Alignment of IL_73700.1 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
3

2
5
4
I

6
5

3
7
6
I

8
7

4
9
8
I

10
9

5
11
9
I

12
9

6
13
9
I

14
9

7
15
10
I

16
11


17
10
I

18
9

8
19
9
I

20
9

9
21
9
I

22
9

10
23
9
I

24
9

11
25
9
I

26
9

12
27
2
I

28
2

13
29
1
I


In
acceptance
region

Cutoff
score
Full
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distance
Interior
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distance
Alignment
score
deficit
IL_73700.1_Instance_1 IL_73700.1,IL_6N5P_004,C36_G99CGCUUUUUGGCGACAG
IL_73700.1_Sequence_1 IL_73700.16N5P_C36_G99CGCUUUUUGG*CGACAGtrue100000.00

Conserved interactions between motif group positions in IL_73700.1:
1 2 s35 
1 13 cWW 
2 3 s35 
2 13 s55 
3 4 s35 
5 6 s35 
5 10 cWW 
6 7 s35 
6 9 tHS 
6 10 s55 
6 11 cWW 
7 8 cWW 
7 11 s55 
8 9 s35 
8 12 tSW 
10 11 s53 
11 12 s53 
11 9 7BR
JAR3D SCFG/MRF model for IL_73700.1:
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
BasepairNode | Deletion Probability [0.0000224390099112] | 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]] | 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 [1] | Right Index [13] // Basepair C36 - G99 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Position [1] | Left Index [2] | Right Index [12] // Fixed node on left for 6N5P|1|A|G|37
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 [3] | Right Index [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [3] | Right Index [12] // Fixed node on left for 6N5P|1|A|C|38
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 [4] | Right Index [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [1] | Left Index [4] | Right Index [12] // Fixed node on left for 6N5P|1|A|U|39
InitialNode  | Left Length Distribution [0.000000000,0.045351474,0.907029478,0.045351474,0.002267574] | Left Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [12] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000000000001906753397244242883095262764002054089856] | Num Left Bases [3] | Num Right Bases [5] | Left Index [5] | Right Index [12] | Norm Constant [0.080004212503668] // Cluster node 6N5P|1|A|U|42:6N5P|1|A|G|45 and 6N5P|1|A|C|94:6N5P|1|A|A|98
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.009830065,0.020472507,0.011193821,0.203314028,0.000000000],[0.017266777,0.009639366,0.205036802,0.013415526,0.000000000],[0.011069507,0.220897605,0.002109966,0.027030175,0.000000000],[0.200711998,0.013924020,0.023693165,0.010394672,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6N5P|1|A|G|45 - 6N5P|1|A|C|94 cWW 
Interaction  | Interacting Bases [2,5] | 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 6N5P|1|A|G|44 - 6N5P|1|A|G|95 tHS 
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.009123784,0.017718471,0.010008206,0.198264936,0.000000000],[0.022262210,0.009929018,0.198931998,0.011154256,0.000000000],[0.010027726,0.196386049,0.002064490,0.023275738,0.000000000],[0.216349992,0.010477281,0.053822220,0.010203624,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6N5P|1|A|U|42 - 6N5P|1|A|A|96 cWW 
Interaction  | Interacting Bases [2,7] | Pair Probability [[0.004841606,0.050416664,0.005513298,0.100138349,0.000000000],[0.008504413,0.023738407,0.100986868,0.006607555,0.000000000],[0.005452069,0.529512277,0.001039223,0.013313184,0.000000000],[0.098856770,0.034290020,0.011669605,0.005119692,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6N5P|1|A|G|44 - 6N5P|1|A|C|97 cWW 
Interaction  | Interacting Bases [4,8] | Pair Probability [[0.170304962,0.164498591,0.002050808,0.010080909,0.000000000],[0.214981783,0.009370211,0.002050808,0.008338571,0.000000000],[0.191910242,0.002050808,0.002050808,0.006664609,0.000000000],[0.182461924,0.009260672,0.013913556,0.010010739,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6N5P|1|A|C|94 - 6N5P|1|A|A|98 tSW 
Insertion    | Location [1] | 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 5, position 1 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 [8] | Right Index [7] // New Initial node after Cluster
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_73700.1:
> IL_73700.1  6N5P C   36 G   99
CGCUUUUUGG*CGACAG