Alignment of IL_44874.1 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
6
I

10
7

5
11
8
I

12
9

6
13
10
I

14
11

7
15
11
I

16
12


17
11
I

18
11

8
19
4
I

20
4

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_44874.1_Instance_1 IL_44874.1,IL_3NDB_007,C192_G226CGAACCCGUAG
IL_44874.1_Sequence_1 IL_44874.13NDB_C192_G226CGAACCC*GUAGtrue100000.00

Conserved interactions between motif group positions in IL_44874.1:
1 2 s35 
1 11 cWW 
2 9 s33 
2 10 tSH 
2 11 s55 
3 7 s35 
3 9 tHW 
3 10 s55 
4 5 s35 
5 6 s35 
7 8 cWW 
8 9 s35 
9 10 s35 
10 11 s35 
5 4 7BPh
7 5 7BPh
10 2 6BR
JAR3D SCFG/MRF model for IL_44874.1:
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 [11] // 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 [11] // Basepair C192 - G226 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.113862076,0.120538352,0.001366838,0.006441913,0.000000000],[0.114707989,0.120259235,0.001366838,0.001366838,0.000000000],[0.146584821,0.001366838,0.006682038,0.116012068,0.000000000],[0.127100484,0.119609993,0.001366838,0.001366838,0.000000000],[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 [10] // Basepair G193 - A225 tSH 
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 [3] | Right Index [9] // Basepair A194 - U224 tHW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [4] | Right Index [8] // Fixed node on left for 3NDB|1|M|A|195
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 [5] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.833333333,0.055555556,0.055555556,0.000000000] | Position [1] | Left Index [5] | Right Index [8] // Fixed node on left for 3NDB|1|M|C|196
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 [6] | Right Index [8] // 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 [6] | Right Index [8] // Fixed node on left for 3NDB|1|M|C|197
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 [8] // 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 [7] | Right Index [8] // Basepair C198 - G223 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_44874.1:
> IL_44874.1  3NDB C  192 G  226
CGAACCC*GUAG