Alignment of HL_69752.2 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
2
I

6
2

3
7
1
I


In
acceptance
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Cutoff
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Full
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Interior
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Alignment
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HL_69752.2_Instance_1 HL_69752.2,HL_8Y03_001,C11_G17CUAAGUG
HL_69752.2_Sequence_1 HL_69752.28Y03_C11_G17CUAAGUGtrue89001.02
HL_69752.2_Instance_2 HL_69752.2,HL_5ID6_001,C11_G17CUAAGUG
HL_69752.2_Sequence_2 HL_69752.25ID6_C11_G17CUAAGUGtrue89001.02
HL_69752.2_Instance_3 HL_69752.2,HL_5XUZ_001,C-12_G-6CUAAGUG
HL_69752.2_Sequence_3 HL_69752.25XUZ_C-12_G-6CUAAGUGtrue89001.02
HL_69752.2_Instance_4 HL_69752.2,HL_8Y05_001,C-12_G-6CUAAGUG
HL_69752.2_Sequence_4 HL_69752.28Y05_C-12_G-6CUAAGUGtrue89001.02
HL_69752.2_Instance_5 HL_69752.2,HL_5NFV_001,C-10_G-5CUGUUG
HL_69752.2_Sequence_5 HL_69752.25NFV_C-10_G-5CUGUUGtrue93000.69
HL_69752.2_Instance_6 HL_69752.2,HL_8Y0B_001,C-11_G-6CUGUUG
HL_69752.2_Sequence_6 HL_69752.28Y0B_C-11_G-6CUGUUGtrue93000.69
HL_69752.2_Instance_7 HL_69752.2,HL_4M6D_004,C32_G36CUUAG
HL_69752.2_Sequence_7 HL_69752.24M6D_C32_G36CUUAGtrue100000.00

Conserved interactions between motif group positions in HL_69752.2:
1 2 s35 
1 3 cWW 
2 3 s55
JAR3D SCFG/MRF model for HL_69752.2:
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 [3] // Initial node
BasepairNode | Deletion Probability [0.0000000000003180] | Pair Probability [[0.009090944,0.016302246,0.010451159,0.189500131,0.000000000],[0.019328903,0.009258863,0.264630806,0.013146218,0.000000000],[0.010568529,0.193583350,0.001992102,0.022369654,0.000000000],[0.191956811,0.012666128,0.025520256,0.009633898,0.000000000],[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 [0.000000000,0.001005682,0.142806859,0.286619400,0.565243626,0.004123297,0.000201136] | Right Letter Distribution [0.365384615,0.019230769,0.250000000,0.365384615,0.000000000] | Left Index [1] | Right Index [3] // Basepair C11 - G17 cWW 
HairpinNode  | Num Bases [1] | Left Index [2] | Right Index [2] | Norm Constant [1.000000000000000] // Hairpin node U12:U12
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.833333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U12
Sequences of instances from HL_69752.2:
> HL_69752.2  8Y03 C   11 G   17
CUAAGUG
> HL_69752.2  5ID6 C   11 G   17
CUAAGUG
> HL_69752.2  5XUZ C  -12 G   -6
CUAAGUG
> HL_69752.2  8Y05 C  -12 G   -6
CUAAGUG
> HL_69752.2  5NFV C  -10 G   -5
CUGUUG
> HL_69752.2  8Y0B C  -11 G   -6
CUGUUG
> HL_69752.2  4M6D C   32 G   36
CUUAG