Alignment of HL_92681.4 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
3

3
7
3
I

8
3

4
9
3
I

10
3

5
11
3
I

12
3

6
13
2
I

14
2

7
15
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
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Alignment
score
deficit
HL_92681.4_Instance_1 HL_92681.4_HL_4Y4O_164_U2528_G2535UGAAGAAG
HL_92681.4_Sequence_1 HL_92681.4_HL_4Y4O_164_U_2528_G_2535UGAAGAAGtrue100000.00
HL_92681.4_Instance_2 HL_92681.4_HL_5J7L_194_U2528_G2535UGAAGUAG
HL_92681.4_Sequence_2 HL_92681.4_HL_5J7L_194_U_2528_G_2535UGAAGUAGtrue93000.79
HL_92681.4_Instance_3 HL_92681.4_HL_4V9F_063_U2563_G2570UGCAGAAG
HL_92681.4_Sequence_3 HL_92681.4_HL_4V9F_063_U_2563_G_2570UGCAGAAGtrue97000.34
HL_92681.4_Instance_4 HL_92681.4_HL_4WF9_057_U2555_G2562UGUAGUCG
HL_92681.4_Sequence_4 HL_92681.4_HL_4WF9_057_U_2555_G_2562UGUAGUCGtrue79002.42
HL_92681.4_Instance_5 HL_92681.4_HL_7A0S_060_U2507_G2514UGAAGAAG
HL_92681.4_Sequence_5 HL_92681.4_HL_7A0S_060_U_2507_G_2514UGAAGAAGtrue100000.00
HL_92681.4_Instance_6 HL_92681.4_HL_5TBW_062_A2897_U2904AGCAGAAU
HL_92681.4_Sequence_6 HL_92681.4_HL_5TBW_062_A_2897_U_2904AGCAGAAUtrue80002.31
HL_92681.4_Instance_7 HL_92681.4_HL_3OXE_001_G17_C24GUUUAAUC
HL_92681.4_Sequence_7 HL_92681.4_HL_3OXE_001_G17_C24GUUUAAUCtrue32008.01

Conserved interactions between motif group positions in HL_92681.4:
1 2 s35 
1 7 cWW 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35 
7 2 6BPh
JAR3D SCFG/MRF model for HL_92681.4:
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 [7] // Initial node U2528 - G2535 from junction 
BasepairNode | Deletion Probability [0.0000001232089072] | Pair Probability [[0.004848468,0.008566714,0.022932889,0.072045187,0.000000000],[0.065477894,0.008218312,0.113637192,0.006440127,0.000000000],[0.005770601,0.072039064,0.005210697,0.013838489,0.000000000],[0.071071676,0.006327700,0.517878680,0.005696310,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.007039775,0.985568462,0.007039775,0.000351989] | Left Letter Distribution [0.055555556,0.055555556,0.722222222,0.166666667,0.000000000] | 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 [7] // Basepair U2528 - G2535 cWW 
HairpinNode  | Num Bases [5] | Left Index [2] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node A2530:A2534
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.388888889,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.277777778,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.277777778,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2530
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.722222222,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2531
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.722222222,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2532
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.611111111,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.277777778,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2533
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.611111111,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2534
Sequences of instances from HL_92681.4:
> HL_92681.4 HL_4Y4O_164 U 2528 G 2535
UGAAGAAG
> HL_92681.4 HL_5J7L_194 U 2528 G 2535
UGAAGUAG
> HL_92681.4 HL_4V9F_063 U 2563 G 2570
UGCAGAAG
> HL_92681.4 HL_4WF9_057 U 2555 G 2562
UGUAGUCG
> HL_92681.4 HL_7A0S_060 U 2507 G 2514
UGAAGAAG
> HL_92681.4 HL_5TBW_062 A 2897 U 2904
AGCAGAAU
> HL_92681.4 HL_3OXE_001 G   17 C   24
GUUUAAUC