Alignment of IL_67095.2 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
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distance
Alignment
score
deficit
IL_67095.2_Instance_1 IL_67095.2,IL_4WF9_063,U1707_A2024UAAUCA
IL_67095.2_Sequence_1 IL_67095.24WF9_U_1707_A_2024UAA*UCAtrue100000.00
IL_67095.2_Instance_2 IL_67095.2,IL_8CRE_080,A1891_U2318AAGCCU
IL_67095.2_Sequence_2 IL_67095.28CRE_A_1891_U_2318AAG*CCUtrue99000.08
IL_67095.2_Instance_3 IL_67095.2,IL_7A0S_060,U1680_A1980UAAUCA
IL_67095.2_Sequence_3 IL_67095.27A0S_U_1680_A_1980UAA*UCAtrue100000.00
IL_67095.2_Instance_4 IL_67095.2,IL_5J7L_305,G1663_C1997GAAUCC
IL_67095.2_Sequence_4 IL_67095.25J7L_G_1663_C_1997GAA*UCCtrue99000.14
IL_67095.2_Instance_5 IL_67095.2,IL_8P9A_303,A1895_U2340AAGCCU
IL_67095.2_Sequence_5 IL_67095.28P9A_A_1895_U_2340AAG*CCUtrue99000.08
IL_67095.2_Instance_6 IL_67095.2,IL_9DFE_064,C1663_G1997CAAUCG
IL_67095.2_Sequence_6 IL_67095.29DFE_C_1663_G_1997CAA*UCGtrue99000.13
IL_67095.2_Instance_7 IL_67095.2,IL_4V9F_060,U1741_A2038UAGCCA
IL_67095.2_Sequence_7 IL_67095.24V9F_U_1741_A_2038UAG*CCAtrue100000.00
IL_67095.2_Instance_8 IL_67095.2,IL_9DFE_055,U1433_G1560UAGCAGG
IL_67095.2_Sequence_8 IL_67095.29DFE_U_1433_G_1560UAG*CAGGtrue46005.12

Conserved interactions between motif group positions in IL_67095.2:
1 6 cWW 
2 3 s35 
2 5 tWW 
3 4 cWW 
4 5 s33
JAR3D SCFG/MRF model for IL_67095.2:
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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000123078457223] | Pair Probability [[0.008994095,0.017473699,0.010139100,0.187878483,0.000000000],[0.052071973,0.011317263,0.178507624,0.011446803,0.000000000],[0.010178292,0.177591655,0.002089611,0.028389242,0.000000000],[0.203872482,0.011207449,0.078529039,0.010313190,0.000000000],[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 [0.869396619,0.129517605,0.001046999,0.000038778] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [1] | Right Index [6] // Basepair U1707 - A2024 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.079371218,0.381823760,0.003594008,0.039224897,0.000000000],[0.017478854,0.015453019,0.010565705,0.015598029,0.000000000],[0.003594008,0.013590840,0.060797022,0.290335951,0.000000000],[0.016908297,0.015073879,0.016699524,0.019890989,0.000000000],[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 A1708 - C2023 tWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008980070,0.019966660,0.009915932,0.228492889,0.000000000],[0.016346286,0.009031307,0.187563177,0.011164675,0.000000000],[0.009848690,0.228575642,0.001950482,0.037767838,0.000000000],[0.186418153,0.011718511,0.021945816,0.010313871,0.000000000],[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 A1709 - U2022 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_67095.2:
> IL_67095.2  4WF9 U 1707 A 2024
UAA*UCA
> IL_67095.2  8CRE A 1891 U 2318
AAG*CCU
> IL_67095.2  7A0S U 1680 A 1980
UAA*UCA
> IL_67095.2  5J7L G 1663 C 1997
GAA*UCC
> IL_67095.2  8P9A A 1895 U 2340
AAG*CCU
> IL_67095.2  9DFE C 1663 G 1997
CAA*UCG
> IL_67095.2  4V9F U 1741 A 2038
UAG*CCA
> IL_67095.2  9DFE U 1433 G 1560
UAG*CAGG