Alignment of HL_77082.1 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
3
I

14
3

7
15
2
I

16
2

8
17
1
I


In
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Full
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Alignment
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HL_77082.1_Instance_1 HL_77082.1,HL_9DE7_001,C29_G36CCGAAAAG
HL_77082.1_Sequence_1 HL_77082.19DE7_C29_G36CCGAAAAGtrue100000.00
HL_77082.1_Instance_2 HL_77082.1,HL_5UD5_002,A31_U39ACUCUAAAU
HL_77082.1_Sequence_2 HL_77082.15UD5_A31_U39ACUCUAAAUtrue95000.55
HL_77082.1_Instance_3 HL_77082.1,HL_4V9F_032,A1274_U1282ACUCAUACU
HL_77082.1_Sequence_3 HL_77082.14V9F_A_1274_U_1282ACUCAUACUtrue78002.47
HL_77082.1_Instance_4 HL_77082.1,HL_1H3E_002,U31_A39UCUGUAAAA
HL_77082.1_Sequence_4 HL_77082.11H3E_U31_A39UCUGUAAAAtrue89001.19
HL_77082.1_Instance_5 HL_77082.1,HL_7PMQ_003,G8_C15GUUUCGAC
HL_77082.1_Sequence_5 HL_77082.17PMQ_G8_C15GUUUCGACtrue60004.43
HL_77082.1_Instance_6 HL_77082.1,HL_6UFM_004,G13_C20GCCAUCAC
HL_77082.1_Sequence_6 HL_77082.16UFM_G13_C20GCCAUCACtrue96000.43
HL_77082.1_Instance_7 HL_77082.1,HL_8P9A_148,G1680_U1688GUUAUCUUU
HL_77082.1_Sequence_7 HL_77082.18P9A_G_1680_U_1688GUUAUCUUUtrue74002.94
HL_77082.1_Instance_8 HL_77082.1,HL_8CRE_036,G1676_U1684GUUAUCUUU
HL_77082.1_Sequence_8 HL_77082.18CRE_G_1676_U_1684GUUAUCUUUtrue74002.94

Conserved interactions between motif group positions in HL_77082.1:
1 2 s35 
1 8 cWW 
2 3 s35 
2 7 bif 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35
JAR3D SCFG/MRF model for HL_77082.1:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [8] // Initial node
BasepairNode | Deletion Probability [0.0000063567332629] | Pair Probability [[0.010422393,0.084171809,0.010802758,0.180862374,0.000000000],[0.016409392,0.009842698,0.159568300,0.011915480,0.000000000],[0.010713531,0.171032329,0.002229320,0.119497327,0.000000000],[0.159010822,0.012367757,0.023824636,0.017329073,0.000000000],[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 [0.745505270,0.252634842,0.001782393,0.000077495] | Right Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair C29 - G36 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.022712169,0.025768374,0.006040802,0.006040802,0.000000000],[0.524097199,0.218069008,0.006040802,0.006040802,0.000000000],[0.006040802,0.006040802,0.023379250,0.034656894,0.000000000],[0.036343832,0.006040802,0.006040802,0.066646862,0.000000000],[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 [7] // Basepair C30 - A35 bif 
HairpinNode  | Num Bases [4] | Left Index [3] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node G31:A34
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.050000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.150000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.150000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.650000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G31
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.450000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.150000000,0.000000000,0.000000000],[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 A32
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.450000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.150000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.050000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.350000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A33
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.450000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.350000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.150000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.050000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A34
Insertion    | Location [2] | Length Distribution [0.745505270,0.252634842,0.001782393,0.000077495] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion in Hairpin after nucleotide 4, position 2
Insertion    | Location [3] | Length Distribution [0.869396619,0.129517605,0.001046999,0.000038778] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 5, position 3
Sequences of instances from HL_77082.1:
> HL_77082.1  9DE7 C   29 G   36
CCGAAAAG
> HL_77082.1  5UD5 A   31 U   39
ACUCUAAAU
> HL_77082.1  4V9F A 1274 U 1282
ACUCAUACU
> HL_77082.1  1H3E U   31 A   39
UCUGUAAAA
> HL_77082.1  7PMQ G    8 C   15
GUUUCGAC
> HL_77082.1  6UFM G   13 C   20
GCCAUCAC
> HL_77082.1  8P9A G 1680 U 1688
GUUAUCUUU
> HL_77082.1  8CRE G 1676 U 1684
GUUAUCUUU