Alignment of IL_23038.1 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
7

4
9
7
I

10
7

5
11
7
I

12
7

6
13
8
I

14
9

7
15
9
I

16
10


17
9
I

18
9

8
19
8
I

20
7

9
21
6
I

22
5

10
23
4
I

24
4

11
25
3
I

26
3

12
27
2
I

28
2

13
29
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_23038.1_Instance_1 IL_23038.1,IL_8P9A_300,U1737_A1707UCUUAUGUUAUCA
IL_23038.1_Sequence_1 IL_23038.18P9A_U_1737_A_1707UCUUAUG*UUAUCAtrue100000.00
IL_23038.1_Instance_2 IL_23038.1,IL_8CRE_077,U1733_A1703UCUUAUGUUAUCA
IL_23038.1_Sequence_2 IL_23038.18CRE_U_1733_A_1703UCUUAUG*UUAUCAtrue100000.00

Conserved interactions between motif group positions in IL_23038.1:
1 2 s35 
1 13 cWW 
2 3 s35 
2 12 bif 
2 13 s55 
3 4 perp 
3 10 s33 
3 11 tWH 
4 5 cSH 
4 9 s33 
5 6 s35 
5 10 s35 
6 7 s35 
6 9 cWW 
7 8 cWW 
7 9 s55 
8 9 s35 
10 11 s35 
11 12 s35 
12 13 s35 
4 3 7BPh
6 5 7BPh
5 10 6BR
JAR3D SCFG/MRF model for IL_23038.1:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [13] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009034335,0.017544761,0.009910087,0.196321162,0.000000000],[0.022043953,0.009831675,0.196981684,0.011044900,0.000000000],[0.009929415,0.194460696,0.002044250,0.023047545,0.000000000],[0.224032836,0.010374563,0.053294552,0.010103588,0.000000000],[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 [13] // Basepair U1737 - A1707 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.020329716,0.024021902,0.007285362,0.007285362,0.000000000],[0.085321476,0.748144029,0.007285362,0.007285362,0.000000000],[0.007285362,0.007285362,0.021397370,0.027931888,0.000000000],[0.007285362,0.007285362,0.007285362,0.007285362,0.000000000],[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 [12] // Basepair C1738 - C1706 bif 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.019059668,0.003911733,0.033938098,0.003911733,0.000000000],[0.338291337,0.045646942,0.003911733,0.003911733,0.000000000],[0.003911733,0.012240000,0.025155457,0.036900503,0.000000000],[0.038529923,0.003911733,0.015986500,0.410781171,0.000000000],[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 [3] | Right Index [11] // Basepair U1739 - U1705 tWH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [4] | Right Index [10] // Fixed node on right for 8P9A|1|AR|U|1740
InitialNode  | Left Length Distribution [1.000000000] | 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 [4] | Right Index [9] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [4] | Right Index [9] | Norm Constant [1.000000000000000] // Cluster node 8P9A|1|AR|U|1740:8P9A|1|AR|U|1742 and 8P9A|1|AR|U|1703:8P9A|1|AR|U|1703
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.003917817,0.071857546,0.003497950,0.006109389,0.000000000],[0.004330118,0.004668938,0.005222068,0.003839941,0.000000000],[0.003424890,0.005319704,0.001079822,0.013794930,0.000000000],[0.037358709,0.029110573,0.030984372,0.775483232,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|U|1742 - 8P9A|1|AR|U|1703 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.070874096,0.013425181,0.000686145,0.001914373,0.000000000],[0.069224509,0.012956333,0.000147304,0.001233407,0.000000000],[0.006286575,0.000147304,0.012409326,0.012058850,0.000000000],[0.624297629,0.088485288,0.001031126,0.084822554,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|U|1740 - 8P9A|1|AR|A|1741 cSH 
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 [7] | Right Index [8] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.015839826,0.296886961,0.014317634,0.084582798,0.000000000],[0.013722760,0.012789399,0.036431816,0.014404953,0.000000000],[0.014010903,0.041562971,0.003244391,0.344046970,0.000000000],[0.036578332,0.015734627,0.014397948,0.041447713,0.000000000],[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 G1743 - U1702 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_23038.1:
> IL_23038.1  8P9A U 1737 A 1707
UCUUAUG*UUAUCA
> IL_23038.1  8CRE U 1733 A 1703
UCUUAUG*UUAUCA