Alignment of HL_21400.1 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
3

3
7
3
I

8
3

4
9
3
I

10
3

5
11
3
I

12
3

6
13
3
I

14
3

7
15
3
I

16
3

8
17
3
I

18
3

9
19
3
I

20
3

10
21
3
I

22
3

11
23
3
I

24
3

12
25
3
I

26
3

13
27
3
I

28
3

14
29
3
I

30
3

15
31
3
I

32
3

16
33
3
I

34
3

17
35
2
I

36
2

18
37
1
I


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Alignment
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HL_21400.1_Instance_1 HL_21400.1,HL_8EYU_003,A16_U38AGGUGGGUGGUGUGGAGGAGUAU
HL_21400.1_Sequence_1 HL_21400.18EYU_A16_U38AGGUGGGUGGUGUGGAGGAGUAUtrue100000.00

Conserved interactions between motif group positions in HL_21400.1:
1 18 cWW 
2 3 s33 
2 6 s33 
2 9 tWH 
2 15 tSW 
3 5 s53 
3 6 cWH 
3 14 s53 
3 15 s33 
3 16 cHW 
4 5 s35 
4 7 cWH 
4 13 cHW 
4 14 s35 
5 6 s35 
5 7 s53 
5 8 cWH 
5 14 cHW 
6 8 s53 
6 9 s35 
6 10 cWH 
7 8 s35 
7 11 cWH 
8 10 s35 
8 11 s53 
8 12 cWH 
9 10 s53 
9 17 cWW 
10 12 s53 
10 16 cWH 
10 17 s33 
11 12 s35 
11 13 cWH 
12 13 s53 
12 14 cWH 
12 16 s35 
13 14 s35 
16 17 s33 
12 13 2BPh
16 15 2BPh
14 3 2BR
8 10 2BR
JAR3D SCFG/MRF model for HL_21400.1:
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 [18] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009374836,0.022228469,0.010012528,0.216037101,0.000000000],[0.017691617,0.009675113,0.196088410,0.010461402,0.000000000],[0.009993038,0.198630499,0.002061361,0.053740648,0.000000000],[0.197964449,0.011137350,0.023240462,0.011662716,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [18] // Basepair A16 - U38 cWW 
HairpinNode  | Num Bases [16] | Left Index [2] | Right Index [17] | Norm Constant [0.000344517752562] // Hairpin node G17:A37
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G18 - G22 cWH 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G20 - G24 cWH 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.001506979,0.001506979,0.077492300,0.012766885,0.000000000],[0.001506979,0.015973364,0.007534897,0.005435124,0.000000000],[0.062660010,0.001506979,0.763390658,0.001506979,0.000000000],[0.005208458,0.001506979,0.023570892,0.016925537,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G21 - G25 cWH 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.044078439,0.004118062,0.330370325,0.004118062,0.000000000],[0.037959457,0.019394613,0.004118062,0.004118062,0.000000000],[0.004118062,0.007198246,0.041471646,0.421707145,0.000000000],[0.018315720,0.004118062,0.015949182,0.038846857,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G17 - U26 tWH 
Interaction  | Interacting Bases [5,9] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G22 - G27 cWH 
Interaction  | Interacting Bases [6,10] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G24 - G29 cWH 
Interaction  | Interacting Bases [7,11] | Pair Probability [[0.000256492,0.000256492,0.018465170,0.002172960,0.000000000],[0.000256492,0.002718711,0.001795445,0.000925073,0.000000000],[0.053324547,0.001282461,0.907623372,0.001282461,0.000000000],[0.000886494,0.000256492,0.005616565,0.002880774,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G25 - G30 cWH 
Interaction  | Interacting Bases [3,12] | Pair Probability [[0.004966430,0.004966430,0.206503547,0.017165095,0.000000000],[0.004966430,0.052642128,0.004966430,0.004966430,0.000000000],[0.051077026,0.004966430,0.506544030,0.015536138,0.000000000],[0.042074794,0.017912101,0.004966430,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G20 - G32 cHW 
Interaction  | Interacting Bases [10,12] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G29 - G32 cWH 
Interaction  | Interacting Bases [4,13] | Pair Probability [[0.001279730,0.001279730,0.266055152,0.004423035,0.000000000],[0.001279730,0.013564619,0.006398652,0.001279730,0.000000000],[0.013161329,0.001279730,0.649766220,0.004003292,0.000000000],[0.010841669,0.004615521,0.006398652,0.014373206,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G21 - G33 cHW 
Interaction  | Interacting Bases [11,13] | Pair Probability [[0.000252674,0.000252674,0.012993057,0.002140611,0.000000000],[0.000252674,0.002678238,0.001263369,0.000911302,0.000000000],[0.073542989,0.001768716,0.894259015,0.001768716,0.000000000],[0.000873297,0.000252674,0.003952108,0.002837888,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G30 - G33 cWH 
Interaction  | Interacting Bases [1,14] | Pair Probability [[0.166586913,0.165788799,0.002070551,0.010011986,0.000000000],[0.193757756,0.009129710,0.002070551,0.008278035,0.000000000],[0.216956090,0.002070551,0.002070551,0.006790033,0.000000000],[0.179185112,0.008998530,0.016291903,0.009942930,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G17 - A34 tSW 
Interaction  | Interacting Bases [2,15] | Pair Probability [[0.000933318,0.000933318,0.271650781,0.003225757,0.000000000],[0.000933318,0.009892791,0.006533228,0.000933318,0.000000000],[0.009598669,0.000933318,0.663223761,0.002919634,0.000000000],[0.007906921,0.003366138,0.006533228,0.010482501,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G18 - G35 cHW 
Interaction  | Interacting Bases [9,15] | Pair Probability [[0.001117702,0.001117702,0.080464698,0.009468992,0.000000000],[0.001117702,0.011847185,0.007823915,0.004031144,0.000000000],[0.046473914,0.001117702,0.792292506,0.001117702,0.000000000],[0.003863029,0.001117702,0.024475008,0.012553396,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G27 - G35 cWH 
Interaction  | Interacting Bases [8,16] | Pair Probability [[0.009123784,0.017718471,0.010008206,0.198264936,0.000000000],[0.022262210,0.009929018,0.198931998,0.011154256,0.000000000],[0.010027726,0.196386049,0.002064490,0.023275738,0.000000000],[0.216349992,0.010477281,0.053822220,0.010203624,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U26 - A37 cWW 
Insertion    | Location [2] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2
Insertion    | Location [5] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 6, position 5
Insertion    | Location [9] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 10, position 9
Insertion    | Location [11] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 12, position 11
Insertion    | Location [15] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 16, position 15
Sequences of instances from HL_21400.1:
> HL_21400.1  8EYU A   16 U   38
AGGUGGGUGGUGUGGAGGAGUAU