Alignment of HL_38901.2 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
3

3
7
3
I

8
3

4
9
2
I

10
2

5
11
1
I


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HL_38901.2_Instance_1 HL_38901.2,HL_3AM1_001,U18_A23UUGGUA
HL_38901.2_Sequence_1 HL_38901.23AM1_U18_A23UUGGUAtrue98000.15
HL_38901.2_Instance_2 HL_38901.2,HL_3W3S_001,C15_G20ACUGGUG
HL_38901.2_Sequence_2 HL_38901.23W3S_C15_G20ACUGGUGtrue99000.09
HL_38901.2_Instance_3 HL_38901.2,HL_3ADD_001,G15_C20AGUGGUC
HL_38901.2_Sequence_3 HL_38901.23ADD_G15_C20AGUGGUCtrue100000.00
HL_38901.2_Instance_4 HL_38901.2,HL_3RG5_005,G15_C20AGUGGUC
HL_38901.2_Sequence_4 HL_38901.23RG5_G15_C20AGUGGUCtrue100000.00
HL_38901.2_Instance_5 HL_38901.2,HL_5F9R_004,G105_C109GAGUC
HL_38901.2_Sequence_5 HL_38901.25F9R_G105_C109GAGUCtrue81001.76
HL_38901.2_Instance_6 HL_38901.2,HL_8P9A_219,C1359_G1364CAUUUG
HL_38901.2_Sequence_6 HL_38901.28P9A_C_1359_G_1364CAUUUGtrue79001.97
HL_38901.2_Instance_7 HL_38901.2,HL_4KR9_004,G19_C24GGAAAC
HL_38901.2_Sequence_7 HL_38901.24KR9_G19_C24GGAAACtrue74002.51

Conserved interactions between motif group positions in HL_38901.2:
1 2 s35 
1 5 cWW 
2 5 s55 
3 4 cSH
JAR3D SCFG/MRF model for HL_38901.2:
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 [5] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009129921,0.018089638,0.010373405,0.190542929,0.000000000],[0.017837979,0.009183620,0.213028027,0.012496319,0.000000000],[0.010342519,0.232983258,0.001985647,0.024109674,0.000000000],[0.200290726,0.012542138,0.027328996,0.009735204,0.000000000],[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 [5] // Basepair U18 - A23 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node U19:U22
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.100002531,0.074061717,0.004072143,0.072379495,0.000000000],[0.054263395,0.081775889,0.000901642,0.072531229,0.000000000],[0.063504210,0.000901642,0.077464311,0.136893122,0.000000000],[0.073811815,0.073368713,0.000901642,0.113166507,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G21 - U22 cSH 
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.277777778,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U19
Insertion    | Location [1] | Length Distribution [0.146977400,0.846630090,0.006090502,0.000302008] | Letter Distribution [0.187500000,0.062500000,0.562500000,0.187500000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_38901.2:
> HL_38901.2  3AM1 U   18 A   23
UUGGUA
> HL_38901.2  3W3S C   15 G  20A
CUGGUG
> HL_38901.2  3ADD G   15 C  20A
GUGGUC
> HL_38901.2  3RG5 G   15 C  20A
GUGGUC
> HL_38901.2  5F9R G  105 C  109
GAGUC
> HL_38901.2  8P9A C 1359 G 1364
CAUUUG
> HL_38901.2  4KR9 G   19 C   24
GGAAAC