Alignment of IL_45794.1 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
5

2
5
5
I

6
6

3
7
6
I

8
7

4
9
7
I

10
8

5
11
8
I

12
9


13
8
I

14
8

6
15
7
I

16
7

7
17
6
I

18
6

8
19
5
I

20
5

9
21
4
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_45794.1_Instance_1 IL_45794.1_IL_3U5H_090_C2156_G2180CGAUGGUGUUGACG
IL_45794.1_Sequence_1 IL_45794.1_IL_3U5H_090_C_2156_G_2180CGAUGG*UGUUGACGtrue100000.00
IL_45794.1_Instance_2 IL_45794.1_IL_4A1B_085_U2152_A2175UGACGGUGAUGACA
IL_45794.1_Sequence_2 IL_45794.1_IL_4A1B_085_U_2152_A_2175UGACGG*UGAUGACAtrue100000.00

Conserved interactions between motif group positions in IL_45794.1:
1 10 s35 
1 11 cWW 
2 9 tSS 
2 10 s53 
3 4 s55 
3 7 s55 
3 8 tWW 
3 9 s35 
4 5 s35 
4 7 tWW 
5 6 cWW 
6 7 s33 
7 8 s55 
10 11 s55 
10 2 6BPh
2 10 6BPh
9 3 6BR
2 9 6BR
JAR3D SCFG/MRF model for IL_45794.1:
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 C2156 - G2180 from junction 
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.009573432,0.018670696,0.010738592,0.199847452,0.000000000],[0.022636955,0.009050270,0.214230681,0.012151330,0.000000000],[0.010821283,0.200582138,0.002151860,0.023718468,0.000000000],[0.214249849,0.011785171,0.027717608,0.012074217,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Left Index [1] | Right Index [11] // Basepair C2156 - G2180 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.906250000,0.031250000,0.031250000,0.031250000,0.000000000] | Position [2] | Left Index [2] | Right Index [10] // 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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [9] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.000828022,0.001039259,0.008821390,0.001017059,0.000000000],[0.000180669,0.000180669,0.000903347,0.000180669,0.000000000],[0.113707142,0.117192079,0.651951059,0.102553278,0.000000000],[0.000180669,0.000180669,0.000903347,0.000180669,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [9] // Basepair G2157 - G2177 tSS 
BasepairNode | Deletion Probability [0.0000000006094467] | Pair Probability [[0.022062116,0.052061168,0.004657104,0.485318270,0.000000000],[0.021929599,0.060153984,0.019602286,0.060262558,0.000000000],[0.004657104,0.026684972,0.023169287,0.051844976,0.000000000],[0.048915432,0.051457529,0.021223473,0.046000141,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000] | Right Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Left Index [3] | Right Index [8] // Basepair A2158 - U2176 tWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.350791599,0.040670272,0.003713382,0.018474231,0.000000000],[0.038122680,0.015188207,0.012119555,0.015027400,0.000000000],[0.003713382,0.012224256,0.390946071,0.024547920,0.000000000],[0.018369341,0.015013760,0.022729598,0.018348346,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // Basepair G2160 - G2174 tWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.016500430,0.310288742,0.015571103,0.044672112,0.000000000],[0.014475176,0.011549597,0.038212544,0.015431970,0.000000000],[0.015226490,0.044298882,0.003453650,0.364972803,0.000000000],[0.037922120,0.017096803,0.015161977,0.035165601,0.000000000],[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 [5] | Right Index [6] // Basepair G2161 - U2173 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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_45794.1:
> IL_45794.1 IL_3U5H_090 C 2156 G 2180
CGAUGG*UGUUGACG
> IL_45794.1 IL_4A1B_085 U 2152 A 2175
UGACGG*UGAUGACA