Alignment of IL_40892.1 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
3

3
7
3
I

8
3

4
9
3
I

10
3

5
11
3
I

12
3

6
13
4
I

14
5


15
4
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_40892.1_Instance_1 IL_40892.1_IL_3U5H_101_A2520_U2587AUGAAGCGGGU
IL_40892.1_Sequence_1 IL_40892.1_IL_3U5H_101_A_2520_U_2587AUGAAGC*GGGUtrue100000.00
IL_40892.1_Instance_2 IL_40892.1_IL_4A1B_099_G2515_C2576GUGAAGAUUGC
IL_40892.1_Sequence_2 IL_40892.1_IL_4A1B_099_G_2515_C_2576GUGAAGA*UUGCtrue95000.85

Conserved interactions between motif group positions in IL_40892.1:
1 2 s35 
1 8 cWW 
2 3 cWS 
3 8 s35 
6 7 cWW 
JAR3D SCFG/MRF model for IL_40892.1:
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 A2520 - U2587 from junction 
BasepairNode | Deletion Probability [0.0000000005912491] | Pair Probability [[0.009722986,0.022602524,0.010807110,0.213946067,0.000000000],[0.018642384,0.008854915,0.200306720,0.011770232,0.000000000],[0.010724456,0.213953122,0.002148800,0.027678057,0.000000000],[0.199554445,0.012136228,0.023684855,0.013467100,0.000000000],[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 [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.083333333,0.083333333,0.583333333,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair A2520 - U2587 cWW 
ClusterNode  | Deletion Probability [0.000000000000000077146797411633740000000000000000000000000000] | Num Left Bases [5] | Num Right Bases [1] | Left Index [2] | Right Index [7] | Norm Constant [1.000000000000000] // Cluster node U2521:C2526 and G2584:G2584
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.009640843,0.020820542,0.010733993,0.213406915,0.000000000],[0.020428208,0.008935347,0.213416622,0.012101297,0.000000000],[0.010799946,0.200886051,0.002149018,0.025786435,0.000000000],[0.200132635,0.011807914,0.025581673,0.013372561,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C2526 - G2584 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.007512069,0.008360159,0.007186863,0.008188381,0.000000000],[0.014137583,0.014479854,0.010969251,0.014468650,0.000000000],[0.010578210,0.009148700,0.008845779,0.007931851,0.000000000],[0.327000080,0.177983196,0.181398224,0.191811151,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2521 - A2523 cWS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A2524
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion G2525
Insertion    | Location [1] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000]// Insertion after nucleotide 2, position 1 in cluster node
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 [7] | Right Index [6] // New Initial node after Cluster
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_40892.1:
> IL_40892.1 IL_3U5H_101 A 2520 U 2587
AUGAAGC*GGGU
> IL_40892.1 IL_4A1B_099 G 2515 C 2576
GUGAAGA*UUGC