Alignment of HL_75293.5 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
4
I

6
7

3
7
7
I

8
8

4
9
8
I

10
8

5
11
8
I

12
8

6
13
8
I

14
8

7
15
7
I

16
7

8
17
6
I

18
5

9
19
2
I

20
2

10
21
1
I


In
acceptance
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Cutoff
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Full
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Interior
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Alignment
score
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HL_75293.5_Instance_1 HL_75293.5,HL_8CRE_210,A885_U894AGGUGAAAUU
HL_75293.5_Sequence_1 HL_75293.58CRE_A885_U894AGGUGAAAUUtrue100000.00
HL_75293.5_Instance_2 HL_75293.5,HL_5J7L_015,C689_G698CGGUGAAAUG
HL_75293.5_Sequence_2 HL_75293.55J7L_C689_G698CGGUGAAAUGtrue98000.29
HL_75293.5_Instance_3 HL_75293.5,HL_4LFB_015,C689_G698CGGUGAAAUG
HL_75293.5_Sequence_3 HL_75293.54LFB_C689_G698CGGUGAAAUGtrue98000.29
HL_75293.5_Instance_4 HL_75293.5,HL_8P9A_209,A900_U909AGGUGAAAUU
HL_75293.5_Sequence_4 HL_75293.58P9A_A900_U909AGGUGAAAUUtrue100000.00
HL_75293.5_Instance_5 HL_75293.5,HL_8P9A_211,G997_C1007GAUCAGAUACC
HL_75293.5_Sequence_5 HL_75293.58P9A_G997_C_1007GAUCAGAUACCtrue89001.60
HL_75293.5_Instance_6 HL_75293.5,HL_5J7L_017,G786_C796GAUUAGAUACC
HL_75293.5_Sequence_6 HL_75293.55J7L_G786_C796GAUUAGAUACCtrue98000.24
HL_75293.5_Instance_7 HL_75293.5,HL_8CRE_212,G982_C992GAUCAGAUACC
HL_75293.5_Sequence_7 HL_75293.58CRE_G982_C992GAUCAGAUACCtrue89001.60
HL_75293.5_Instance_8 HL_75293.5,HL_4LFB_017,G786_C796GAUUAGAUACC
HL_75293.5_Sequence_8 HL_75293.54LFB_G786_C796GAUUAGAUACCtrue98000.24
HL_75293.5_Instance_9 HL_75293.5,HL_4TUE_219,C31_G40CCUUGGUAAG
HL_75293.5_Sequence_9 HL_75293.54TUE_C31_G40CCUUGGUAAGtrue80002.98
HL_75293.5_Instance_10 HL_75293.5,HL_5J7L_212,G1091_C1100GCGUAAUAGC
HL_75293.5_Sequence_10 HL_75293.55J7L_G_1091_C_1100GCGUAAUAGCtrue90001.57
HL_75293.5_Instance_11 HL_75293.5,HL_4WSM_251,C47_G56CCCAAUAGGG
HL_75293.5_Sequence_11 HL_75293.54WSM_C47_G56CCCAAUAGGGtrue57006.42

Conserved interactions between motif group positions in HL_75293.5:
1 2 s35 
1 10 cWW 
2 3 s35 
2 10 s55 
3 4 s35 
3 8 tSH 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
9 10 s35 
4 7 6BPh
10 9 7BPh
JAR3D SCFG/MRF model for HL_75293.5:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [10] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.005850100,0.027393284,0.006655921,0.215812969,0.000000000],[0.011528573,0.013404573,0.161453244,0.011933967,0.000000000],[0.006669430,0.334471092,0.001272985,0.036564873,0.000000000],[0.122069314,0.018941238,0.015404638,0.010573800,0.000000000],[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 [10] // Basepair A885 - U894 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.346153846,0.269230769,0.346153846,0.038461538,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left for 8CRE|1|CM|G|886
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.115384615,0.346153846,0.192307692,0.346153846,0.000000000] | Position [2] | Left Index [3] | Right Index [9] // Fixed node on right for 8CRE|1|CM|U|893
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 [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000035196243062] | Pair Probability [[0.106056673,0.104321352,0.001223907,0.005893693,0.000000000],[0.106649285,0.105900781,0.019152727,0.001223907,0.000000000],[0.163171360,0.001223907,0.006768990,0.102750762,0.000000000],[0.163118923,0.110095920,0.001223907,0.001223907,0.000000000],[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 [0.633943052,0.364188787,0.001786044,0.000082117] | Right Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000] | Left Index [3] | Right Index [8] // Basepair G887 - A892 tSH 
HairpinNode  | Num Bases [4] | Left Index [4] | Right Index [7] | Norm Constant [0.999999999999999] // Hairpin node U888:A891
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.094936709,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.183544304,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.006329114,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.715189873,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U888
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.423076923,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G889
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.423076923,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.423076923,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.115384615,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A890
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.730769231,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.038461538,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.192307692,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A891
Sequences of instances from HL_75293.5:
> HL_75293.5  8CRE A  885 U  894
AGGUGAAAUU
> HL_75293.5  5J7L C  689 G  698
CGGUGAAAUG
> HL_75293.5  4LFB C  689 G  698
CGGUGAAAUG
> HL_75293.5  8P9A A  900 U  909
AGGUGAAAUU
> HL_75293.5  8P9A G  997 C 1007
GAUCAGAUACC
> HL_75293.5  5J7L G  786 C  796
GAUUAGAUACC
> HL_75293.5  8CRE G  982 C  992
GAUCAGAUACC
> HL_75293.5  4LFB G  786 C  796
GAUUAGAUACC
> HL_75293.5  4TUE C   31 G   40
CCUUGGUAAG
> HL_75293.5  5J7L G 1091 C 1100
GCGUAAUAGC
> HL_75293.5  4WSM C   47 G   56
CCCAAUAGGG