Alignment of HL_60266.1 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
5
I

12
5

6
13
4
I

14
4

7
15
3
I

16
3

8
17
2
I

18
2

9
19
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
HL_60266.1_Instance_1 HL_60266.1,HL_6DME_003,G78_C88GGAUAAAAGAC
HL_60266.1_Sequence_1 HL_60266.16DME_G78_C88GGAUAAAAGACtrue100000.00
HL_60266.1_Instance_2 HL_60266.1,HL_7A0S_045,G1767_C1779GUUUACCAAAAUC
HL_60266.1_Sequence_2 HL_60266.17A0S_G_1767_C_1779GUUUACCAAAAUCtrue91001.49

Conserved interactions between motif group positions in HL_60266.1:
1 2 s35 
1 9 cWW 
2 3 s35 
2 8 cWW 
3 4 s35 
3 6 s35 
3 7 tWH 
3 8 s55 
4 5 s33 
4 6 tWH 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
5 4 7BR
JAR3D SCFG/MRF model for HL_60266.1:
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 [9] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[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 [9] // Basepair G78 - C88 cWW 
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.019182405,0.148655525,0.180909616,0.020809685,0.000000000],[0.015872069,0.014270336,0.019891162,0.030121973,0.000000000],[0.197677357,0.019976682,0.003937382,0.034983187,0.000000000],[0.019305959,0.029541285,0.016708444,0.228156930,0.000000000],[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 [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair G79 - A87 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.199980210,0.003885421,0.169238699,0.003885421,0.000000000],[0.036366779,0.175081720,0.003885421,0.003885421,0.000000000],[0.003885421,0.009458368,0.082252671,0.028591197,0.000000000],[0.225726841,0.003885421,0.020718805,0.029272186,0.000000000],[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 [7] // Basepair A80 - A85 tWH 
BasepairNode | Deletion Probability [0.0000000005912491] | Pair Probability [[0.017068734,0.003777338,0.017728674,0.003777338,0.000000000],[0.037986112,0.304381264,0.003777338,0.003777338,0.000000000],[0.003777338,0.009054529,0.028726337,0.016800299,0.000000000],[0.486468209,0.003777338,0.021915662,0.037206152,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.011890606,0.475624257,0.023781213,0.476218787,0.011890606,0.000594530] | Left Letter Distribution [0.416666667,0.416666667,0.083333333,0.083333333,0.000000000] | 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 [6] // Basepair U81 - A84 tWH 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A83:A83
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.875000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A83
Sequences of instances from HL_60266.1:
> HL_60266.1  6DME G   78 C   88
GGAUAAAAGAC
> HL_60266.1  7A0S G 1767 C 1779
GUUUACCAAAAUC