Alignment of IL_37053.1 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
5

4
9
5
I

10
5

5
11
5
I

12
5

6
13
6
I

14
7


15
6
I

16
5

7
17
5
I

18
5

8
19
5
I

20
5

9
21
4
I

22
4

10
23
3
I

24
3

11
25
2
I

26
2

12
27
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_37053.1_Instance_1 IL_37053.1_IL_4A1B_077_U1735_A1757UGAAAUUAGAGAUA
IL_37053.1_Sequence_1 IL_37053.1_IL_4A1B_077_U_1735_A_1757UGAAAUU*AGAGAUAtrue97000.40
IL_37053.1_Instance_2 IL_37053.1_IL_3U5H_081_C1711_G1733CGGAAUUGGAGAUG
IL_37053.1_Sequence_2 IL_37053.1_IL_3U5H_081_C_1711_G_1733CGGAAUU*GGAGAUGtrue100000.00
IL_37053.1_Instance_3 IL_37053.1_IL_1S72_058_U1587_G1608UGGAAGCAGGAAG
IL_37053.1_Sequence_3 IL_37053.1_IL_1S72_058_U_1587_G_1608UGGAAG*CAGGAAGtrue92001.30

Conserved interactions between motif group positions in IL_37053.1:
1 2 s35 
1 12 cWW 
2 3 s35 
2 11 tSH 
2 12 s55 
3 4 s35 
3 9 s33 
3 10 tSH 
4 7 tSS 
4 8 s33 
4 9 tHS 
4 10 s55 
6 7 cWW 
10 11 s35 
11 12 s35 
2 10 6BPh
3 10 6BPh
4 7 6BR
3 9 6BR
4 9 6BR
JAR3D SCFG/MRF model for IL_37053.1:
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 [12] // Initial node U1735 - A1757 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.010617565,0.017207514,0.012224139,0.144725988,0.000000000],[0.119578446,0.011276938,0.159608290,0.013787516,0.000000000],[0.012394940,0.145308958,0.002585264,0.020771623,0.000000000],[0.159746803,0.012984375,0.144469588,0.012712053,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair U1735 - A1757 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.019680511,0.052135779,0.000598716,0.003321980,0.000000000],[0.019508401,0.020008761,0.000598716,0.000598716,0.000000000],[0.378788100,0.004191009,0.025571885,0.418046764,0.000000000],[0.035351914,0.020401319,0.000598716,0.000598716,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair G1736 - U1756 tSH 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.168008325,0.137401149,0.001642125,0.011900428,0.000000000],[0.047047609,0.037864462,0.000532653,0.000532653,0.000000000],[0.278182915,0.002619096,0.013399396,0.204760253,0.000000000],[0.048415624,0.046628008,0.000532653,0.000532653,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // Basepair A1737 - A1755 tSH 
ClusterNode  | Deletion Probability [0.000000000000000002141016935993338200000000000000000000000000] | Num Left Bases [3] | Num Right Bases [3] | Left Index [4] | Right Index [9] | Norm Constant [0.203059297941871] // Cluster node A1738:U1741 and A1751:G1754
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.246133399,0.253695198,0.246453931,0.224620956,0.000000000],[0.000520662,0.000520662,0.000520662,0.000520662,0.000000000],[0.002474039,0.002668836,0.003464906,0.016323442,0.000000000],[0.000520662,0.000520662,0.000520662,0.000520662,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1738 - A1751 tSS 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.010671796,0.018383968,0.012272411,0.145081933,0.000000000],[0.118399456,0.011223837,0.147716963,0.013568949,0.000000000],[0.012345101,0.157172007,0.002585120,0.022020461,0.000000000],[0.159365085,0.013201127,0.143217320,0.012774467,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1741 - A1751 cWW 
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.186964122,0.188627543,0.254394136,0.203223383,0.000000000],[0.043586124,0.039541834,0.000450536,0.039155962,0.000000000],[0.000450536,0.000450536,0.002182752,0.000450536,0.000000000],[0.002145394,0.000450536,0.037475536,0.000450536,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1738 - G1754 tHS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A1739
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G1752
Insertion    | Location [2] | Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion after nucleotide 5, position 2 in cluster node
Insertion    | Location [5] | Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000]// Insertion after nucleotide 8, position 5 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_37053.1:
> IL_37053.1 IL_4A1B_077 U 1735 A 1757
UGAAAUU*AGAGAUA
> IL_37053.1 IL_3U5H_081 C 1711 G 1733
CGGAAUU*GGAGAUG
> IL_37053.1 IL_1S72_058 U 1587 G 1608
UGGAAG*CAGGAAG