Alignment of HL_16898.2 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
4

3
7
3
I

8
3

4
9
2
I

10
2

5
11
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
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Alignment
score
deficit
HL_16898.2_Instance_1 HL_16898.2_HL_5J7L_156_U779_G785UGAAAGG
HL_16898.2_Sequence_1 HL_16898.2_HL_5J7L_156_U779_G785UGAAAGGtrue90000.96
HL_16898.2_Instance_2 HL_16898.2_HL_4V9F_025_U872_G878UGAAAGG
HL_16898.2_Sequence_2 HL_16898.2_HL_4V9F_025_U872_G878UGAAAGGtrue90000.96
HL_16898.2_Instance_3 HL_16898.2_HL_4LGT_001_C2594_G2599CGUGAG
HL_16898.2_Sequence_3 HL_16898.2_HL_4LGT_001_C_2594_G_2599CGUGAGtrue100000.00
HL_16898.2_Instance_4 HL_16898.2_HL_6VMY_004_C287_G293CCAAGCG
HL_16898.2_Sequence_4 HL_16898.2_HL_6VMY_004_C287_G293CCAAGCGtrue65003.29
HL_16898.2_Instance_5 HL_16898.2_HL_3DH3_001_C2594_G2599CGUGAG
HL_16898.2_Sequence_5 HL_16898.2_HL_3DH3_001_C_2594_G_2599CGUGAGtrue100000.00
HL_16898.2_Instance_6 HL_16898.2_HL_3DH3_003_C2594_G2599CGUGAG
HL_16898.2_Sequence_6 HL_16898.2_HL_3DH3_003_C_2594_G_2599CGUGAGtrue100000.00

Conserved interactions between motif group positions in HL_16898.2:
1 2 s35 
1 5 cWW 
2 3 s35 
2 4 tSW 
2 5 s55 
4 5 s55 
JAR3D SCFG/MRF model for HL_16898.2:
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 [5] // Initial node U779 - G785 from junction 
BasepairNode | Deletion Probability [0.0000016853335170] | Pair Probability [[0.009725060,0.015456119,0.011612777,0.139481247,0.000000000],[0.110048040,0.015196140,0.185380856,0.013989850,0.000000000],[0.011792020,0.142181183,0.002401060,0.019759909,0.000000000],[0.156825235,0.013232153,0.142088180,0.010830171,0.000000000],[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 [0.497737557,0.497737557,0.004319210,0.000205677] | Right Letter Distribution [0.100000000,0.300000000,0.500000000,0.100000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair U779 - G785 cWW 
BasepairNode | Deletion Probability [0.0000001231336240] | Pair Probability [[0.155616705,0.154871150,0.001934200,0.009352669,0.000000000],[0.180998274,0.008528493,0.029866127,0.007732903,0.000000000],[0.240589762,0.001934200,0.001934200,0.006342891,0.000000000],[0.167385278,0.008405952,0.015219036,0.009288161,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Left Letter Distribution [0.437500000,0.062500000,0.062500000,0.437500000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [4] // Basepair G780 - A783 tSW 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node A782:A782
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.437500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.437500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A782
Sequences of instances from HL_16898.2:
> HL_16898.2 HL_5J7L_156 U  779 G  785
UGAAAGG
> HL_16898.2 HL_4V9F_025 U  872 G  878
UGAAAGG
> HL_16898.2 HL_4LGT_001 C 2594 G 2599
CGUGAG
> HL_16898.2 HL_6VMY_004 C  287 G  293
CCAAGCG
> HL_16898.2 HL_3DH3_001 C 2594 G 2599
CGUGAG
> HL_16898.2 HL_3DH3_003 C 2594 G 2599
CGUGAG