Alignment of IL_76319.5 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

4
9
6
I

10
7


11
6
I

12
6

5
13
5
I

14
5

6
15
2
I

16
2

7
17
1
I


In
acceptance
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Cutoff
score
Full
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distance
Interior
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Alignment
score
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IL_76319.5_Instance_1 IL_76319.5,IL_8CRE_452,U1257_G1424UGCAUAUG
IL_76319.5_Sequence_1 IL_76319.58CRE_U_1257_G_1424UGCAU*AUGtrue100000.00
IL_76319.5_Instance_2 IL_76319.5,IL_4LFB_044,U1052_G1206UGCAUAUG
IL_76319.5_Sequence_2 IL_76319.54LFB_U_1052_G_1206UGCAU*AUGtrue100000.00
IL_76319.5_Instance_3 IL_76319.5,IL_8P9A_438,U1272_G1438UGCAUAUG
IL_76319.5_Sequence_3 IL_76319.58P9A_U_1272_G_1438UGCAU*AUGtrue100000.00

Conserved interactions between motif group positions in IL_76319.5:
1 7 cWW 
2 4 s53 
3 4 s35 
3 6 cWS 
3 7 s55 
4 5 cWW 
5 6 s35
JAR3D SCFG/MRF model for IL_76319.5:
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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.011136961,0.013848204,0.014138980,0.036912705,0.000000000],[0.299600889,0.027679377,0.041942910,0.015878461,0.000000000],[0.014448515,0.036764849,0.003274049,0.014529563,0.000000000],[0.085355993,0.014536633,0.356531131,0.013420778,0.000000000],[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 [7] // Basepair U1257 - G1424 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [6] // Fixed node on left for 8CRE|1|CM|G|1258
InitialNode  | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.177014145,0.169762925,0.174600796,0.217520950,0.000000000],[0.016824339,0.013609444,0.001883947,0.013791422,0.000000000],[0.024400012,0.001883947,0.152081736,0.009268302,0.000000000],[0.007067753,0.007412749,0.005925146,0.006952386,0.000000000],[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 [6] // Basepair A1260 - U1423 cWS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008946623,0.017374423,0.009813872,0.194415132,0.000000000],[0.021829934,0.009736222,0.195069241,0.010937668,0.000000000],[0.009833013,0.192572728,0.002024403,0.022823782,0.000000000],[0.231566497,0.010273839,0.052777129,0.010005495,0.000000000],[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 [4] | Right Index [5] // Basepair U1261 - A1422 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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_76319.5:
> IL_76319.5  8CRE U 1257 G 1424
UGCAU*AUG
> IL_76319.5  4LFB U 1052 G 1206
UGCAU*AUG
> IL_76319.5  8P9A U 1272 G 1438
UGCAU*AUG