Alignment of IL_97509.1 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
4

3
7
4
I

8
4

4
9
5
I

10
6

5
11
6
I

12
7


13
6
I

14
6

6
15
5
I

16
4

7
17
4
I

18
4

8
19
3
I

20
3

9
21
2
I

22
2

10
23
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_97509.1_Instance_1 IL_97509.1_IL_4BPP_046_G863_C905GUAUUAGGAC
IL_97509.1_Sequence_1 IL_97509.1_IL_4BPP_046_G863_C905GUAUU*AGGACtrue100000.00
IL_97509.1_Instance_2 IL_97509.1_IL_3U5F_003_U37_A471UCAAAUGACAA
IL_97509.1_Sequence_2 IL_97509.1_IL_3U5F_003_U37_A471UCAAA*UGACAAtrue88001.65

Conserved interactions between motif group positions in IL_97509.1:
1 2 s35 
1 10 cWW 
2 3 s35 
2 9 cWW 
2 10 s55 
3 4 s35 
3 7 wat 
3 8 cWW 
4 5 s35 
4 7 tHS 
4 8 s55 
5 6 cWW 
5 7 s55 
6 7 s35 
7 8 s35 
8 9 s35 
9 10 s35 
JAR3D SCFG/MRF model for IL_97509.1:
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 [10] // Initial node G863 - C905 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009655575,0.020452677,0.010811709,0.200386604,0.000000000],[0.020851131,0.008969837,0.201120779,0.011820265,0.000000000],[0.010745793,0.213649208,0.002151642,0.025610090,0.000000000],[0.213671659,0.012113485,0.025820790,0.012168755,0.000000000],[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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair G863 - C905 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.010610815,0.017566445,0.012200287,0.120859047,0.000000000],[0.206134582,0.013915363,0.114716350,0.013364208,0.000000000],[0.012383976,0.111101518,0.002917694,0.019539880,0.000000000],[0.138432870,0.012521397,0.179314102,0.014421465,0.000000000],[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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [9] // Basepair U864 - A904 cWW 
ClusterNode  | Deletion Probability [0.0000000000396545] | Num Left Bases [2] | Num Right Bases [2] | Left Index [3] | Right Index [8] | Norm Constant [0.181109043621461] // Cluster node A865:U866 and G902:G903
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.007750136,0.007750136,0.883747966,0.007750136,0.000000000],[0.007750136,0.007750136,0.007750136,0.007750136,0.000000000],[0.007750136,0.007750136,0.007750136,0.007750136,0.000000000],[0.007750136,0.007750136,0.007750136,0.007750136,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A865 - G902 wat 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.101728279,0.102633356,0.132373524,0.110575038,0.000000000],[0.118577332,0.107574724,0.001225696,0.106524945,0.000000000],[0.001225696,0.001225696,0.005938240,0.001225696,0.000000000],[0.005836608,0.001225696,0.200883780,0.001225696,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U866 - G902 tHS 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.177190689,0.109960849,0.281763742,0.012419737,0.000000000],[0.010771367,0.004154329,0.014747163,0.031379647,0.000000000],[0.261287932,0.014935165,0.002719598,0.012261563,0.000000000],[0.012398575,0.033379576,0.011990196,0.008639871,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A865 - G903 cWW 
Insertion    | Location [3] | Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 7, position 3 in cluster node
InitialNode  | 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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009183469,0.022285751,0.009814417,0.220857782,0.000000000],[0.022291510,0.009418174,0.193045342,0.010327057,0.000000000],[0.009814439,0.193043865,0.002150936,0.025717104,0.000000000],[0.220868443,0.010326961,0.025722659,0.015132092,0.000000000],[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 [5] | Right Index [6] // Basepair U867 - A901 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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_97509.1:
> IL_97509.1 IL_4BPP_046 G  863 C  905
GUAUU*AGGAC
> IL_97509.1 IL_3U5F_003 U   37 A  471
UCAAA*UGACAA