Alignment of HL_61996.2 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
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
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Full
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Alignment
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HL_61996.2_Instance_1 HL_61996.2,HL_5J7L_183,G2027_C2036GUGAAGAUGC
HL_61996.2_Sequence_1 HL_61996.25J7L_G_2027_C_2036GUGAAGAUGCtrue100000.00
HL_61996.2_Instance_2 HL_61996.2,HL_4WF9_047,G2054_C2063GUGAAGAUGC
HL_61996.2_Sequence_2 HL_61996.24WF9_G_2054_C_2063GUGAAGAUGCtrue100000.00
HL_61996.2_Instance_3 HL_61996.2,HL_9DFE_048,G2027_C2036GUGAAGAUGC
HL_61996.2_Sequence_3 HL_61996.29DFE_G_2027_C_2036GUGAAGAUGCtrue100000.00
HL_61996.2_Instance_4 HL_61996.2,HL_4V9F_052,G2068_C2077GUGCGGAGUC
HL_61996.2_Sequence_4 HL_61996.24V9F_G_2068_C_2077GUGCGGAGUCtrue83002.74
HL_61996.2_Instance_5 HL_61996.2,HL_7A0S_049,G2010_C2019GUAAAGAUGC
HL_61996.2_Sequence_5 HL_61996.27A0S_G_2010_C_2019GUAAAGAUGCtrue89001.73
HL_61996.2_Instance_6 HL_61996.2,HL_8P9A_162,G2369_C2378GGGAACGGGC
HL_61996.2_Sequence_6 HL_61996.28P9A_G_2369_C_2378GGGAACGGGCtrue90001.54
HL_61996.2_Instance_7 HL_61996.2,HL_8CRE_049,G2347_C2356GGGAACGGGC
HL_61996.2_Sequence_7 HL_61996.28CRE_G_2347_C_2356GGGAACGGGCtrue90001.54
HL_61996.2_Instance_8 HL_61996.2,HL_5E7K_220,G53_C61GUUCGAAUC
HL_61996.2_Sequence_8 HL_61996.25E7K_G53_C61GUUCGAAUCtrue62006.02

Conserved interactions between motif group positions in HL_61996.2:
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_61996.2:
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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003611448,0.052649480,0.004112476,0.074695145,0.000000000],[0.006343607,0.024789716,0.075328071,0.004928704,0.000000000],[0.004066805,0.616697523,0.000775176,0.009930563,0.000000000],[0.073739190,0.035808631,0.008704586,0.003818878,0.000000000],[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 [0.050000000,0.050000000,0.650000000,0.250000000,0.000000000] | Position [2] | Left Index [2] | Right Index [6] // Fixed node on right for 5J7L|1|DA|G|2032
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 [0.150000000,0.050000000,0.350000000,0.450000000,0.000000000] | Position [2] | Left Index [2] | Right Index [5] // Fixed node on right for 5J7L|1|DA|A|2031
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 [0.0000000000059760] | Pair Probability [[0.058028385,0.004002498,0.036753177,0.004002498,0.000000000],[0.038932436,0.230291093,0.004002498,0.004002498,0.000000000],[0.004002498,0.008544631,0.163430289,0.024768382,0.000000000],[0.354373440,0.004002498,0.025675301,0.035187881,0.000000000],[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 [0.000000000,0.000771367,0.128818266,0.864702252,0.005438136,0.000269978] | Right Letter Distribution [0.500000000,0.180000000,0.300000000,0.020000000,0.000000000] | 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 [[0.129310345,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.008620690,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.732758621,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.129310345,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2029
Sequences of instances from HL_61996.2:
> HL_61996.2  5J7L G 2027 C 2036
GUGAAGAUGC
> HL_61996.2  4WF9 G 2054 C 2063
GUGAAGAUGC
> HL_61996.2  9DFE G 2027 C 2036
GUGAAGAUGC
> HL_61996.2  4V9F G 2068 C 2077
GUGCGGAGUC
> HL_61996.2  7A0S G 2010 C 2019
GUAAAGAUGC
> HL_61996.2  8P9A G 2369 C 2378
GGGAACGGGC
> HL_61996.2  8CRE G 2347 C 2356
GGGAACGGGC
> HL_61996.2  5E7K G   53 C   61
GUUCGAAUC