Alignment of IL_42251.1 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
3
I

4
6

2
5
6
I

6
7


7
6
I

8
6

3
9
5
I

10
4

4
11
3
I

12
2

5
13
2
I

14
2

6
15
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_42251.1_Instance_1 IL_42251.1_IL_4FNJ_003_U27_A11UGCUAA
IL_42251.1_Sequence_1 IL_42251.1_IL_4FNJ_003_U27_A11UG*CUAAtrue100000.00
IL_42251.1_Instance_2 IL_42251.1_IL_1U6B_009_U162_A150UGCUAA
IL_42251.1_Sequence_2 IL_42251.1_IL_1U6B_009_U162_A150UG*CUAAtrue100000.00
IL_42251.1_Instance_3 IL_42251.1_IL_1QA6_001_G109_C129GUAGCAUC
IL_42251.1_Sequence_3 IL_42251.1_IL_1QA6_001_G109_C129GUAG*CAUCtrue84001.51
IL_42251.1_Instance_4 IL_42251.1_IL_2QBG_043_G1059_C1079GUUGCAUC
IL_42251.1_Sequence_4 IL_42251.1_IL_2QBG_043_G_1059_C_1079GUUG*CAUCtrue93000.66

Conserved interactions between motif group positions in IL_42251.1:
1 6 cWW 
2 3 cWW 
2 4 s55 
3 4 s35 
4 5 s35 
5 6 cSH 
JAR3D SCFG/MRF model for IL_42251.1:
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 [6] // Initial node U27 - A11 from junction 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [1] | Right Index [6] | Norm Constant [0.254951209121093] // Cluster node U27:U27 and A10:A11
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.009469891,0.020059356,0.010603791,0.196533016,0.000000000],[0.020450148,0.008797341,0.197253072,0.011592952,0.000000000],[0.010539143,0.219155954,0.002110264,0.025117588,0.000000000],[0.219177973,0.011880534,0.025324236,0.011934740,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U27 - A11 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.137818189,0.103088651,0.005213033,0.004518119,0.000000000],[0.106359205,0.100311682,0.001185874,0.104577052,0.000000000],[0.005542935,0.005354284,0.005993321,0.099240131,0.000000000],[0.010111954,0.209208468,0.001185874,0.100291229,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A10 - A11 cSH 
InitialNode  | Left Length Distribution [0.490496628,0.012262416,0.490803188,0.006131208,0.000306560] | Left Letter Distribution [0.250000000,0.083333333,0.083333333,0.583333333,0.000000000] | 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 [4] // Initial node G28 - U9 from junction 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.083333333,0.083333333,0.416666667,0.000000000] | Position [2] | Left Index [2] | Right Index [4] // 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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [3] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009999033,0.020370037,0.011577394,0.189754219,0.000000000],[0.016871198,0.008244913,0.204374808,0.013008374,0.000000000],[0.011431659,0.249278495,0.002108170,0.027040831,0.000000000],[0.188658474,0.013655008,0.023325621,0.010301767,0.000000000],[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 [2] | Right Index [3] // Basepair G28 - C8 cWW 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | 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_42251.1:
> IL_42251.1 IL_4FNJ_003 U   27 A   11
UG*CUAA
> IL_42251.1 IL_1U6B_009 U  162 A  150
UG*CUAA
> IL_42251.1 IL_1QA6_001 G  109 C  129
GUAG*CAUC
> IL_42251.1 IL_2QBG_043 G 1059 C 1079
GUUG*CAUC