Alignment of HL_46546.1 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
3

3
7
2
I

8
2

4
9
1
I


In
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Cutoff
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Full
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Interior
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Alignment
score
deficit
HL_46546.1_Instance_1 HL_46546.1_HL_5TBW_068_C3194_G3197CUUG
HL_46546.1_Sequence_1 HL_46546.1_HL_5TBW_068_C_3194_G_3197CUUGtrue95000.51
HL_46546.1_Instance_2 HL_46546.1_HL_5AH5_007_C46A_G46ECUCUG
HL_46546.1_Sequence_2 HL_46546.1_HL_5AH5_007_C46A_G46ECUCUGtrue95000.47
HL_46546.1_Instance_3 HL_46546.1_HL_5J7L_176_C1728_G1731CUCG
HL_46546.1_Sequence_3 HL_46546.1_HL_5J7L_176_C_1728_G_1731CUCGtrue100000.00
HL_46546.1_Instance_4 HL_46546.1_HL_2Y8Y_001_C11_G16CGCGUG
HL_46546.1_Sequence_4 HL_46546.1_HL_2Y8Y_001_C11_G16CGCGUGtrue62003.59

Conserved interactions between motif group positions in HL_46546.1:
1 3 s33 
1 4 cWW 
3 4 s35 
JAR3D SCFG/MRF model for HL_46546.1:
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 [4] // Initial node C3194 - G3197 from junction 
BasepairNode | Deletion Probability [0.0000004157377304] | Pair Probability [[0.009353183,0.016772504,0.010752635,0.194966481,0.000000000],[0.019886467,0.009525946,0.243418233,0.013525436,0.000000000],[0.010873390,0.199167485,0.002049567,0.023014932,0.000000000],[0.197494026,0.013031497,0.026256418,0.009911799,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.741082411,0.255227552,0.003536285,0.000153752] | Left Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Right Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Right Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Left Index [1] | Right Index [4] // Basepair C3194 - G3197 cWW 
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node U3195:U3196
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.583333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U3195
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.416666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U3196
Sequences of instances from HL_46546.1:
> HL_46546.1 HL_5TBW_068 C 3194 G 3197
CUUG
> HL_46546.1 HL_5AH5_007 C  46A G  46E
CUCUG
> HL_46546.1 HL_5J7L_176 C 1728 G 1731
CUCG
> HL_46546.1 HL_2Y8Y_001 C   11 G   16
CGCGUG