Alignment of HL_43613.3 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
4
I

10
4

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
edit
distance

Alignment
score
deficit
HL_43613.3_Instance_1 HL_43613.3_HL_5J7L_178_U1777_A1787UUUAUUAAAAA
HL_43613.3_Sequence_1 HL_43613.3_HL_5J7L_178_U_1777_A_1787UUUAUUAAAAAtrue100000.00
HL_43613.3_Instance_2 HL_43613.3_HL_4Y4O_147_U1777_A1787UUUACCAAAAA
HL_43613.3_Sequence_2 HL_43613.3_HL_4Y4O_147_U_1777_A_1787UUUACCAAAAAtrue95000.90
HL_43613.3_Instance_3 HL_43613.3_HL_4V9F_047_U1833_A1843UCUAGUAACAA
HL_43613.3_Sequence_3 HL_43613.3_HL_4V9F_047_U_1833_A_1843UCUAGUAACAAtrue92001.46
HL_43613.3_Instance_4 HL_43613.3_HL_5TBW_046_U2135_A2145UCUAAUUAAAA
HL_43613.3_Sequence_4 HL_43613.3_HL_5TBW_046_U_2135_A_2145UCUAAUUAAAAtrue88002.29
HL_43613.3_Instance_5 HL_43613.3_HL_4WF9_043_U1804_A1814UUUAUCAAAAA
HL_43613.3_Sequence_5 HL_43613.3_HL_4WF9_043_U_1804_A_1814UUUAUCAAAAAtrue98000.45

Conserved interactions between motif group positions in HL_43613.3:
1 2 s35 
1 7 cWW 
2 5 s35 
2 6 tWH 
2 7 s55 
3 4 s53 
3 5 tWH 
6 7 s35 
5 3 6BPh
4 3 7BR
JAR3D SCFG/MRF model for HL_43613.3:
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 U1777 - A1787 from junction 
BasepairNode | Deletion Probability [0.0000001230289089] | Pair Probability [[0.008776211,0.017043482,0.009626941,0.190711986,0.000000000],[0.021414125,0.009550770,0.191353636,0.010729332,0.000000000],[0.009645717,0.188904676,0.001985843,0.022389043,0.000000000],[0.246203326,0.010078147,0.051771850,0.009814914,0.000000000],[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 [0.009799118,0.979911808,0.009799118,0.000489956] | Right Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Left Index [1] | Right Index [7] // Basepair U1777 - A1787 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.020410803,0.003943665,0.035057120,0.003943665,0.000000000],[0.109609892,0.292216935,0.003943665,0.003943665,0.000000000],[0.003943665,0.009440547,0.029747413,0.021082024,0.000000000],[0.344212553,0.003943665,0.020785752,0.093774971,0.000000000],[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 [6] // Basepair U1778 - A1785 tWH 
BasepairNode | Deletion Probability [0.0000000000030757] | Pair Probability [[0.031622574,0.000999732,0.004692174,0.000999732,0.000000000],[0.070375380,0.080559320,0.000999732,0.000999732,0.000000000],[0.006998126,0.002396424,0.007602880,0.004446465,0.000000000],[0.770660471,0.000999732,0.005800327,0.009847197,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.000000000,0.000000000,0.009799118,0.979911808,0.009799118,0.000489956] | Left Letter Distribution [0.382352941,0.205882353,0.088235294,0.323529412,0.000000000] | 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 U1779 - A1784 tWH 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A1783:A1783
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.759259259,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.018518519,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.018518519,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.203703704,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1783
Sequences of instances from HL_43613.3:
> HL_43613.3 HL_5J7L_178 U 1777 A 1787
UUUAUUAAAAA
> HL_43613.3 HL_4Y4O_147 U 1777 A 1787
UUUACCAAAAA
> HL_43613.3 HL_4V9F_047 U 1833 A 1843
UCUAGUAACAA
> HL_43613.3 HL_5TBW_046 U 2135 A 2145
UCUAAUUAAAA
> HL_43613.3 HL_4WF9_043 U 1804 A 1814
UUUAUCAAAAA