Alignment of HL_68304.6 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
3
I

6
4

3
7
4
I

8
4

4
9
3
I

10
3

5
11
2
I

12
2

6
13
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
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Alignment
score
deficit
HL_68304.6_Instance_1 HL_68304.6_HL_4LFB_012_C458_G474CGACGAG
HL_68304.6_Sequence_1 HL_68304.6_HL_4LFB_012_C458_G474CGACGAGtrue95000.44
HL_68304.6_Instance_2 HL_68304.6_HL_6CZR_083_C453_G459CGACGAG
HL_68304.6_Sequence_2 HL_68304.6_HL_6CZR_083_C453_G459CGACGAGtrue95000.44
HL_68304.6_Instance_3 HL_68304.6_HL_5J7L_148_C487_G493CGGCGAG
HL_68304.6_Sequence_3 HL_68304.6_HL_5J7L_148_C487_G493CGGCGAGtrue95000.44
HL_68304.6_Instance_4 HL_68304.6_HL_6ASO_001_U70_A76UGCAUAA
HL_68304.6_Sequence_4 HL_68304.6_HL_6ASO_001_U70_A76UGCAUAAtrue67003.10
HL_68304.6_Instance_5 HL_68304.6_HL_5J7L_026_U1165_A1171UGAUAAA
HL_68304.6_Sequence_5 HL_68304.6_HL_5J7L_026_U_1165_A_1171UGAUAAAtrue88001.16
HL_68304.6_Instance_6 HL_68304.6_HL_4WF9_031_C1260_G1265CGUAAG
HL_68304.6_Sequence_6 HL_68304.6_HL_4WF9_031_C_1260_G_1265CGUAAGtrue91000.85
HL_68304.6_Instance_7 HL_68304.6_HL_7A0S_031_C1235_G1240CGGAAG
HL_68304.6_Sequence_7 HL_68304.6_HL_7A0S_031_C_1235_G_1240CGGAAGtrue100000.00
HL_68304.6_Instance_8 HL_68304.6_HL_3KTW_001_U163_G168UGGAGG
HL_68304.6_Sequence_8 HL_68304.6_HL_3KTW_001_U163_G168UGGAGGtrue78002.08

Conserved interactions between motif group positions in HL_68304.6:
1 2 s35 
1 6 cWW 
2 5 tSH 
2 6 s55 
3 4 s35 
4 5 s35 
5 6 s35 
JAR3D SCFG/MRF model for HL_68304.6:
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 [6] // Initial node C458 - G474 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009090007,0.015887961,0.010496925,0.168095018,0.000000000],[0.052889839,0.011354317,0.221159565,0.012641051,0.000000000],[0.010611065,0.170166497,0.002106515,0.021025473,0.000000000],[0.195823217,0.012025535,0.076676079,0.009950935,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair C458 - G474 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.094627850,0.097558487,0.001614695,0.053331582,0.000000000],[0.094362199,0.097387718,0.001614695,0.001614695,0.000000000],[0.188489829,0.001614695,0.067988736,0.095513706,0.000000000],[0.103750567,0.097301154,0.001614695,0.001614695,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [5] // Basepair G459 - A463 tSH 
HairpinNode  | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A460:G462
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.350000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.150000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.350000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.150000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A460
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.450000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.050000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.350000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.150000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G462
Insertion    | Location [1] | Length Distribution [0.374980671,0.620844286,0.003981754,0.000193289] | Letter Distribution [0.214285714,0.500000000,0.071428571,0.214285714,0.000000000]// Insertion in Hairpin after nucleotide 3, position 1
Sequences of instances from HL_68304.6:
> HL_68304.6 HL_4LFB_012 C  458 G  474
CGACGAG
> HL_68304.6 HL_6CZR_083 C  453 G  459
CGACGAG
> HL_68304.6 HL_5J7L_148 C  487 G  493
CGGCGAG
> HL_68304.6 HL_6ASO_001 U   70 A   76
UGCAUAA
> HL_68304.6 HL_5J7L_026 U 1165 A 1171
UGAUAAA
> HL_68304.6 HL_4WF9_031 C 1260 G 1265
CGUAAG
> HL_68304.6 HL_7A0S_031 C 1235 G 1240
CGGAAG
> HL_68304.6 HL_3KTW_001 U  163 G  168
UGGAGG