Alignment of HL_90642.4 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_90642.4
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
7

2
5
7
I

6
8

3
7
7
I

8
7

4
9
6
I

10
5

5
11
4
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_90642.4_Instance_1 HL_90642.4_HL_4Y4O_153_G2027_C2036GUGAAGAUGC
HL_90642.4_Sequence_1 HL_90642.4_HL_4Y4O_153_G_2027_C_2036GUGAAGAUGCtrue100000.00
HL_90642.4_Instance_2 HL_90642.4_HL_7A0S_049_G2010_C2019GUAAAGAUGC
HL_90642.4_Sequence_2 HL_90642.4_HL_7A0S_049_G_2010_C_2019GUAAAGAUGCtrue92001.34
HL_90642.4_Instance_3 HL_90642.4_HL_4WF9_047_G2054_C2063GUGAAGAUGC
HL_90642.4_Sequence_3 HL_90642.4_HL_4WF9_047_G_2054_C_2063GUGAAGAUGCtrue100000.00
HL_90642.4_Instance_4 HL_90642.4_HL_4V9F_052_G2068_C2077GUGCGGAGUC
HL_90642.4_Sequence_4 HL_90642.4_HL_4V9F_052_G_2068_C_2077GUGCGGAGUCtrue82003.09
HL_90642.4_Instance_5 HL_90642.4_HL_5TBW_051_G2369_C2378GGGAACGGGC
HL_90642.4_Sequence_5 HL_90642.4_HL_5TBW_051_G_2369_C_2378GGGAACGGGCtrue87002.21

Conserved interactions between motif group positions in HL_90642.4:
1 2 s35 
1 7 cWW 
2 3 s35 
2 4 tWH 
3 4 s55 
4 7 s35 
5 6 s35 
3 4 6BPh
7 6 7BPh
JAR3D SCFG/MRF model for HL_90642.4:
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 [7] // Initial node G2027 - C2036 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003714633,0.054153751,0.004229975,0.076829292,0.000000000],[0.006524853,0.025497993,0.077480302,0.005069524,0.000000000],[0.004182999,0.605746023,0.000797324,0.010214294,0.000000000],[0.075846024,0.036831735,0.008953288,0.003927989,0.000000000],[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 [7] // Basepair G2027 - C2036 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.071428571,0.642857143,0.214285714,0.000000000] | Position [2] | Left Index [2] | 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 [2] | Right Index [5] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.071428571,0.357142857,0.500000000,0.000000000] | Position [2] | Left Index [2] | Right Index [5] // 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 [2] | Right Index [4] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000000000030757] | Pair Probability [[0.047849049,0.004133874,0.032523626,0.004133874,0.000000000],[0.040609064,0.265754232,0.004133874,0.004133874,0.000000000],[0.004133874,0.009142645,0.124559648,0.023473691,0.000000000],[0.367884526,0.004133874,0.025775841,0.037624437,0.000000000],[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 [0.000000000,0.000000000,0.009799118,0.979911808,0.009799118,0.000489956] | Right Letter Distribution [0.500000000,0.147058824,0.323529412,0.029411765,0.000000000] | Left Index [2] | Right Index [4] // Basepair U2028 - A2033 tWH 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node G2029:G2029
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.202702703,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.013513514,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.770270270,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.013513514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2029
Sequences of instances from HL_90642.4:
> HL_90642.4 HL_4Y4O_153 G 2027 C 2036
GUGAAGAUGC
> HL_90642.4 HL_7A0S_049 G 2010 C 2019
GUAAAGAUGC
> HL_90642.4 HL_4WF9_047 G 2054 C 2063
GUGAAGAUGC
> HL_90642.4 HL_4V9F_052 G 2068 C 2077
GUGCGGAGUC
> HL_90642.4 HL_5TBW_051 G 2369 C 2378
GGGAACGGGC