Alignment of IL_89047.1 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
3
I

12
4

6
13
5
I

14
8

7
15
8
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16
9

8
17
9
I

18
10

9
19
10
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20
11


21
10
I

22
10

10
23
9
I

24
9

11
25
8
I

26
8

12
27
7
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28
6

13
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3
I

30
2

14
31
2
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32
2

15
33
2
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34
2

16
35
1
I


In
acceptance
region

Cutoff
score
Full
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distance
Interior
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Alignment
score
deficit
IL_89047.1_Instance_1 IL_89047.1,IL_8CRE_436,C895_G884CUUGGAUUUAUUGUCAG
IL_89047.1_Sequence_1 IL_89047.18CRE_C895_G884CUUGGAUUUA*UUGUCAGtrue100000.00

Conserved interactions between motif group positions in IL_89047.1:
1 2 s35 
1 5 cSS 
1 16 cWW 
2 16 s55 
3 4 s55 
3 15 s53 
4 14 s33 
5 6 s35 
5 14 tHS 
5 15 s55 
5 16 perp 
6 7 s35 
7 8 s35 
7 12 cSW 
8 9 s35 
8 11 cWH 
8 12 s55 
9 10 cWW 
9 11 s53 
10 11 s33 
11 12 s55 
12 13 s35 
13 14 s35 
15 16 perp 
6 5 7BPh
14 4 6BR
JAR3D SCFG/MRF model for IL_89047.1:
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 [16] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000001906753397244242883095262764002054089856] | Num Left Bases [5] | Num Right Bases [3] | Left Index [1] | Right Index [16] | Norm Constant [0.072090933854857] // Cluster node 8CRE|1|CM|C|895:8CRE|1|CM|A|900 and 8CRE|1|CM|C|882:8CRE|1|CM|G|884
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.075973411,0.401665643,0.065755452,0.070826497,0.000000000],[0.009836802,0.274109705,0.000783529,0.071609913,0.000000000],[0.000783529,0.003917647,0.005436875,0.000783529,0.000000000],[0.003896848,0.003917647,0.009919445,0.000783529,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|A|900 - 8CRE|1|CM|C|882 tHS 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|C|895 - 8CRE|1|CM|G|884 cWW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.074958370,0.074522986,0.072592901,0.075257560,0.000000000],[0.093663030,0.076039825,0.003534873,0.067669678,0.000000000],[0.079480999,0.003480647,0.006829583,0.080842831,0.000000000],[0.075739436,0.073025027,0.072599406,0.069762848,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|C|895 - 8CRE|1|CM|A|900 cSS 
Interaction  | Interacting Bases [2,2] | 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 8CRE|1|CM|U|896
Interaction  | Interacting Bases [3,3] | 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 8CRE|1|CM|U|897
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],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8CRE|1|CM|G|899
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 8CRE|1|CM|A|883
Insertion    | Location [3] | 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 3, position 3 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 [6] | Right Index [13] // Initial node 8CRE|1|CM|U|901 - 8CRE|1|CM|U|881 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.055555556,0.055555556,0.833333333,0.000000000] | Position [1] | Left Index [6] | Right Index [13] // Fixed node on left for 8CRE|1|CM|A|883
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [13] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [2] | Left Index [7] | Right Index [13] // Fixed node on right for 8CRE|1|CM|A|900
InitialNode  | Left Length Distribution [1.000000000] | 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 [12] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.028639612,0.025585386,0.063264876,0.021611744,0.000000000],[0.026641307,0.024110226,0.006020808,0.020957404,0.000000000],[0.028329055,0.021492269,0.029037104,0.016761760,0.000000000],[0.029620074,0.024577439,0.611981755,0.021369182,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [12] // Basepair U902 - G880 cSW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.003549050,0.003549050,0.138176698,0.034470642,0.000000000],[0.003549050,0.314587998,0.003549050,0.017233117,0.000000000],[0.033909983,0.003549050,0.039860910,0.003549050,0.000000000],[0.016648517,0.003549050,0.015462842,0.364805947,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [8] | Right Index [11] // Basepair U903 - U879 cWH 
BasepairNode | Deletion Probability [0.0000249735224443] | 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]] | 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 [9] | Right Index [10] // Basepair A904 - U878 cWW 
HairpinNode  | Num Bases [1] | Left Index [10] | Right Index [10] | 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_89047.1:
> IL_89047.1  8CRE C  895 G  884
CUUGGAUUUA*UUGUCAG