Alignment of HL_53760.2 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
6

3
7
6
I

8
7

4
9
6
I

10
6

5
11
5
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
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distance

Interior
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distance

Alignment
score
deficit
HL_53760.2_Instance_1 HL_53760.2_HL_4Y4O_151_G1949_C1957GGUAAGUUC
HL_53760.2_Sequence_1 HL_53760.2_HL_4Y4O_151_G_1949_C_1957GGUAAGUUCtrue100000.00
HL_53760.2_Instance_2 HL_53760.2_HL_5J7L_182_G1949_C1957GGUAAGUUC
HL_53760.2_Sequence_2 HL_53760.2_HL_5J7L_182_G_1949_C_1957GGUAAGUUCtrue100000.00
HL_53760.2_Instance_3 HL_53760.2_HL_4WF9_046_G1976_C1984GGUAAGUUC
HL_53760.2_Sequence_3 HL_53760.2_HL_4WF9_046_G_1976_C_1984GGUAAGUUCtrue100000.00
HL_53760.2_Instance_4 HL_53760.2_HL_7A0S_048_G1932_C1940GGUAAGUUC
HL_53760.2_Sequence_4 HL_53760.2_HL_7A0S_048_G_1932_C_1940GGUAAGUUCtrue100000.00
HL_53760.2_Instance_5 HL_53760.2_HL_4V9F_051_C1990_G1998CAUCAGUAG
HL_53760.2_Sequence_5 HL_53760.2_HL_4V9F_051_C_1990_G_1998CAUCAGUAGtrue77003.25
HL_53760.2_Instance_6 HL_53760.2_HL_5TBW_050_U2292_G2300UCUAAUUAG
HL_53760.2_Sequence_6 HL_53760.2_HL_5TBW_050_U_2292_G_2300UCUAAUUAGtrue76003.42
HL_53760.2_Instance_7 HL_53760.2_HL_4R4V_003_G689_C697GUUGACUAC
HL_53760.2_Sequence_7 HL_53760.2_HL_4R4V_003_G689_C697GUUGACUACtrue78003.09
HL_53760.2_Instance_8 HL_53760.2_HL_4R4V_007_G689_C697GUUGACUAC
HL_53760.2_Sequence_8 HL_53760.2_HL_4R4V_007_G689_C697GUUGACUACtrue78003.09
HL_53760.2_Instance_9 HL_53760.2_HL_4V9F_049_C1916_G1923CGUACAAG
HL_53760.2_Sequence_9 HL_53760.2_HL_4V9F_049_C_1916_G_1923CGUACAAGtrue62005.32
HL_53760.2_Instance_10 HL_53760.2_HL_4V9F_038_G1557_C1564GCAUUCGC
HL_53760.2_Sequence_10 HL_53760.2_HL_4V9F_038_G_1557_C_1564GCAUUCGCtrue42008.23

Conserved interactions between motif group positions in HL_53760.2:
1 2 s35 
1 8 cWW 
2 3 s35 
2 6 s33 
2 7 bif 
3 5 tSH 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
3 6 6BPh
JAR3D SCFG/MRF model for HL_53760.2:
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 G1949 - C1957 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009129477,0.017626462,0.010551722,0.170998231,0.000000000],[0.042911716,0.010588550,0.192647392,0.012666863,0.000000000],[0.010523640,0.240352930,0.002050257,0.023085440,0.000000000],[0.174339825,0.012774643,0.059941008,0.009811843,0.000000000],[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 [8] // Basepair G1949 - C1957 cWW 
BasepairNode | Deletion Probability [0.0000003525527566] | Pair Probability [[0.062029806,0.212148009,0.003700315,0.003700315,0.000000000],[0.142492471,0.023420514,0.029320149,0.003700315,0.000000000],[0.029320149,0.003700315,0.123744185,0.296682531,0.000000000],[0.054939984,0.003700315,0.003700315,0.003700315,0.000000000],[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 [0.202130295,0.793658657,0.004012881,0.000198167] | Right Letter Distribution [0.050000000,0.050000000,0.050000000,0.850000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair G1950 - U1956 bif 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.291666667,0.458333333,0.125000000,0.000000000] | Position [2] | Left Index [3] | Right Index [6] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | 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 [3] | Right Index [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.040394532,0.036896519,0.000448597,0.025502196,0.000000000],[0.040550578,0.038154183,0.000448597,0.000448597,0.000000000],[0.041714457,0.000448597,0.002772552,0.037241903,0.000000000],[0.415154383,0.313543947,0.003140180,0.003140180,0.000000000],[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 [3] | Right Index [5] // Basepair U1951 - A1953 tSH 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A1952:A1952
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.541666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.208333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1952
Sequences of instances from HL_53760.2:
> HL_53760.2 HL_4Y4O_151 G 1949 C 1957
GGUAAGUUC
> HL_53760.2 HL_5J7L_182 G 1949 C 1957
GGUAAGUUC
> HL_53760.2 HL_4WF9_046 G 1976 C 1984
GGUAAGUUC
> HL_53760.2 HL_7A0S_048 G 1932 C 1940
GGUAAGUUC
> HL_53760.2 HL_4V9F_051 C 1990 G 1998
CAUCAGUAG
> HL_53760.2 HL_5TBW_050 U 2292 G 2300
UCUAAUUAG
> HL_53760.2 HL_4R4V_003 G  689 C  697
GUUGACUAC
> HL_53760.2 HL_4R4V_007 G  689 C  697
GUUGACUAC
> HL_53760.2 HL_4V9F_049 C 1916 G 1923
CGUACAAG
> HL_53760.2 HL_4V9F_038 G 1557 C 1564
GCAUUCGC