Alignment of IL_60649.1 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
2

2
5
2
I

6
2

3
7
2
I

8
2

4
9
2
I

10
2

5
11
3
I

12
4

6
13
5
I

14
6

7
15
6
I

16
7


17
6
I

18
6

8
19
3
I

20
2

9
21
2
I

22
2

10
23
2
I

24
2

11
25
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_60649.1_Instance_1 IL_60649.1_IL_4FAW_006_A149_U225AUAUGAGGUAAAU
IL_60649.1_Sequence_1 IL_60649.1_IL_4FAW_006_A149_U225AUAUGAGG*UAAAUtrue100000.00

Conserved interactions between motif group positions in IL_60649.1:
1 2 s35 
1 5 cSS 
1 11 cWW 
3 10 s35 
5 6 s35 
5 9 tHW 
5 10 s53 
5 11 tSS 
6 7 s35 
6 9 s55 
7 8 cWW 
9 10 s33 
10 2 7BR
9 4 7BR
3 10 6BR
JAR3D SCFG/MRF model for IL_60649.1:
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 [11] // Initial node A149 - U225 from junction 
ClusterNode  | Deletion Probability [0.000000000000000000000009307413805830298700000000000000000000] | Num Left Bases [5] | Num Right Bases [3] | Left Index [1] | Right Index [11] | Norm Constant [0.009387342401780] // Cluster node A149:A154 and A222:U225
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.506438116,0.007840179,0.000993074,0.004735160,0.000000000],[0.004965371,0.003648161,0.000993074,0.000993074,0.000000000],[0.425788143,0.005684564,0.012301188,0.005879059,0.000000000],[0.004965371,0.000993074,0.008860898,0.004921494,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A154 - A222 tHW 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.009342473,0.024677534,0.009906945,0.226837217,0.000000000],[0.020281602,0.009395363,0.194134563,0.010378776,0.000000000],[0.009890064,0.195262113,0.002169362,0.028060170,0.000000000],[0.208798271,0.010452176,0.023820256,0.016593115,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A149 - U225 cWW 
Interaction  | Interacting Bases [5,8] | Pair Probability [[0.207800644,0.221738047,0.219780639,0.260581942,0.000000000],[0.002506810,0.002506810,0.002506810,0.002506810,0.000000000],[0.011813840,0.011879886,0.014111804,0.032238722,0.000000000],[0.002506810,0.002506810,0.002506810,0.002506810,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A154 - U225 tSS 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.086939953,0.072624236,0.070524287,0.073782299,0.000000000],[0.067518845,0.063767557,0.006019939,0.070392706,0.000000000],[0.070843756,0.067331062,0.042601166,0.069586592,0.000000000],[0.072918886,0.034751210,0.055201728,0.075195777,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A149 - A154 cSS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion U150
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.785714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A151
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion G153
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.785714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A224
Insertion    | Location [3] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 3, position 3 in cluster node
Insertion    | Location [6] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 9, position 6 in cluster node
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [8] // Initial node G155 - U221 from junction 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Position [1] | Left Index [6] | Right Index [8] // Fixed node on left
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [7] | Right Index [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.016663800,0.313360908,0.015725272,0.045114411,0.000000000],[0.014618495,0.011663950,0.038590886,0.015584762,0.000000000],[0.015377247,0.044737484,0.003487844,0.358685405,0.000000000],[0.038297587,0.017266078,0.015312095,0.035513776,0.000000000],[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 [7] | Right Index [8] // Basepair G156 - U221 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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_60649.1:
> IL_60649.1 IL_4FAW_006 A  149 U  225
AUAUGAGG*UAAAU