Alignment of HL_53987.3 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_53987.3_Instance_1 HL_53987.3_HL_4M6D_004_C32_G36CUUAG
HL_53987.3_Sequence_1 HL_53987.3_HL_4M6D_004_C32_G36CUUAGtrue100000.00
HL_53987.3_Instance_2 HL_53987.3_HL_4M4O_001_C32_G36CUUAG
HL_53987.3_Sequence_2 HL_53987.3_HL_4M4O_001_C32_G36CUUAGtrue100000.00
HL_53987.3_Instance_3 HL_53987.3_HL_4V88_190_C230_G235CUUCGG
HL_53987.3_Sequence_3 HL_53987.3_HL_4V88_190_C230_G235CUUCGGtrue78002.06

Conserved interactions between motif group positions in HL_53987.3:
1 2 s35 
1 4 cWW 
2 3 cWS 
3 4 s35 
JAR3D SCFG/MRF model for HL_53987.3:
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 C32 - G36 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [4] // Basepair C32 - G36 cWW 
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node U33:A35
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.007861111,0.007975876,0.007642854,0.008260816,0.000000000],[0.014262644,0.013529871,0.003070167,0.014596640,0.000000000],[0.010173082,0.002201965,0.009282757,0.007903972,0.000000000],[0.239613933,0.198615943,0.238666258,0.216342112,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U33 - A35 cWS 
Insertion    | Location [1] | Length Distribution [0.010744024,0.650013430,0.333064733,0.005909213,0.000268601] | Letter Distribution [0.083333333,0.250000000,0.083333333,0.583333333,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_53987.3:
> HL_53987.3 HL_4M6D_004 C   32 G   36
CUUAG
> HL_53987.3 HL_4M4O_001 C   32 G   36
CUUAG
> HL_53987.3 HL_4V88_190 C  230 G  235
CUUCGG