Alignment of IL_14688.1 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


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
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distance
Interior
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Alignment
score
deficit
IL_14688.1_Instance_1 IL_14688.1,IL_8F4O_005,G18_C48GGUAUAC
IL_14688.1_Sequence_1 IL_14688.18F4O_G18_C48GGU*AUACtrue96000.41
IL_14688.1_Instance_2 IL_14688.1,IL_7TZS_001,G18_C48GGUAUAC
IL_14688.1_Sequence_2 IL_14688.17TZS_G18_C48GGU*AUACtrue96000.41
IL_14688.1_Instance_3 IL_14688.1,IL_7A0S_052,U1447_G1576UACGACG
IL_14688.1_Sequence_3 IL_14688.17A0S_U_1447_G_1576UAC*GACGtrue75002.41
IL_14688.1_Instance_4 IL_14688.1,IL_6RTI_005,A4_U40ACCGUU
IL_14688.1_Sequence_4 IL_14688.16RTI_A4_U40ACC*GUUtrue99000.08
IL_14688.1_Instance_5 IL_14688.1,IL_8P9A_436,U1249_A1236UUUACA
IL_14688.1_Sequence_5 IL_14688.18P9A_U_1249_A_1236UUU*ACAtrue100000.00

Conserved interactions between motif group positions in IL_14688.1:
1 2 s35 
1 6 cWW 
2 3 s35 
2 5 cWW 
3 4 cWW 
4 5 s35 
5 6 s35
JAR3D SCFG/MRF model for IL_14688.1:
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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000081095392462] | Pair Probability [[0.009525982,0.018278957,0.010932497,0.172792282,0.000000000],[0.073108794,0.012910753,0.163113552,0.012435427,0.000000000],[0.010945399,0.183437652,0.002247907,0.028067229,0.000000000],[0.181297618,0.012367625,0.097699156,0.010839170,0.000000000],[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 [0.792098765,0.205432099,0.002370370,0.000098765] | Right Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Left Index [1] | Right Index [6] // Basepair G18 - C48 cWW 
BasepairNode | Deletion Probability [0.0000028285212255] | Pair Probability [[0.165425970,0.016921130,0.187036293,0.019227550,0.000000000],[0.015263490,0.010326070,0.021382444,0.125551631,0.000000000],[0.210660180,0.021202834,0.004012122,0.018229317,0.000000000],[0.019352363,0.135034846,0.016664346,0.013709415,0.000000000],[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 [0.595367176,0.400197141,0.004238541,0.000197141] | Right Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Left Index [2] | Right Index [5] // Basepair G19 - A47 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008681156,0.016522734,0.009641720,0.186645272,0.000000000],[0.020473036,0.009289642,0.231804626,0.011118199,0.000000000],[0.009684631,0.186337727,0.001948189,0.021942164,0.000000000],[0.221587518,0.010522397,0.044224855,0.009576133,0.000000000],[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 U20 - A45 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_14688.1:
> IL_14688.1  8F4O G   18 C   48
GGU*AUAC
> IL_14688.1  7TZS G   18 C   48
GGU*AUAC
> IL_14688.1  7A0S U 1447 G 1576
UAC*GACG
> IL_14688.1  6RTI A    4 U   40
ACC*GUU
> IL_14688.1  8P9A U 1249 A 1236
UUU*ACA