Alignment of HL_81545.2 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
3

2
5
3
I

6
6

3
7
6
I

8
7

4
9
6
I

10
6

5
11
5
I

12
4

6
13
3
I

14
3

7
15
2
I

16
2

8
17
1
I


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Alignment
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HL_81545.2_Instance_1 HL_81545.2,HL_4V9F_037,G1498_C1507GUUAAUAUUC
HL_81545.2_Sequence_1 HL_81545.24V9F_G_1498_C_1507GUUAAUAUUCtrue100000.00
HL_81545.2_Instance_2 HL_81545.2,HL_5J7L_168,G1389_C1398GUUAAUAUUC
HL_81545.2_Sequence_2 HL_81545.25J7L_G_1389_C_1398GUUAAUAUUCtrue100000.00
HL_81545.2_Instance_3 HL_81545.2,HL_4WF9_035,G1426_C1435GUUGAUAUUC
HL_81545.2_Sequence_3 HL_81545.24WF9_G_1426_C_1435GUUGAUAUUCtrue92001.47
HL_81545.2_Instance_4 HL_81545.2,HL_8P9A_146,G1599_C1608GUUAAGAUUC
HL_81545.2_Sequence_4 HL_81545.28P9A_G_1599_C_1608GUUAAGAUUCtrue97000.59
HL_81545.2_Instance_5 HL_81545.2,HL_8CRE_034,G1595_C1604GUUAAAAUUC
HL_81545.2_Sequence_5 HL_81545.28CRE_G_1595_C_1604GUUAAAAUUCtrue94001.10
HL_81545.2_Instance_6 HL_81545.2,HL_9DFE_034,G1389_C1398GUUAAUAUUC
HL_81545.2_Sequence_6 HL_81545.29DFE_G_1389_C_1398GUUAAUAUUCtrue100000.00
HL_81545.2_Instance_7 HL_81545.2,HL_7A0S_035,G1402_C1411GUCAAGAUUC
HL_81545.2_Sequence_7 HL_81545.27A0S_G_1402_C_1411GUCAAGAUUCtrue87002.34

Conserved interactions between motif group positions in HL_81545.2:
1 2 s35 
1 8 cWW 
2 7 tWH 
3 5 tSH 
3 6 s55 
4 5 s35 
6 7 s35 
7 8 s35 
3 6 6BPh
JAR3D SCFG/MRF model for HL_81545.2:
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 [8] // Initial node
BasepairNode | Deletion Probability [0.0000000006160445] | Pair Probability [[0.009278847,0.019324516,0.010566130,0.191913241,0.000000000],[0.016298546,0.009098841,0.193539411,0.012663253,0.000000000],[0.010448787,0.264585590,0.001991650,0.025514464,0.000000000],[0.189457119,0.013143234,0.022364576,0.009811793,0.000000000],[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 [0.000000000,0.007039775,0.985568462,0.007039775,0.000351989] | Right Letter Distribution [0.031250000,0.031250000,0.031250000,0.906250000,0.000000000] | Left Index [1] | Right Index [8] // Basepair G1498 - C1507 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.017898242,0.003960910,0.018590254,0.003960910,0.000000000],[0.039832166,0.319173624,0.003960910,0.003960910,0.000000000],[0.003960910,0.009494562,0.030122383,0.017616762,0.000000000],[0.461511524,0.003960910,0.022980723,0.039014302,0.000000000],[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 [2] | Right Index [7] // Basepair U1499 - A1504 tWH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.055555556,0.277777778,0.500000000,0.000000000] | Position [2] | Left Index [3] | Right Index [6] // Fixed node on right for 4V9F|1|0|U|1503
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 [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.043569405,0.039796460,0.000483855,0.002380184,0.000000000],[0.068404485,0.041152972,0.000483855,0.000483855,0.000000000],[0.044993071,0.000483855,0.002990465,0.040168990,0.000000000],[0.394773534,0.313061037,0.003386988,0.003386988,0.000000000],[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 [3] | Right Index [5] // Basepair U1500 - A1502 tSH 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A1501:A1501
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.722222222,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1501
Sequences of instances from HL_81545.2:
> HL_81545.2  4V9F G 1498 C 1507
GUUAAUAUUC
> HL_81545.2  5J7L G 1389 C 1398
GUUAAUAUUC
> HL_81545.2  4WF9 G 1426 C 1435
GUUGAUAUUC
> HL_81545.2  8P9A G 1599 C 1608
GUUAAGAUUC
> HL_81545.2  8CRE G 1595 C 1604
GUUAAAAUUC
> HL_81545.2  9DFE G 1389 C 1398
GUUAAUAUUC
> HL_81545.2  7A0S G 1402 C 1411
GUCAAGAUUC