Alignment of HL_39334.4 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_39334.4
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
2

2
5
2
I

6
2

3
7
2
I

8
2

4
9
2
I

10
2

5
11
2
I

12
2

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_39334.4_Instance_1 HL_39334.4_HL_4WF9_023_C789_G798CGUUGAAAAG
HL_39334.4_Sequence_1 HL_39334.4_HL_4WF9_023_C789_G798CGUUGAAAAGtrue97000.46
HL_39334.4_Instance_2 HL_39334.4_HL_7A0S_022_U757_A766UGCUGAAACA
HL_39334.4_Sequence_2 HL_39334.4_HL_7A0S_022_U757_A766UGCUGAAACAtrue89001.62
HL_39334.4_Instance_3 HL_39334.4_HL_4Y4O_125_G744_C753GGAUGCAAAC
HL_39334.4_Sequence_3 HL_39334.4_HL_4Y4O_125_G744_C753GGAUGCAAACtrue100000.00
HL_39334.4_Instance_4 HL_39334.4_HL_4V9F_024_U837_A846UCCUACAAUA
HL_39334.4_Sequence_4 HL_39334.4_HL_4V9F_024_U837_A846UCCUACAAUAtrue83002.54
HL_39334.4_Instance_5 HL_39334.4_HL_5TBW_020_A876_U885ACGUGCAAAU
HL_39334.4_Sequence_5 HL_39334.4_HL_5TBW_020_A876_U885ACGUGCAAAUtrue100000.05

Conserved interactions between motif group positions in HL_39334.4:
1 2 s35 
1 7 cWW 
2 3 s35 
2 4 s33 
2 6 tSW 
2 7 s55 
4 6 s33 
5 6 s35 
5 7 cWS 
6 7 s55 
6 2 7BR
4 3 2BR
JAR3D SCFG/MRF model for HL_39334.4:
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 C789 - G798 from junction 
HairpinNode  | Num Bases [7] | Left Index [1] | Right Index [7] | Norm Constant [0.249973259348243] // Hairpin node C789:G798
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.161671308,0.158976612,0.001984076,0.009657096,0.000000000],[0.209780801,0.008874447,0.001984076,0.007985973,0.000000000],[0.221911551,0.001984076,0.001984076,0.006483107,0.000000000],[0.173619805,0.008756591,0.014756162,0.009590242,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G790 - A795 tSW 
Interaction  | Interacting Bases [1,7] | Pair Probability [[0.009057963,0.018354800,0.010060520,0.203200943,0.000000000],[0.019230394,0.009423090,0.203835059,0.011564523,0.000000000],[0.010064286,0.203344265,0.002002830,0.029053534,0.000000000],[0.214301711,0.011434067,0.034939147,0.010132867,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction C789 - G798 cWW 
Interaction  | Interacting Bases [5,7] | Pair Probability [[0.104247946,0.091635700,0.103157231,0.092253245,0.000000000],[0.163558958,0.163026387,0.002395318,0.163725761,0.000000000],[0.023016496,0.002395318,0.027010747,0.010380352,0.000000000],[0.012877755,0.018619515,0.009694589,0.012004682,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction A794 - G798 cWS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.357142857,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.214285714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U791
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.203703704,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.018518519,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.759259259,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.018518519,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G793
Insertion    | Location [3] | Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Letter Distribution [0.071428571,0.071428571,0.071428571,0.785714286,0.000000000]// Insertion in Hairpin after nucleotide 3, position 3
Insertion    | Location [6] | Length Distribution [0.000000000,0.009799118,0.979911808,0.009799118,0.000489956] | Letter Distribution [0.708333333,0.125000000,0.041666667,0.125000000,0.000000000]// Insertion in Hairpin after nucleotide 6, position 6
Sequences of instances from HL_39334.4:
> HL_39334.4 HL_4WF9_023 C  789 G  798
CGUUGAAAAG
> HL_39334.4 HL_7A0S_022 U  757 A  766
UGCUGAAACA
> HL_39334.4 HL_4Y4O_125 G  744 C  753
GGAUGCAAAC
> HL_39334.4 HL_4V9F_024 U  837 A  846
UCCUACAAUA
> HL_39334.4 HL_5TBW_020 A  876 U  885
ACGUGCAAAU