Alignment of IL_49867.1 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
3
I

6
4

3
7
4
I

8
5

4
9
5
I

10
8

5
11
8
I

12
9

6
13
10
I

14
11

7
15
12
I

16
13

8
17
13
I

18
14


19
13
I

20
13

9
21
8
I

22
8

10
23
7
I

24
6

11
25
5
I

26
5

12
27
4
I

28
4

13
29
3
I

30
3

14
31
2
I

32
2

15
33
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_49867.1_Instance_1 IL_49867.1,IL_1YLS_011,C228_G217CAAUACUCGUGCCGG
IL_49867.1_Sequence_1 IL_49867.11YLS_C228_G217CAAUACUC*GUGCCGGtrue100000.00

Conserved interactions between motif group positions in IL_49867.1:
1 2 s35 
1 15 cWW 
2 3 s35 
2 14 cWW 
2 15 s55 
3 4 s35 
3 13 bif 
4 11 s33 
4 12 tSH 
5 8 s35 
5 10 tHW 
5 11 s55 
6 7 s35 
8 9 cWW 
9 10 s35 
10 11 s35 
12 13 s35 
13 14 s35 
14 15 s35 
11 5 6BPh
7 6 7BPh
8 7 7BPh
8 5 7BR
4 11 6BR
JAR3D SCFG/MRF model for IL_49867.1:
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 [15] // 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 [15] // Basepair C228 - G217 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.030079776,0.014734320,0.373183812,0.017645523,0.000000000],[0.014388349,0.009799453,0.019058893,0.042827032,0.000000000],[0.349027357,0.019272929,0.003632828,0.016031822,0.000000000],[0.017611175,0.045250265,0.015688367,0.011768099,0.000000000],[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 [2] | Right Index [14] // Basepair A229 - G216 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.211919560,0.299977801,0.002900768,0.002900768,0.000000000],[0.013355096,0.009564654,0.002900768,0.002900768,0.000000000],[0.002900768,0.002900768,0.198951064,0.237224144,0.000000000],[0.002900768,0.002900768,0.002900768,0.002900768,0.000000000],[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 [3] | Right Index [13] // Basepair A230 - C215 bif 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.061560371,0.044363437,0.000685096,0.003245107,0.000000000],[0.062613719,0.058708606,0.000685096,0.000685096,0.000000000],[0.059951758,0.000685096,0.003555276,0.027342227,0.000000000],[0.316619026,0.352449124,0.003425481,0.003425481,0.000000000],[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 [4] | Right Index [12] // Basepair U231 - C214 tSH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.055555556,0.833333333,0.055555556,0.000000000] | Position [2] | Left Index [5] | Right Index [11] // Fixed node on right for 1YLS|1|B|U|231
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 [5] | Right Index [10] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.018961504,0.042198433,0.004196211,0.429522110,0.000000000],[0.004196211,0.338134433,0.010058595,0.004196211,0.000000000],[0.019694625,0.004196211,0.031911832,0.024345914,0.000000000],[0.004196211,0.004196211,0.018663303,0.041331983,0.000000000],[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 [5] | Right Index [10] // Basepair A232 - U212 tHW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [6] | Right Index [9] // Fixed node on left for 1YLS|1|B|G|216
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 [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.055555556,0.055555556,0.833333333,0.000000000] | Position [1] | Left Index [7] | Right Index [9] // Fixed node on left for 1YLS|1|B|G|217
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 [8] | Right Index [9] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003781516,0.006781167,0.004347319,0.078825460,0.000000000],[0.056281056,0.026959555,0.589952696,0.038278585,0.000000000],[0.004396140,0.080523937,0.000828645,0.009304998,0.000000000],[0.079847353,0.005268669,0.010615539,0.004007366,0.000000000],[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 [8] | Right Index [9] // Basepair C235 - G211 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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_49867.1:
> IL_49867.1  1YLS C  228 G  217
CAAUACUC*GUGCCGG