Alignment of HL_36421.4 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
4

3
7
4
I

8
4

4
9
4
I

10
4

5
11
4
I

12
4

6
13
4
I

14
4

7
15
3
I

16
3

8
17
2
I

18
2

9
19
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_36421.4_Instance_1 HL_36421.4_HL_5J7L_193_A2471_U2479AGUUCAUAU
HL_36421.4_Sequence_1 HL_36421.4_HL_5J7L_193_A_2471_U_2479AGUUCAUAUtrue100000.00
HL_36421.4_Instance_2 HL_36421.4_HL_4Y4O_163_C2471_G2479CGUCCACAG
HL_36421.4_Sequence_2 HL_36421.4_HL_4Y4O_163_C_2471_G_2479CGUCCACAGtrue88001.96
HL_36421.4_Instance_3 HL_36421.4_HL_4WF9_056_A2498_U2506AGUUCACAU
HL_36421.4_Sequence_3 HL_36421.4_HL_4WF9_056_A_2498_U_2506AGUUCACAUtrue97000.59
HL_36421.4_Instance_4 HL_36421.4_HL_7A0S_059_A2450_U2458AGUCCAUAU
HL_36421.4_Sequence_4 HL_36421.4_HL_7A0S_059_A_2450_U_2458AGUCCAUAUtrue98000.39
HL_36421.4_Instance_5 HL_36421.4_HL_4V9F_062_A2506_U2514AGCACAUAU
HL_36421.4_Sequence_5 HL_36421.4_HL_4V9F_062_A_2506_U_2514AGCACAUAUtrue86002.35
HL_36421.4_Instance_6 HL_36421.4_HL_5TBW_061_C2840_G2848CGUUCAUAG
HL_36421.4_Sequence_6 HL_36421.4_HL_5TBW_061_C_2840_G_2848CGUUCAUAGtrue94000.98

Conserved interactions between motif group positions in HL_36421.4:
1 2 s35 
1 9 cWW 
2 5 s33 
2 8 tSH 
3 4 s35 
4 5 s35 
6 7 s35 
8 9 s35 
4 3 7BPh
5 3 6BPh
5 4 7BPh
2 7 6BPh
9 8 7BPh
8 2 6BR
1 6 7BR
JAR3D SCFG/MRF model for HL_36421.4:
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 [9] // Initial node A2471 - U2479 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.004620414,0.010085180,0.005057588,0.548501215,0.000000000],[0.018014501,0.008765314,0.206090237,0.019188450,0.000000000],[0.002883321,0.054580502,0.000563633,0.046343014,0.000000000],[0.054235572,0.003360490,0.006861583,0.010848985,0.000000000],[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 [9] // Basepair A2471 - U2479 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.042049014,0.044514549,0.000504770,0.002378984,0.000000000],[0.042361408,0.044411471,0.000504770,0.000504770,0.000000000],[0.409943044,0.003533393,0.017273635,0.299901013,0.000000000],[0.046937930,0.044171708,0.000504770,0.000504770,0.000000000],[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 [8] // Basepair G2472 - A2478 tSH 
HairpinNode  | Num Bases [5] | Left Index [3] | Right Index [7] | Norm Constant [0.999999999999999] // Hairpin node U2473:U2477
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.687500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U2473
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.170454545,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.329545455,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.011363636,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.488636364,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U2474
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.001689189,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.994932432,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.001689189,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.001689189,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C2475
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[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 A2476
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.312500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.562500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U2477
Sequences of instances from HL_36421.4:
> HL_36421.4 HL_5J7L_193 A 2471 U 2479
AGUUCAUAU
> HL_36421.4 HL_4Y4O_163 C 2471 G 2479
CGUCCACAG
> HL_36421.4 HL_4WF9_056 A 2498 U 2506
AGUUCACAU
> HL_36421.4 HL_7A0S_059 A 2450 U 2458
AGUCCAUAU
> HL_36421.4 HL_4V9F_062 A 2506 U 2514
AGCACAUAU
> HL_36421.4 HL_5TBW_061 C 2840 G 2848
CGUUCAUAG