Alignment of HL_89567.2 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_89567.2_Instance_1 HL_89567.2,HL_5J7L_173,C1612_G1619CGACACAG
HL_89567.2_Sequence_1 HL_89567.25J7L_C_1612_G_1619CGACACAGtrue100000.00
HL_89567.2_Instance_2 HL_89567.2,HL_4WF9_038,C1656_G1663CGACACAG
HL_89567.2_Sequence_2 HL_89567.24WF9_C_1656_G_1663CGACACAGtrue100000.00
HL_89567.2_Instance_3 HL_89567.2,HL_7A0S_040,C1628_G1635CGACACAG
HL_89567.2_Sequence_3 HL_89567.27A0S_C_1628_G_1635CGACACAGtrue100000.00
HL_89567.2_Instance_4 HL_89567.2,HL_9DFE_038,C1612_G1619CGACACAG
HL_89567.2_Sequence_4 HL_89567.29DFE_C_1612_G_1619CGACACAGtrue100000.00
HL_89567.2_Instance_5 HL_89567.2,HL_4V9F_042,C1687_G1694CGACACAG
HL_89567.2_Sequence_5 HL_89567.24V9F_C_1687_G_1694CGACACAGtrue100000.00
HL_89567.2_Instance_6 HL_89567.2,HL_8P9A_152,C1844_G1851CGCAGCAG
HL_89567.2_Sequence_6 HL_89567.28P9A_C_1844_G_1851CGCAGCAGtrue87001.69
HL_89567.2_Instance_7 HL_89567.2,HL_8CRE_040,C1840_G1847CGCAGCAG
HL_89567.2_Sequence_7 HL_89567.28CRE_C_1840_G_1847CGCAGCAGtrue87001.69
HL_89567.2_Instance_8 HL_89567.2,HL_1S03_001,A22_U29AGGCAAUU
HL_89567.2_Sequence_8 HL_89567.21S03_A22_U29AGGCAAUUtrue60005.07

Conserved interactions between motif group positions in HL_89567.2:
1 2 s35 
1 5 cWW 
2 4 s33 
2 5 s55 
3 4 s35 
4 3 7BPh
2 4 6BR
JAR3D SCFG/MRF model for HL_89567.2:
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 [0.0000001232656381] | Pair Probability [[0.008976824,0.016730854,0.010230537,0.197633502,0.000000000],[0.018824307,0.009157494,0.260432179,0.012619351,0.000000000],[0.010330006,0.191036585,0.001967919,0.025674394,0.000000000],[0.189548681,0.012282179,0.024840230,0.009714959,0.000000000],[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 [0.006170935,0.987349583,0.006170935,0.000308547] | Right Letter Distribution [0.750000000,0.050000000,0.050000000,0.150000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair C1612 - G1619 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G1613:C1617
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.011904762,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.011904762,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.964285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.011904762,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1613
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.350000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.550000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.050000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.050000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C1615
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.129310345,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.853448276,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.008620690,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.008620690,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C1617
Insertion    | Location [1] | Length Distribution [0.005399568,0.864702252,0.128818266,0.001041345,0.000038568] | Letter Distribution [0.500000000,0.318181818,0.136363636,0.045454545,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Insertion    | Location [2] | Length Distribution [0.128917709,0.865369770,0.005442334,0.000270187] | Letter Distribution [0.611111111,0.055555556,0.277777778,0.055555556,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2
Sequences of instances from HL_89567.2:
> HL_89567.2  5J7L C 1612 G 1619
CGACACAG
> HL_89567.2  4WF9 C 1656 G 1663
CGACACAG
> HL_89567.2  7A0S C 1628 G 1635
CGACACAG
> HL_89567.2  9DFE C 1612 G 1619
CGACACAG
> HL_89567.2  4V9F C 1687 G 1694
CGACACAG
> HL_89567.2  8P9A C 1844 G 1851
CGCAGCAG
> HL_89567.2  8CRE C 1840 G 1847
CGCAGCAG
> HL_89567.2  1S03 A   22 U   29
AGGCAAUU