Alignment of IL_61438.4 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
5
I

8
6


9
5
I

10
5

4
11
2
I

12
2

5
13
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
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distance
Alignment
score
deficit
IL_61438.4_Instance_1 IL_61438.4,IL_8P9A_452,C1764_G1638CAAGCCG
IL_61438.4_Sequence_1 IL_61438.48P9A_C_1764_G_1638CAAG*CCGtrue100000.00
IL_61438.4_Instance_2 IL_61438.4,IL_8CRE_466,C1751_G1625CAAGCCG
IL_61438.4_Sequence_2 IL_61438.48CRE_C_1751_G_1625CAAG*CCGtrue100000.00
IL_61438.4_Instance_3 IL_61438.4,IL_5J7L_058,C1501_G1401CAAGCCG
IL_61438.4_Sequence_3 IL_61438.45J7L_C_1501_G_1401CAAG*CCGtrue100000.00
IL_61438.4_Instance_4 IL_61438.4,IL_4LFB_056,C1501_G1401CAAGCCG
IL_61438.4_Sequence_4 IL_61438.44LFB_C_1501_G_1401CAAG*CCGtrue100000.00

Conserved interactions between motif group positions in IL_61438.4:
1 3 s33 
1 5 cWW 
2 3 s55 
2 4 s53 
3 4 cWW 
4 5 s55 
1 3 7BR
2 4 6BR
JAR3D SCFG/MRF model for IL_61438.4:
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 [5] // Initial node
BasepairNode | Deletion Probability [0.0000001215781528] | Pair Probability [[0.004604664,0.008257268,0.005293628,0.095983909,0.000000000],[0.048951514,0.023448583,0.542972485,0.033293523,0.000000000],[0.005353077,0.098052105,0.001009022,0.011330477,0.000000000],[0.097228245,0.006415534,0.012926292,0.004879676,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | Left Index [1] | Right Index [5] // Basepair C1764 - G1638 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.931818182,0.022727273,0.022727273,0.022727273,0.000000000] | Position [1] | Left Index [2] | Right Index [4] // Fixed node on left for 8P9A|1|sR|C|1637
InitialNode  | Left Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Left Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [4] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009546506,0.019881954,0.010870922,0.197449200,0.000000000],[0.016768697,0.009361308,0.199122279,0.013028540,0.000000000],[0.010750195,0.243371713,0.002049102,0.026250458,0.000000000],[0.194922229,0.013522366,0.023009709,0.010094826,0.000000000],[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 [3] | Right Index [4] // Basepair G1767 - C1636 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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_61438.4:
> IL_61438.4  8P9A C 1764 G 1638
CAAG*CCG
> IL_61438.4  8CRE C 1751 G 1625
CAAG*CCG
> IL_61438.4  5J7L C 1501 G 1401
CAAG*CCG
> IL_61438.4  4LFB C 1501 G 1401
CAAG*CCG