Alignment of HL_68257.1 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
5
I

10
6

5
11
6
I

12
7

6
13
6
I

14
6

7
15
5
I

16
5

8
17
4
I

18
4

9
19
3
I

20
3

10
21
2
I

22
2

11
23
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
HL_68257.1_Instance_1 HL_68257.1,HL_7A0S_075,A253_U266AAACGCUUGCGUUU
HL_68257.1_Sequence_1 HL_68257.17A0S_A253_U266AAACGCUUGCGUUUtrue76004.41
HL_68257.1_Instance_2 HL_68257.1,HL_5J7L_138,U158_G168UGAAUCCAUAG
HL_68257.1_Sequence_2 HL_68257.15J7L_U158_G168UGAAUCCAUAGtrue100000.00

Conserved interactions between motif group positions in HL_68257.1:
1 2 s35 
1 11 cWW 
2 3 s35 
2 10 tSH 
3 4 s35 
3 8 s33 
3 9 tHW 
3 10 s55 
4 5 s35 
4 8 tHW 
5 6 s35 
5 7 cSH 
5 8 s35 
6 7 s35 
7 8 s35 
8 9 s35 
9 10 s35 
10 11 s35
JAR3D SCFG/MRF model for HL_68257.1:
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 [11] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.010264537,0.017997257,0.012095982,0.130498803,0.000000000],[0.160028161,0.018765501,0.118260045,0.013196486,0.000000000],[0.012242617,0.116904215,0.002673650,0.033942895,0.000000000],[0.141108219,0.012853655,0.186617613,0.012550365,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [11] // Basepair A253 - U266 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.102496164,0.108506004,0.001230398,0.104729351,0.000000000],[0.103257637,0.108254748,0.001230398,0.001230398,0.000000000],[0.132843734,0.001230398,0.006015026,0.104431541,0.000000000],[0.114413092,0.107670315,0.001230398,0.001230398,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [10] // Basepair A254 - U265 tSH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.017068734,0.037986112,0.003777338,0.486468209,0.000000000],[0.003777338,0.304381264,0.009054529,0.003777338,0.000000000],[0.017728674,0.003777338,0.028726337,0.021915662,0.000000000],[0.003777338,0.003777338,0.016800299,0.037206152,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [9] // Basepair A255 - U264 tHW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.338510258,0.028135304,0.003287063,0.014853320,0.000000000],[0.003287063,0.013949136,0.107072985,0.003287063,0.000000000],[0.289978051,0.003287063,0.120823975,0.015754893,0.000000000],[0.003287063,0.003287063,0.035183695,0.016016004,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [8] // Basepair C256 - G263 tHW 
BasepairNode | Deletion Probability [0.0000000071284465] | Pair Probability [[0.082442164,0.088350897,0.007680972,0.084139219,0.000000000],[0.084342963,0.086292904,0.000981194,0.011079913,0.000000000],[0.012396638,0.099911675,0.089503806,0.079842104,0.000000000],[0.084200391,0.107923341,0.000981194,0.079930624,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.481347774,0.012033694,0.012635379,0.481347774,0.012033694,0.000601685] | Right Letter Distribution [0.100000000,0.100000000,0.300000000,0.500000000,0.000000000] | Left Index [5] | Right Index [7] // Basepair G257 - C262 cSH 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node C258:C258
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.625000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[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 C258
Sequences of instances from HL_68257.1:
> HL_68257.1  7A0S A  253 U  266
AAACGCUUGCGUUU
> HL_68257.1  5J7L U  158 G  168
UGAAUCCAUAG