Alignment of HL_73793.2 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
4
I

8
5

4
9
5
I

10
5

5
11
4
I

12
4

6
13
3
I

14
3

7
15
2
I

16
2

8
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_73793.2_Instance_1 HL_73793.2_HL_5T83_003_G77_C85GAUAAAAGC
HL_73793.2_Sequence_1 HL_73793.2_HL_5T83_003_G77_C85GAUAAAAGCtrue96000.51
HL_73793.2_Instance_2 HL_73793.2_HL_6DLR_003_G82_C90GAUAGAAGC
HL_73793.2_Sequence_2 HL_73793.2_HL_6DLR_003_G82_C90GAUAGAAGCtrue100000.00
HL_73793.2_Instance_3 HL_73793.2_HL_6UFH_003_G70_C77GGUUGGCC
HL_73793.2_Sequence_3 HL_73793.2_HL_6UFH_003_G70_C77GGUUGGCCtrue66004.59
HL_73793.2_Instance_4 HL_73793.2_HL_5TBW_037_G1680_U1688GUUAUCUUU
HL_73793.2_Sequence_4 HL_73793.2_HL_5TBW_037_G_1680_U_1688GUUAUCUUUtrue62005.11

Conserved interactions between motif group positions in HL_73793.2:
1 2 s35 
1 8 cWW 
2 3 s35 
2 7 tWH 
3 5 s33 
3 6 tWH 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
JAR3D SCFG/MRF model for HL_73793.2:
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 [8] // Initial node G77 - C85 from junction 
BasepairNode | Deletion Probability [0.0000004444241139] | Pair Probability [[0.011043683,0.087705864,0.011663765,0.168825951,0.000000000],[0.015941238,0.010156843,0.158274510,0.013303388,0.000000000],[0.011498012,0.192719706,0.002332326,0.108853206,0.000000000],[0.155160397,0.013999784,0.020787547,0.017733780,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.253667482,0.736552567,0.009321516,0.000458435] | Right Letter Distribution [0.100000000,0.100000000,0.500000000,0.300000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair G77 - C85 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.341615830,0.003223851,0.284401550,0.003223851,0.000000000],[0.027594241,0.013680883,0.003223851,0.003223851,0.000000000],[0.003223851,0.061307595,0.118500437,0.034507085,0.000000000],[0.014567679,0.003223851,0.015451914,0.069029682,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair A78 - A83 tWH 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.016740489,0.003704697,0.017387738,0.003704697,0.000000000],[0.037255609,0.298527778,0.003704697,0.003704697,0.000000000],[0.003704697,0.008880403,0.028173908,0.016477216,0.000000000],[0.389700464,0.057026375,0.074815886,0.036490649,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair U79 - A82 tWH 
HairpinNode  | Num Bases [2] | Left Index [4] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A80:A81
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.583333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A80
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A81
Sequences of instances from HL_73793.2:
> HL_73793.2 HL_5T83_003 G   77 C   85
GAUAAAAGC
> HL_73793.2 HL_6DLR_003 G   82 C   90
GAUAGAAGC
> HL_73793.2 HL_6UFH_003 G   70 C   77
GGUUGGCC
> HL_73793.2 HL_5TBW_037 G 1680 U 1688
GUUAUCUUU