Alignment of IL_37104.3 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
4
I

8
5


9
4
I

10
4

4
11
3
I

12
3

5
13
2
I

14
2

6
15
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_37104.3_Instance_1 IL_37104.3_IL_1S72_076_C2122_G2272CAGCGGG
IL_37104.3_Sequence_1 IL_37104.3_IL_1S72_076_C_2122_G_2272CAG*CGGGtrue100000.00
IL_37104.3_Instance_2 IL_37104.3_IL_3V2F_079_C2081_G2239CAGCGGG
IL_37104.3_Sequence_2 IL_37104.3_IL_3V2F_079_C_2081_G_2239CAG*CGGGtrue100000.00
IL_37104.3_Instance_3 IL_37104.3_IL_3V2F_012_C288_G353CAGUGGG
IL_37104.3_Sequence_3 IL_37104.3_IL_3V2F_012_C288_G353CAG*UGGGtrue96000.40
IL_37104.3_Instance_4 IL_37104.3_IL_4IOA_082_C2276_G2300CAAUGUAG
IL_37104.3_Sequence_4 IL_37104.3_IL_4IOA_082_C_2276_G_2300CAA*UGUAGtrue75002.34
IL_37104.3_Instance_5 IL_37104.3_IL_4A1B_102_C2655_G2679CAGCGUAG
IL_37104.3_Sequence_5 IL_37104.3_IL_4A1B_102_C_2655_G_2679CAG*CGUAGtrue78002.09
IL_37104.3_Instance_6 IL_37104.3_IL_3U5H_104_C2666_G2690CAUAGUAG
IL_37104.3_Sequence_6 IL_37104.3_IL_3U5H_104_C_2666_G_2690CAU*AGUAGtrue75002.35
IL_37104.3_Instance_7 IL_37104.3_IL_1S72_078_C2331_G2355CAGCGAAG
IL_37104.3_Sequence_7 IL_37104.3_IL_1S72_078_C_2331_G_2355CAG*CGAAGtrue83001.64
IL_37104.3_Instance_8 IL_37104.3_IL_2QBG_082_U2081_G2239UAGUGGG
IL_37104.3_Sequence_8 IL_37104.3_IL_2QBG_082_U_2081_G_2239UAG*UGGGtrue90000.93
IL_37104.3_Instance_9 IL_37104.3_IL_3U5H_100_U2423_G2607UAGUGGG
IL_37104.3_Sequence_9 IL_37104.3_IL_3U5H_100_U_2423_G_2607UAG*UGGGtrue90000.93
IL_37104.3_Instance_10 IL_37104.3_IL_4IOA_077_U2064_G2218UAGCGGG
IL_37104.3_Sequence_10 IL_37104.3_IL_4IOA_077_U_2064_G_2218UAG*CGGGtrue94000.53
IL_37104.3_Instance_11 IL_37104.3_IL_4BPP_026_C492_G479CUACGGG
IL_37104.3_Sequence_11 IL_37104.3_IL_4BPP_026_C492_G479CUAC*GGGtrue57004.05

Conserved interactions between motif group positions in IL_37104.3:
1 2 s35 
1 5 s33 
1 6 cWW 
2 3 s35 
2 5 tHS 
2 6 s55 
3 4 cWW 
3 5 s55 
4 5 s35 
2 5 6BR
JAR3D SCFG/MRF model for IL_37104.3:
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 [6] // Initial node C2122 - G2272 from junction 
BasepairNode | Deletion Probability [0.0000000176048942] | Pair Probability [[0.009966159,0.015204404,0.011689454,0.138288258,0.000000000],[0.093322444,0.009751015,0.227094929,0.013683603,0.000000000],[0.011877006,0.149074025,0.002321010,0.019779227,0.000000000],[0.140763174,0.012816665,0.133876049,0.010492577,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.904811823,0.094550986,0.000616637,0.000020555] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [0.092564150,0.542688047,0.362904712,0.001761176,0.000081915] | Right Letter Distribution [0.343750000,0.031250000,0.406250000,0.218750000,0.000000000] | Left Index [1] | Right Index [6] // Basepair C2122 - G2272 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.102828044,0.103742905,0.222993778,0.111770444,0.000000000],[0.119859249,0.108737694,0.001238947,0.107676566,0.000000000],[0.001238947,0.001238947,0.006002437,0.001238947,0.000000000],[0.005899707,0.001238947,0.103055496,0.001238947,0.000000000],[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 [5] // Basepair A2123 - G2270 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010765928,0.091598712,0.011446582,0.152351597,0.000000000],[0.016272570,0.008695101,0.155838320,0.012296204,0.000000000],[0.011310571,0.195594189,0.002302334,0.131380470,0.000000000],[0.150288428,0.012933719,0.020335074,0.016590203,0.000000000],[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 [3] | Right Index [4] // Basepair G2124 - C2269 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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_37104.3:
> IL_37104.3 IL_1S72_076 C 2122 G 2272
CAG*CGGG
> IL_37104.3 IL_3V2F_079 C 2081 G 2239
CAG*CGGG
> IL_37104.3 IL_3V2F_012 C  288 G  353
CAG*UGGG
> IL_37104.3 IL_4IOA_082 C 2276 G 2300
CAA*UGUAG
> IL_37104.3 IL_4A1B_102 C 2655 G 2679
CAG*CGUAG
> IL_37104.3 IL_3U5H_104 C 2666 G 2690
CAU*AGUAG
> IL_37104.3 IL_1S72_078 C 2331 G 2355
CAG*CGAAG
> IL_37104.3 IL_2QBG_082 U 2081 G 2239
UAG*UGGG
> IL_37104.3 IL_3U5H_100 U 2423 G 2607
UAG*UGGG
> IL_37104.3 IL_4IOA_077 U 2064 G 2218
UAG*CGGG
> IL_37104.3 IL_4BPP_026 C  492 G  479
CUAC*GGG