Alignment of HL_69353.6 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
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_69353.6_Instance_1 HL_69353.6_HL_4ZT0_005_C55_G58CUAG
HL_69353.6_Sequence_1 HL_69353.6_HL_4ZT0_005_C55_G58CUAGtrue100000.00
HL_69353.6_Instance_2 HL_69353.6_HL_5B2T_002_C55_G58CUAG
HL_69353.6_Sequence_2 HL_69353.6_HL_5B2T_002_C55_G58CUAGtrue100000.00
HL_69353.6_Instance_3 HL_69353.6_HL_5FQ5_002_C55_G58CUAG
HL_69353.6_Sequence_3 HL_69353.6_HL_5FQ5_002_C55_G58CUAGtrue100000.00
HL_69353.6_Instance_4 HL_69353.6_HL_2F8K_001_U6_A9UUGA
HL_69353.6_Sequence_4 HL_69353.6_HL_2F8K_001_U6_A9UUGAtrue86001.28
HL_69353.6_Instance_5 HL_69353.6_HL_5VW1_002_C55_G58CUAG
HL_69353.6_Sequence_5 HL_69353.6_HL_5VW1_002_C55_G58CUAGtrue100000.00
HL_69353.6_Instance_6 HL_69353.6_HL_4Y4O_141_C1565_G1568CAAG
HL_69353.6_Sequence_6 HL_69353.6_HL_4Y4O_141_C_1565_G_1568CAAGtrue92000.74
HL_69353.6_Instance_7 HL_69353.6_HL_5J7L_172_C1565_G1568CAGG
HL_69353.6_Sequence_7 HL_69353.6_HL_5J7L_172_C_1565_G_1568CAGGtrue83001.62
HL_69353.6_Instance_8 HL_69353.6_HL_5U30_001_U4_A7UAGA
HL_69353.6_Sequence_8 HL_69353.6_HL_5U30_001_U4_A7UAGAtrue79002.02
HL_69353.6_Instance_9 HL_69353.6_HL_5TBW_040_C1792_G1796CCGUG
HL_69353.6_Sequence_9 HL_69353.6_HL_5TBW_040_C_1792_G_1796CCGUGtrue39005.83
HL_69353.6_Instance_10 HL_69353.6_HL_7A0S_039_C1581_G1584CAAG
HL_69353.6_Sequence_10 HL_69353.6_HL_7A0S_039_C_1581_G_1584CAAGtrue92000.74
HL_69353.6_Instance_11 HL_69353.6_HL_5F9R_002_C73_G76CUAG
HL_69353.6_Sequence_11 HL_69353.6_HL_5F9R_002_C73_G76CUAGtrue100000.00
HL_69353.6_Instance_12 HL_69353.6_HL_6JOO_002_C58_G61CUCG
HL_69353.6_Sequence_12 HL_69353.6_HL_6JOO_002_C58_G61CUCGtrue87001.22
HL_69353.6_Instance_13 HL_69353.6_HL_4V9F_041_C1651_G1655CCAUG
HL_69353.6_Sequence_13 HL_69353.6_HL_4V9F_041_C_1651_G_1655CCAUGtrue48004.95
HL_69353.6_Instance_14 HL_69353.6_HL_5TBW_071_C3350_G3353CUUG
HL_69353.6_Sequence_14 HL_69353.6_HL_5TBW_071_C_3350_G_3353CUUGtrue93000.64
HL_69353.6_Instance_15 HL_69353.6_HL_4V88_192_C276_G279CUUG
HL_69353.6_Sequence_15 HL_69353.6_HL_4V88_192_C276_G279CUUGtrue93000.64
HL_69353.6_Instance_16 HL_69353.6_HL_5SWD_005_U47_A52UUUCUA
HL_69353.6_Sequence_16 HL_69353.6_HL_5SWD_005_U47_A52UUUCUAtrue24007.22
HL_69353.6_Instance_17 HL_69353.6_HL_4WF9_037_C1612_G1615CGAG
HL_69353.6_Sequence_17 HL_69353.6_HL_4WF9_037_C_1612_G_1615CGAGtrue84001.53

Conserved interactions between motif group positions in HL_69353.6:
1 2 s35 
1 3 cWW 
2 3 s55 
JAR3D SCFG/MRF model for HL_69353.6:
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 [3] // Initial node C55 - G58 from junction 
BasepairNode | Deletion Probability [0.0000000352713031] | Pair Probability [[0.008236672,0.014977105,0.009395839,0.172923817,0.000000000],[0.017948791,0.008485807,0.299996653,0.011600188,0.000000000],[0.009487208,0.175712836,0.001814837,0.020393308,0.000000000],[0.201661815,0.011135483,0.027419546,0.008810094,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.002407629,0.819109693,0.177820580,0.000636302,0.000025796] | Left Letter Distribution [0.250000000,0.113636364,0.113636364,0.522727273,0.000000000] | Right Length Distribution [0.938289488,0.061391483,0.000310406,0.000008622] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [1] | Right Index [3] // Basepair C55 - G58 cWW 
HairpinNode  | Num Bases [1] | Left Index [2] | Right Index [2] | Norm Constant [1.000000000000000] // Hairpin node A57:A57
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.447368421,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.131578947,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.184210526,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.236842105,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A57
Sequences of instances from HL_69353.6:
> HL_69353.6 HL_4ZT0_005 C   55 G   58
CUAG
> HL_69353.6 HL_5B2T_002 C   55 G   58
CUAG
> HL_69353.6 HL_5FQ5_002 C   55 G   58
CUAG
> HL_69353.6 HL_2F8K_001 U    6 A    9
UUGA
> HL_69353.6 HL_5VW1_002 C   55 G   58
CUAG
> HL_69353.6 HL_4Y4O_141 C 1565 G 1568
CAAG
> HL_69353.6 HL_5J7L_172 C 1565 G 1568
CAGG
> HL_69353.6 HL_5U30_001 U    4 A    7
UAGA
> HL_69353.6 HL_5TBW_040 C 1792 G 1796
CCGUG
> HL_69353.6 HL_7A0S_039 C 1581 G 1584
CAAG
> HL_69353.6 HL_5F9R_002 C   73 G   76
CUAG
> HL_69353.6 HL_6JOO_002 C   58 G   61
CUCG
> HL_69353.6 HL_4V9F_041 C 1651 G 1655
CCAUG
> HL_69353.6 HL_5TBW_071 C 3350 G 3353
CUUG
> HL_69353.6 HL_4V88_192 C  276 G  279
CUUG
> HL_69353.6 HL_5SWD_005 U   47 A   52
UUUCUA
> HL_69353.6 HL_4WF9_037 C 1612 G 1615
CGAG