Alignment of IL_61299.4 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
5

2
5
5
I

6
5

3
7
5
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
4
I

18
3

8
19
2
I

20
2

9
21
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_61299.4_Instance_1 IL_61299.4,IL_8P9A_378,U58_G89UCUAAGCUG
IL_61299.4_Sequence_1 IL_61299.48P9A_U58_G89UCUAAG*CUGtrue100000.00
IL_61299.4_Instance_2 IL_61299.4,IL_8CRE_395,U58_G89UCUAAGCUG
IL_61299.4_Sequence_2 IL_61299.48CRE_U58_G89UCUAAG*CUGtrue100000.00
IL_61299.4_Instance_3 IL_61299.4,IL_5UNE_008,C33_G12CGGAAAUGG
IL_61299.4_Sequence_3 IL_61299.45UNE_C33_G12CGGAAA*UGGtrue87001.68

Conserved interactions between motif group positions in IL_61299.4:
1 9 cWW 
2 6 cWH 
4 5 s33 
6 7 cWW 
6 8 s55 
7 8 s35 
8 9 s35 
3 6 6BPh
JAR3D SCFG/MRF model for IL_61299.4:
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 [9] // Initial node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.010572638,0.014877250,0.013044997,0.090228256,0.000000000],[0.206427106,0.021659062,0.106652866,0.015137891,0.000000000],[0.013291996,0.091543616,0.002872521,0.017432502,0.000000000],[0.123374477,0.014077094,0.246524532,0.012283196,0.000000000],[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 [9] // Basepair U58 - G89 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.300000000,0.500000000,0.000000000] | Position [2] | Left Index [2] | Right Index [8] // Fixed node on right for 8P9A|1|sR|U|88
InitialNode  | Left Length Distribution [1.000000000] | 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 [7] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [5] | Num Right Bases [1] | Left Index [2] | Right Index [7] | Norm Constant [0.250430317362017] // Cluster node 8P9A|1|sR|C|59:8P9A|1|sR|G|63 and 8P9A|1|sR|C|87:8P9A|1|sR|C|87
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.009490394,0.020648938,0.010590347,0.209997349,0.000000000],[0.017070363,0.009463878,0.198130626,0.012189443,0.000000000],[0.010502710,0.222275070,0.002053109,0.035235925,0.000000000],[0.195916611,0.012742798,0.023085133,0.010607307,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|G|63 - 8P9A|1|sR|C|87 cWW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.057790106,0.057790106,0.057790106,0.057790106,0.000000000],[0.057790106,0.057790106,0.077207582,0.057790106,0.000000000],[0.113730929,0.057790106,0.057790106,0.057790106,0.000000000],[0.057790106,0.057790106,0.057790106,0.057790106,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|C|59 - 8P9A|1|sR|G|63 cWH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.021739130,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.326086957,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.630434783,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8P9A|1|sR|U|60
Interaction  | Interacting Bases [3,3] | 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 8P9A|1|sR|A|61
Interaction  | Interacting Bases [4,4] | 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 8P9A|1|sR|A|62
InitialNode  | 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 [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_61299.4:
> IL_61299.4  8P9A U   58 G   89
UCUAAG*CUG
> IL_61299.4  8CRE U   58 G   89
UCUAAG*CUG
> IL_61299.4  5UNE C   33 G   12
CGGAAA*UGG