Alignment of HL_94651.1 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
4

4
9
4
I

10
4

5
11
3
I

12
3

6
13
2
I

14
2

7
15
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_94651.1_Instance_1 HL_94651.1_HL_5F5H_001_C8_G15CGUUCUAG
HL_94651.1_Sequence_1 HL_94651.1_HL_5F5H_001_C8_G15CGUUCUAGtrue100000.00
HL_94651.1_Instance_2 HL_94651.1_HL_5F5H_002_C8_G15CGUUCUAG
HL_94651.1_Sequence_2 HL_94651.1_HL_5F5H_002_C8_G15CGUUCUAGtrue100000.00
HL_94651.1_Instance_3 HL_94651.1_HL_5F5F_003_C7_G14CGUUUUAG
HL_94651.1_Sequence_3 HL_94651.1_HL_5F5F_003_C7_G14CGUUUUAGtrue100000.00
HL_94651.1_Instance_4 HL_94651.1_HL_5F5F_001_C7_G14CGUUUUAG
HL_94651.1_Sequence_4 HL_94651.1_HL_5F5F_001_C7_G14CGUUUUAGtrue100000.00

Conserved interactions between motif group positions in HL_94651.1:
1 2 s35 
1 7 cWW 
2 3 s35 
2 6 tSS 
2 7 s55 
4 5 s55 
JAR3D SCFG/MRF model for HL_94651.1:
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 [7] // Initial node C8 - G15 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | 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 [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair C8 - G15 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.021020535,0.017279673,0.019905677,0.012636670,0.000000000],[0.002538690,0.002538690,0.220876798,0.002538690,0.000000000],[0.292330587,0.002538690,0.246790864,0.148849673,0.000000000],[0.002538690,0.002538690,0.002538690,0.002538690,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [6] // Basepair G9 - A14 tSS 
HairpinNode  | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node U10:U13
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.750000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U10
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.750000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U11
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.750000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U13
Insertion    | Location [2] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000]// Insertion in Hairpin after nucleotide 4, position 2
Sequences of instances from HL_94651.1:
> HL_94651.1 HL_5F5H_001 C    8 G   15
CGUUCUAG
> HL_94651.1 HL_5F5H_002 C    8 G   15
CGUUCUAG
> HL_94651.1 HL_5F5F_003 C    7 G   14
CGUUUUAG
> HL_94651.1 HL_5F5F_001 C    7 G   14
CGUUUUAG