.2_IL_1DUQ_001_G123_C107GGUACGGGC
IL_47758.2_Sequence_1 IL_47758.2_IL_1DUQ_001_G123_C107GGUAC*GGGCtrue100000.00
IL_47758.2_Instance_2 IL_47758.2_IL_1CSL_001_G70_C49GGUACGGGC
IL_47758.2_Sequence_2 IL_47758.2_IL_1CSL_001_G70_C49GGUAC*GGGCtrue100000.00
IL_47758.2_Instance_3 IL_47758.2_IL_1S72_037_A965_U1003AUUGCUGU
IL_47758.2_Sequence_3 IL_47758.2_IL_1S72_037_A965_U_1003AUUG*CUGUtrue80001.92
IL_47758.2_Instance_4 IL_47758.2_IL_4BPP_084_G1621_C1704GUAGCAAC
IL_47758.2_Sequence_4 IL_47758.2_IL_4BPP_084_G_1621_C_1704GUAG*CAACtrue84001.50

Conserved interactions between motif group positions in IL_47758.2:
1 2 s35 
1 8 cWW 
2 3 s55 
2 7 cHW 
3 4 s35 
3 6 cWW 
3 7 s55 
4 5 cWW 
4 6 s55 
5 6 s35 
6 7 s35 
7 8 s35 
JAR3D SCFG/MRF model for IL_47758.2:
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 G123 - C107 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009767519,0.021268948,0.011088337,0.204600662,0.000000000],[0.017577537,0.008464771,0.200414738,0.012276127,0.000000000],[0.010974938,0.234366259,0.002107823,0.027093309,0.000000000],[0.192187667,0.012778924,0.023277499,0.011754942,0.000000000],[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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair G123 - C107 cWW 
BasepairNode | Deletion Probability [0.0000016375373120] | Pair Probability [[0.004235055,0.004235055,0.032715145,0.016948065,0.000000000],[0.004235055,0.039851079,0.004235055,0.004235055,0.000000000],[0.042916657,0.197205402,0.442736260,0.013029168,0.000000000],[0.078132752,0.022381797,0.057556733,0.035351667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Left Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair G124 - G106 cHW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.169109165,0.061910562,0.213476799,0.020571755,0.000000000],[0.013854359,0.009362289,0.017745709,0.027302942,0.000000000],[0.186722167,0.018015243,0.003452274,0.024411989,0.000000000],[0.018645523,0.029161868,0.014693075,0.171564282,0.000000000],[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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair A126 - G105 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009918469,0.018622325,0.011505683,0.189225435,0.000000000],[0.018622679,0.008323799,0.226847981,0.013333072,0.000000000],[0.011505698,0.226847329,0.002108383,0.025185586,0.000000000],[0.189225546,0.013333007,0.025185962,0.010209047,0.000000000],[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 C127 - G104 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_47758.2:
> IL_47758.2 IL_1DUQ_001 G  123 C  107
GGUAC*GGGC
> IL_47758.2 IL_1CSL_001 G   70 C   49
GGUAC*GGGC
> IL_47758.2 IL_1S72_037 A  965 U 1003
AUUG*CUGU
> IL_47758.2 IL_4BPP_084 G 1621 C 1704
GUAG*CAAC