Alignment of IL_49612.1 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
4
I

6
5

3
7
6
I

8
7

4
9
7
I

10
8

5
11
9
I

12
12

6
13
12
I

14
13


15
12
I

16
12

7
17
11
I

18
10

8
19
7
I

20
7

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_49612.1_Instance_1 IL_49612.1,IL_5J7L_362,C1051_G1207CGGCAUAUGG
IL_49612.1_Sequence_1 IL_49612.15J7L_C_1051_G_1207CGGCAU*AUGGtrue100000.00
IL_49612.1_Instance_2 IL_49612.1,IL_8CRE_454,G1415_C1264GUCUGUGAUGGC
IL_49612.1_Sequence_2 IL_49612.18CRE_G_1415_C_1264GUCUGUGA*UGGCtrue99000.09

Conserved interactions between motif group positions in IL_49612.1:
1 2 s35 
1 10 cWW 
2 10 s55 
3 6 s53 
4 5 s35 
4 9 tHS 
5 6 s35 
5 9 s55 
6 7 cWW 
6 8 s55 
7 8 s35 
8 9 s35 
9 10 s35
JAR3D SCFG/MRF model for IL_49612.1:
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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009635135,0.018686586,0.011023774,0.200055053,0.000000000],[0.018686946,0.009628796,0.215804967,0.013537321,0.000000000],[0.011023788,0.215804297,0.002089517,0.025115689,0.000000000],[0.200055346,0.013537264,0.025116064,0.010199456,0.000000000],[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 C1051 - G1207 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left for 5J7L|1|AA|G|1052
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.375000000,0.375000000,0.125000000,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left for 5J7L|1|AA|G|1053
InitialNode  | Left Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.031730993,0.025346635,0.017857393,0.022576124,0.000000000],[0.015700587,0.016041052,0.102583284,0.018956052,0.000000000],[0.003652803,0.003652803,0.375084203,0.003652803,0.000000000],[0.329686787,0.003652803,0.026172876,0.003652803,0.000000000],[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 [4] | Right Index [9] // Basepair C1054 - G1206 tHS 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Position [1] | Left Index [5] | Right Index [8] // Fixed node on left for 5J7L|1|AA|A|1055
InitialNode  | Left Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Left Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000] | Position [2] | Left Index [6] | Right Index [8] // Fixed node on right for 5J7L|1|AA|U|1205
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 [6] | Right Index [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009158630,0.019777652,0.009912226,0.210022087,0.000000000],[0.019781061,0.009705967,0.195573829,0.010701870,0.000000000],[0.009912241,0.195571919,0.002042701,0.038130662,0.000000000],[0.210028228,0.010701362,0.038153583,0.010825982,0.000000000],[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 [6] | Right Index [7] // Basepair U1056 - A1204 cWW 
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_49612.1:
> IL_49612.1  5J7L C 1051 G 1207
CGGCAU*AUGG
> IL_49612.1  8CRE G 1415 C 1264
GUCUGUGA*UGGC