Alignment of HL_25967.2 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
4

3
7
4
I

8
4

4
9
4
I

10
4

5
11
3
I

12
3

6
13
2
I

14
2

7
15
1
I


In
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Alignment
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HL_25967.2_Instance_1 HL_25967.2,HL_8P9A_149,G1719_C1725GUUUAUC
HL_25967.2_Sequence_1 HL_25967.28P9A_G_1719_C_1725GUUUAUCtrue100000.00
HL_25967.2_Instance_2 HL_25967.2,HL_8CRE_037,G1715_C1721GUUUAUC
HL_25967.2_Sequence_2 HL_25967.28CRE_G_1715_C_1721GUUUAUCtrue100000.00
HL_25967.2_Instance_3 HL_25967.2,HL_8P9A_150,C1759_G1766CACCUUUG
HL_25967.2_Sequence_3 HL_25967.28P9A_C_1759_G_1766CACCUUUGtrue60004.91

Conserved interactions between motif group positions in HL_25967.2:
1 2 s35 
1 7 cWW 
2 6 cWW 
3 6 s55 
4 5 s35 
6 7 s35 
3 6 6BPh
5 3 7BR
JAR3D SCFG/MRF model for HL_25967.2:
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 [0.0000234451146992] | Pair Probability [[0.009574124,0.019028436,0.010936653,0.198530575,0.000000000],[0.017980846,0.009507606,0.212727929,0.013322270,0.000000000],[0.010896029,0.224384255,0.002069153,0.025416337,0.000000000],[0.197680266,0.013488440,0.024325847,0.010131233,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair G1719 - C1725 cWW 
BasepairNode | Deletion Probability [0.0000038011627649] | Pair Probability [[0.014550416,0.266872370,0.012991067,0.078630536,0.000000000],[0.016081663,0.017340010,0.019394286,0.014261191,0.000000000],[0.012719729,0.019756895,0.004010360,0.051233113,0.000000000],[0.019820977,0.015444859,0.016439019,0.420453509,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [2] | Right Index [6] // Basepair U1720 - U1724 cWW 
HairpinNode  | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node U1721:A1723
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.326086957,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.021739130,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.630434783,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U1721
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U1722
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.617647059,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.029411765,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.323529412,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1723
Sequences of instances from HL_25967.2:
> HL_25967.2  8P9A G 1719 C 1725
GUUUAUC
> HL_25967.2  8CRE G 1715 C 1721
GUUUAUC
> HL_25967.2  8P9A C 1759 G 1766
CACCUUUG