Alignment of HL_60293.1 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_60293.1_Instance_1 HL_60293.1,HL_5DEA_002,U8_G29UGUGGAAGGAGUGGCUGGGUUG
HL_60293.1_Sequence_1 HL_60293.15DEA_U8_G29UGUGGAAGGAGUGGCUGGGUUGtrue100000.00
HL_60293.1_Instance_2 HL_60293.1,HL_5DE8_001,U8_G29UGUGGAAGGAGUGGCUGGGUUG
HL_60293.1_Sequence_2 HL_60293.15DE8_U8_G29UGUGGAAGGAGUGGCUGGGUUGtrue100000.00

Conserved interactions between motif group positions in HL_60293.1:
1 2 s35 
1 18 cWW 
2 4 s33 
2 14 s33 
2 15 cWH 
2 18 s55 
3 4 s35 
3 5 s53 
3 6 cWH 
3 13 cHW 
4 6 s53 
4 7 cWH 
4 14 cHW 
6 7 s35 
6 10 cWH 
7 9 s33 
7 11 cWH 
8 9 s55 
8 17 tSW 
9 11 s33 
9 15 cHW 
9 17 s55 
10 11 s35 
10 13 cWH 
11 13 s53 
11 14 cWH 
11 15 s33 
13 14 s35 
14 15 s33 
15 18 s55 
9 7 2BR
JAR3D SCFG/MRF model for HL_60293.1:
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 [0.0000229437914523] | Pair Probability [[0.011246147,0.013983971,0.014277598,0.037274594,0.000000000],[0.302538153,0.027950744,0.042354115,0.016034133,0.000000000],[0.014590167,0.037125289,0.003306148,0.014672010,0.000000000],[0.086192816,0.014679149,0.350222612,0.013552354,0.000000000],[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 [18] // Basepair U8 - G29 cWW 
HairpinNode  | Num Bases [16] | Left Index [2] | Right Index [17] | Norm Constant [0.003284219621981] // Hairpin node G9:U28
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.004917740,0.004917740,0.050576271,0.041662297,0.000000000],[0.004917740,0.052126028,0.004917740,0.017736492,0.000000000],[0.204479002,0.004917740,0.511381834,0.004917740,0.000000000],[0.016996810,0.004917740,0.015383823,0.055233263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G11 - G15 cWH 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.004917740,0.004917740,0.050576271,0.041662297,0.000000000],[0.004917740,0.052126028,0.004917740,0.017736492,0.000000000],[0.204479002,0.004917740,0.511381834,0.004917740,0.000000000],[0.016996810,0.004917740,0.015383823,0.055233263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G12 - G16 cWH 
Interaction  | Interacting Bases [5,9] | Pair Probability [[0.004917740,0.004917740,0.050576271,0.041662297,0.000000000],[0.004917740,0.052126028,0.004917740,0.017736492,0.000000000],[0.204479002,0.004917740,0.511381834,0.004917740,0.000000000],[0.016996810,0.004917740,0.015383823,0.055233263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G15 - G20 cWH 
Interaction  | Interacting Bases [6,10] | Pair Probability [[0.004917740,0.004917740,0.050576271,0.041662297,0.000000000],[0.004917740,0.052126028,0.004917740,0.017736492,0.000000000],[0.204479002,0.004917740,0.511381834,0.004917740,0.000000000],[0.016996810,0.004917740,0.015383823,0.055233263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G16 - G21 cWH 
Interaction  | Interacting Bases [2,12] | Pair Probability [[0.004917740,0.004917740,0.204479002,0.016996810,0.000000000],[0.004917740,0.052126028,0.004917740,0.004917740,0.000000000],[0.050576271,0.004917740,0.511381834,0.015383823,0.000000000],[0.041662297,0.017736492,0.004917740,0.055233263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G11 - G24 cHW 
Interaction  | Interacting Bases [9,12] | Pair Probability [[0.004917740,0.004917740,0.050576271,0.041662297,0.000000000],[0.004917740,0.052126028,0.004917740,0.017736492,0.000000000],[0.204479002,0.004917740,0.511381834,0.004917740,0.000000000],[0.016996810,0.004917740,0.015383823,0.055233263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G20 - G24 cWH 
Interaction  | Interacting Bases [3,13] | Pair Probability [[0.004917740,0.004917740,0.204479002,0.016996810,0.000000000],[0.004917740,0.052126028,0.004917740,0.004917740,0.000000000],[0.050576271,0.004917740,0.511381834,0.015383823,0.000000000],[0.041662297,0.017736492,0.004917740,0.055233263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G12 - G25 cHW 
Interaction  | Interacting Bases [10,13] | Pair Probability [[0.004917740,0.004917740,0.050576271,0.041662297,0.000000000],[0.004917740,0.052126028,0.004917740,0.017736492,0.000000000],[0.204479002,0.004917740,0.511381834,0.004917740,0.000000000],[0.016996810,0.004917740,0.015383823,0.055233263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G21 - G25 cWH 
Interaction  | Interacting Bases [1,14] | Pair Probability [[0.004917740,0.004917740,0.050576271,0.041662297,0.000000000],[0.004917740,0.052126028,0.004917740,0.017736492,0.000000000],[0.204479002,0.004917740,0.511381834,0.004917740,0.000000000],[0.016996810,0.004917740,0.015383823,0.055233263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G9 - G26 cWH 
Interaction  | Interacting Bases [8,14] | Pair Probability [[0.001492205,0.001492205,0.062045696,0.005157395,0.000000000],[0.001492205,0.015816762,0.001492205,0.001492205,0.000000000],[0.076732572,0.007461025,0.765710357,0.023339805,0.000000000],[0.012641719,0.005381839,0.001492205,0.016759600,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G18 - G26 cHW 
Interaction  | Interacting Bases [7,16] | Pair Probability [[0.015475941,0.014451115,0.002934097,0.313017499,0.000000000],[0.014422784,0.014585827,0.002934097,0.125809611,0.000000000],[0.014187592,0.002934097,0.002934097,0.014280575,0.000000000],[0.013675905,0.029185846,0.137876263,0.281294655,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction A17 - U28 tSW 
Interaction  | Interacting Bases [4,4] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A14
Interaction  | Interacting Bases [11,11] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U23
Interaction  | Interacting Bases [15,15] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U27
Insertion    | Location [1] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Insertion    | Location [3] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000]// Insertion in Hairpin after nucleotide 4, position 3
Insertion    | Location [8] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion in Hairpin after nucleotide 9, position 8
Insertion    | Location [10] | Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 11, position 10
Insertion    | Location [11] | Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 12, position 11
Sequences of instances from HL_60293.1:
> HL_60293.1  5DEA U    8 G   29
UGUGGAAGGAGUGGCUGGGUUG
> HL_60293.1  5DE8 U    8 G   29
UGUGGAAGGAGUGGCUGGGUUG