Alignment of IL_94403.5 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
4
I

6
5

3
7
6
I

8
7

4
9
7
I

10
7

5
11
7
I

12
7

6
13
7
I

14
7

7
15
7
I

16
7

8
17
7
I

18
7

9
19
8
I

20
9


21
8
I

22
7

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_94403.5_Instance_1 IL_94403.5_IL_3V2F_082_G2110_C2179GCGUAGGAUAGCC
IL_94403.5_Sequence_1 IL_94403.5_IL_3V2F_082_G_2110_C_2179GCGUAGGAUAG*CCtrue100000.00
IL_94403.5_Instance_2 IL_94403.5_IL_1MZP_002_G6_C50GCGUAGGAUAGCC
IL_94403.5_Sequence_2 IL_94403.5_IL_1MZP_002_G6_C50GCGUAGGAUAG*CCtrue100000.00
IL_94403.5_Instance_3 IL_94403.5_IL_3UMY_002_G2110_C2179GCGUAGGAUAGCC
IL_94403.5_Sequence_3 IL_94403.5_IL_3UMY_002_G_2110_C_2179GCGUAGGAUAG*CCtrue100000.00
IL_94403.5_Instance_4 IL_94403.5_IL_4JRC_004_C37_G69CCGAAGCGAGUG
IL_94403.5_Sequence_4 IL_94403.5_IL_4JRC_004_C37_G69CCGAAGCGAG*UGtrue80003.90

Conserved interactions between motif group positions in IL_94403.5:
1 9 s35 
1 11 cWW 
2 3 s35 
3 4 s35 
4 5 s35 
4 8 tWH 
5 7 s33 
6 7 s35 
9 10 cWW 
9 11 s55 
10 11 s35 
5 8 6BPh
JAR3D SCFG/MRF model for IL_94403.5:
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 G2110 - C2179 from junction 
BasepairNode | Deletion Probability [0.0000001215781528] | Pair Probability [[0.009958751,0.019496181,0.011541539,0.189489827,0.000000000],[0.017746938,0.008284356,0.215611394,0.013170723,0.000000000],[0.011468679,0.238062912,0.002108276,0.026113208,0.000000000],[0.188942010,0.013494008,0.024255791,0.010255407,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Left Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | 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 [11] // Basepair G2110 - C2179 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.083333333,0.750000000,0.083333333,0.000000000] | Position [1] | Left Index [2] | Right Index [10] // Fixed node on left
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.250000000,0.083333333,0.083333333,0.583333333,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [10] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000000001418723246459155300000000000000000000000000] | Num Left Bases [6] | Num Right Bases [1] | Left Index [4] | Right Index [10] | Norm Constant [1.000000000000000] // Cluster node A2114:G2120 and C2178:C2178
Interaction  | Interacting Bases [6,7] | Pair Probability [[0.011545053,0.091357941,0.012500960,0.153268922,0.000000000],[0.016202600,0.009015557,0.162650528,0.013540081,0.000000000],[0.012307163,0.197820616,0.002427935,0.114576839,0.000000000],[0.150792068,0.014433261,0.021211816,0.016348660,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2120 - C2178 cWW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.429334136,0.003908726,0.335179201,0.003908726,0.000000000],[0.030858831,0.014359107,0.022374364,0.003908726,0.000000000],[0.003908726,0.003908726,0.048417298,0.034876366,0.000000000],[0.018637522,0.003908726,0.023139890,0.019370929,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A2114 - A2119 tWH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.016666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.016666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.950000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.016666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion G2115
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.583333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion G2116
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.583333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A2117
Insertion    | Location [4] | Length Distribution [0.253667482,0.736552567,0.009321516,0.000458435] | Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000]// Insertion after nucleotide 7, position 4 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 [10] | Right Index [9] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [10] | Right Index [10] | 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_94403.5:
> IL_94403.5 IL_3V2F_082 G 2110 C 2179
GCGUAGGAUAG*CC
> IL_94403.5 IL_1MZP_002 G    6 C   50
GCGUAGGAUAG*CC
> IL_94403.5 IL_3UMY_002 G 2110 C 2179
GCGUAGGAUAG*CC
> IL_94403.5 IL_4JRC_004 C   37 G   69
CCGAAGCGAG*UG