Alignment of IL_86012.1 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
2

2
5
2
I

6
2

3
7
2
I

8
2

4
9
2
I

10
2

5
11
2
I

12
2

6
13
3
I

14
4

7
15
4
I

16
5


17
4
I

18
4

8
19
3
I

20
2

9
21
2
I

22
2

10
23
2
I

24
2

11
25
2
I

26
2

12
27
2
I

28
2

13
29
1
I


In
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Cutoff
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Full
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distance
Interior
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Alignment
score
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IL_86012.1_Instance_1 IL_86012.1,IL_8P9A_439,U1430_G1278UCUGUGAUGUGCAUGG
IL_86012.1_Sequence_1 IL_86012.18P9A_U_1430_G_1278UCUGUGAUG*UGCAUGGtrue100000.00

Conserved interactions between motif group positions in IL_86012.1:
1 9 s33 
1 13 cWW 
2 8 s33 
2 10 tWH 
3 4 s35 
3 13 tHS 
4 5 s35 
5 6 s35 
5 11 cWW 
5 12 s55 
6 10 cSW 
7 8 cWW 
7 10 s55 
9 11 s53 
9 12 cWH 
10 11 s35 
11 12 s35 
12 13 s35 
1 9 7BR
2 9 7BR
JAR3D SCFG/MRF model for IL_86012.1:
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
ClusterNode  | Deletion Probability [0.000000000000000000000000000000005679021726023963487573256378] | Num Left Bases [6] | Num Right Bases [5] | Left Index [1] | Right Index [13] | Norm Constant [0.230642883335851] // Cluster node 8P9A|1|sR|U|1430:8P9A|1|sR|U|1437 and 8P9A|1|sR|G|1273:8P9A|1|sR|G|1278
Interaction  | Interacting Bases [2,8] | Pair Probability [[0.011930598,0.001393858,0.039873965,0.001393858,0.000000000],[0.706830194,0.050775790,0.006969292,0.006969292,0.000000000],[0.001393858,0.004866357,0.012534345,0.012848304,0.000000000],[0.014017083,0.001393858,0.006266816,0.120542530,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|C|1431 - 8P9A|1|sR|A|1275 tWH 
Interaction  | Interacting Bases [6,8] | Pair Probability [[0.180519376,0.017157494,0.024883181,0.007207709,0.000000000],[0.173124567,0.013878938,0.001921253,0.007559536,0.000000000],[0.178058238,0.001921253,0.155093256,0.006042475,0.000000000],[0.202026315,0.014064519,0.009451832,0.007090057,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|U|1437 - 8P9A|1|sR|A|1275 cSW 
Interaction  | Interacting Bases [5,9] | Pair Probability [[0.009374836,0.022228469,0.010012528,0.216037101,0.000000000],[0.017691617,0.009675113,0.196088410,0.010461402,0.000000000],[0.009993038,0.198630499,0.002061361,0.053740648,0.000000000],[0.197964449,0.011137350,0.023240462,0.011662716,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|A|1436 - 8P9A|1|sR|U|1276 cWW 
Interaction  | Interacting Bases [1,11] | Pair Probability [[0.004033546,0.005015494,0.005120807,0.013368915,0.000000000],[0.108508408,0.010024821,0.015190737,0.005750806,0.000000000],[0.005232913,0.013315365,0.001185784,0.005262267,0.000000000],[0.154569684,0.026324136,0.602792863,0.024303454,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|U|1430 - 8P9A|1|sR|G|1278 cWW 
Interaction  | Interacting Bases [3,11] | Pair Probability [[0.035249677,0.028157351,0.019837618,0.025079615,0.000000000],[0.017441642,0.017819861,0.004057866,0.021058110,0.000000000],[0.004057866,0.004057866,0.415687600,0.004057866,0.000000000],[0.366246114,0.004057866,0.029075215,0.004057866,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|G|1433 - 8P9A|1|sR|G|1278 tHS 
Interaction  | Interacting Bases [7,10] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|G|1273 - 8P9A|1|sR|G|1277 cWH 
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8P9A|1|sR|U|1434
Insertion    | Location [2] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node
Insertion    | Location [4] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000]// Insertion after nucleotide 4, position 4 in cluster node
Insertion    | Location [7] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 9, position 7 in cluster node
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [[0.015996656,0.299826436,0.014459392,0.085420251,0.000000000],[0.013858629,0.012916026,0.036792527,0.014547577,0.000000000],[0.014149624,0.041974486,0.003276514,0.337552385,0.000000000],[0.036940494,0.015890415,0.014540501,0.041858086,0.000000000],[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 G1438 - U1272 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_86012.1:
> IL_86012.1  8P9A U 1430 G 1278
UCUGUGAUG*UGCAUGG