Alignment of IL_79083.3 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
3
I

6
4

3
7
5
I

8
6

4
9
7
I

10
10

5
11
10
I

12
11

6
13
11
I

14
12


15
11
I

16
11

7
17
10
I

18
10

8
19
9
I

20
8

9
21
3
I

22
3

10
23
2
I

24
2

11
25
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_79083.3_Instance_1 IL_79083.3_IL_3U5H_139_U3332_G3371UGUAAGCUGAG
IL_79083.3_Sequence_1 IL_79083.3_IL_3U5H_139_U_3332_G_3371UGUAAG*CUGAGtrue96000.63
IL_79083.3_Instance_2 IL_79083.3_IL_4A1B_130_U3290_G3327UGUAAGCUGAG
IL_79083.3_Sequence_2 IL_79083.3_IL_4A1B_130_U_3290_G_3327UGUAAG*CUGAGtrue96000.63
IL_79083.3_Instance_3 IL_79083.3_IL_4IOA_103_U2822_G2844UGCACGUUCAG
IL_79083.3_Sequence_3 IL_79083.3_IL_4IOA_103_U_2822_G_2844UGCACG*UUCAGtrue84002.83
IL_79083.3_Instance_4 IL_79083.3_IL_2QBG_109_U2847_G2869UGUAAGUUGAG
IL_79083.3_Sequence_4 IL_79083.3_IL_2QBG_109_U_2847_G_2869UGUAAG*UUGAGtrue100000.00
IL_79083.3_Instance_5 IL_79083.3_IL_3V2F_106_U2847_G2869UGUAAGUUGAG
IL_79083.3_Sequence_5 IL_79083.3_IL_3V2F_106_U_2847_G_2869UGUAAG*UUGAGtrue100000.00

Conserved interactions between motif group positions in IL_79083.3:
1 2 s35 
1 11 cWW 
2 3 s35 
2 10 tSH 
3 9 perp 
3 10 s55 
4 5 s35 
5 6 s35 
5 8 tHH 
6 7 cWW 
7 8 s33 
10 11 s35 
8 4 6BPh
10 4 2BR
2 9 6BR
3 9 6BR
JAR3D SCFG/MRF model for IL_79083.3:
Character Definition | A,C,G,U,* // Define characters here
InitialNode  | 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 [1] | Right Index [11] // Initial node U3332 - G3371 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.012646166,0.014364762,0.015110345,0.037632857,0.000000000],[0.307921916,0.015603035,0.043960978,0.016966392,0.000000000],[0.015452329,0.037921065,0.003427306,0.015046324,0.000000000],[0.044331362,0.015314258,0.390349627,0.013951278,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [11] // Basepair U3332 - G3371 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.106770229,0.024890874,0.000257289,0.001225177,0.000000000],[0.107720164,0.022581288,0.000257289,0.000257289,0.000000000],[0.514059910,0.000932882,0.004519616,0.077597028,0.000000000],[0.116055460,0.022360926,0.000257289,0.000257289,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [10] // Basepair G3333 - A3370 tSH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.018518519,0.203703704,0.018518519,0.759259259,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Position [1] | Left Index [4] | Right Index [9] // Fixed node on left
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [5] | Right Index [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.214285714,0.642857143,0.071428571,0.000000000] | Position [2] | Left Index [5] | Right Index [9] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.015321660,0.003151887,0.049920537,0.528611003,0.000000000],[0.003399205,0.000747565,0.004119347,0.350157565,0.000000000],[0.003239678,0.014889424,0.000747565,0.005232956,0.000000000],[0.003459265,0.011021822,0.000747565,0.005232956,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair A3336 - U3368 tHH 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.013578915,0.188924424,0.013662582,0.101216274,0.000000000],[0.015121168,0.009998321,0.103243806,0.014148428,0.000000000],[0.013403983,0.128391209,0.002848221,0.240583182,0.000000000],[0.096847870,0.015374978,0.018078655,0.024577984,0.000000000],[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 [6] | Right Index [7] // Basepair G3337 - C3367 cWW 
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_79083.3:
> IL_79083.3 IL_3U5H_139 U 3332 G 3371
UGUAAG*CUGAG
> IL_79083.3 IL_4A1B_130 U 3290 G 3327
UGUAAG*CUGAG
> IL_79083.3 IL_4IOA_103 U 2822 G 2844
UGCACG*UUCAG
> IL_79083.3 IL_2QBG_109 U 2847 G 2869
UGUAAG*UUGAG
> IL_79083.3 IL_3V2F_106 U 2847 G 2869
UGUAAG*UUGAG