Alignment of HL_44730.2 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
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_44730.2_Instance_1 HL_44730.2_HL_4LFB_004_C190B_G190GCCUUGG
HL_44730.2_Sequence_1 HL_44730.2_HL_4LFB_004_C_190B_G_190GCCUUGGtrue100000.00
HL_44730.2_Instance_2 HL_44730.2_HL_6CZR_075_C187_G192CCUUGG
HL_44730.2_Sequence_2 HL_44730.2_HL_6CZR_075_C187_G192CCUUGGtrue100000.00
HL_44730.2_Instance_3 HL_44730.2_HL_5AMQ_001_U3_A9UAGUGUA
HL_44730.2_Sequence_3 HL_44730.2_HL_5AMQ_001_U3_A9UAGUGUAtrue79002.00
HL_44730.2_Instance_4 HL_44730.2_HL_1H4S_002_U32_A38UUCGGGA
HL_44730.2_Sequence_4 HL_44730.2_HL_1H4S_002_U32_A38UUCGGGAtrue87001.27

Conserved interactions between motif group positions in HL_44730.2:
1 2 s35 
1 4 cWW 
2 3 s35 
2 4 s55 
JAR3D SCFG/MRF model for HL_44730.2:
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 C190B - G190G from junction 
BasepairNode | Deletion Probability [0.0000000000429844] | Pair Probability [[0.009106890,0.016989933,0.010236072,0.193756118,0.000000000],[0.020753249,0.009584275,0.218305904,0.012178967,0.000000000],[0.010305927,0.194944276,0.002027252,0.022809627,0.000000000],[0.218224654,0.011603275,0.039263037,0.009910544,0.000000000],[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 [0.000000000,0.006093845,0.493601463,0.493601463,0.006398537,0.000304692] | Right Letter Distribution [0.041666667,0.041666667,0.541666667,0.375000000,0.000000000] | Left Index [1] | Right Index [4] // Basepair C190B - G190G cWW 
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node C190C:U190D
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.416666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C190C
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.416666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U190D
Sequences of instances from HL_44730.2:
> HL_44730.2 HL_4LFB_004 C 190B G 190G
CCUUGG
> HL_44730.2 HL_6CZR_075 C  187 G  192
CCUUGG
> HL_44730.2 HL_5AMQ_001 U    3 A    9
UAGUGUA
> HL_44730.2 HL_1H4S_002 U   32 A   38
UUCGGGA