Alignment of HL_36982.3 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
2
I

6
2

3
7
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_36982.3_Instance_1 HL_36982.3_HL_4ZLD_001_C7_G11CUGUG
HL_36982.3_Sequence_1 HL_36982.3_HL_4ZLD_001_C7_G11CUGUGtrue100000.00
HL_36982.3_Instance_2 HL_36982.3_HL_4Z31_001_C6_G10CUGUG
HL_36982.3_Sequence_2 HL_36982.3_HL_4Z31_001_C6_G10CUGUGtrue100000.00
HL_36982.3_Instance_3 HL_36982.3_HL_4QIL_002_C8_G12CUGUG
HL_36982.3_Sequence_3 HL_36982.3_HL_4QIL_002_C8_G12CUGUGtrue100000.00
HL_36982.3_Instance_4 HL_36982.3_HL_4QI2_003_C10_G14CUGUG
HL_36982.3_Sequence_4 HL_36982.3_HL_4QI2_003_C10_G14CUGUGtrue100000.00
HL_36982.3_Instance_5 HL_36982.3_HL_1ZBH_001_U11_A16UUUUCA
HL_36982.3_Sequence_5 HL_36982.3_HL_1ZBH_001_U11_A16UUUUCAtrue63003.48
HL_36982.3_Instance_6 HL_36982.3_HL_6AAX_001_U933_A938UGGAAA
HL_36982.3_Sequence_6 HL_36982.3_HL_6AAX_001_U933_A938UGGAAAtrue31006.52
HL_36982.3_Instance_7 HL_36982.3_HL_6TQB_001_A10_U14AUAUU
HL_36982.3_Sequence_7 HL_36982.3_HL_6TQB_001_A10_U14AUAUUtrue96000.39
HL_36982.3_Instance_8 HL_36982.3_HL_6TQA_003_A9_U13AUAUU
HL_36982.3_Sequence_8 HL_36982.3_HL_6TQA_003_A9_U13AUAUUtrue96000.39
HL_36982.3_Instance_9 HL_36982.3_HL_5TBW_004_C132_G136CUUCG
HL_36982.3_Sequence_9 HL_36982.3_HL_5TBW_004_C132_G136CUUCGtrue82001.69
HL_36982.3_Instance_10 HL_36982.3_HL_5J7L_204_G86_C90GUCUC
HL_36982.3_Sequence_10 HL_36982.3_HL_5J7L_204_G86_C90GUCUCtrue87001.28

Conserved interactions between motif group positions in HL_36982.3:
1 2 s35 
1 3 cWW 
2 3 s55 
JAR3D SCFG/MRF model for HL_36982.3:
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 [3] // Initial node C7 - G11 from junction 
BasepairNode | Deletion Probability [0.0000000002154747] | Pair Probability [[0.008721103,0.017144279,0.009787395,0.203278453,0.000000000],[0.018323255,0.008988275,0.233709382,0.011595052,0.000000000],[0.009833070,0.195155539,0.001920276,0.027504657,0.000000000],[0.204236657,0.011408055,0.028739099,0.009655453,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.003959416,0.792873051,0.201930215,0.001187825,0.000049493] | Left Letter Distribution [0.035714286,0.035714286,0.178571429,0.750000000,0.000000000] | Right Length Distribution [0.004949270,0.989853997,0.004949270,0.000247463] | Right Letter Distribution [0.125000000,0.208333333,0.041666667,0.625000000,0.000000000] | Left Index [1] | Right Index [3] // Basepair C7 - G11 cWW 
HairpinNode  | Num Bases [1] | Left Index [2] | Right Index [2] | Norm Constant [1.000000000000000] // Hairpin node G9:G9
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.291666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.208333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G9
Sequences of instances from HL_36982.3:
> HL_36982.3 HL_4ZLD_001 C    7 G   11
CUGUG
> HL_36982.3 HL_4Z31_001 C    6 G   10
CUGUG
> HL_36982.3 HL_4QIL_002 C    8 G   12
CUGUG
> HL_36982.3 HL_4QI2_003 C   10 G   14
CUGUG
> HL_36982.3 HL_1ZBH_001 U   11 A   16
UUUUCA
> HL_36982.3 HL_6AAX_001 U  933 A  938
UGGAAA
> HL_36982.3 HL_6TQB_001 A   10 U   14
AUAUU
> HL_36982.3 HL_6TQA_003 A    9 U   13
AUAUU
> HL_36982.3 HL_5TBW_004 C  132 G  136
CUUCG
> HL_36982.3 HL_5J7L_204 G   86 C   90
GUCUC