Alignment of HL_47787.2 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
3
I

10
3

5
11
2
I

12
2

6
13
1
I


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HL_47787.2_Instance_1 HL_47787.2,HL_4V9F_071,C37_G43CAUCCCG
HL_47787.2_Sequence_1 HL_47787.24V9F_C37_G43CAUCCCGtrue89001.10
HL_47787.2_Instance_2 HL_47787.2,HL_9DFE_068,C38_G44CAUUCCG
HL_47787.2_Sequence_2 HL_47787.29DFE_C38_G44CAUUCCGtrue89001.10
HL_47787.2_Instance_3 HL_47787.2,HL_5J7L_203,C38_G44CAUGCCG
HL_47787.2_Sequence_3 HL_47787.25J7L_C38_G44CAUGCCGtrue100000.00
HL_47787.2_Instance_4 HL_47787.2,HL_1MJI_002,C38_G44CAUGCCG
HL_47787.2_Sequence_4 HL_47787.21MJI_C38_G44CAUGCCGtrue100000.00
HL_47787.2_Instance_5 HL_47787.2,HL_8OI5_069,C36_G41CGUUCG
HL_47787.2_Sequence_5 HL_47787.28OI5_C36_G41CGUUCGtrue82001.75
HL_47787.2_Instance_6 HL_47787.2,HL_4WF9_066,C36_G42CAUGCCG
HL_47787.2_Sequence_6 HL_47787.24WF9_C36_G42CAUGCCGtrue100000.00
HL_47787.2_Instance_7 HL_47787.2,HL_8P9A_184,C36_G41CGUCCG
HL_47787.2_Sequence_7 HL_47787.28P9A_C36_G41CGUCCGtrue93000.65
HL_47787.2_Instance_8 HL_47787.2,HL_7A0S_069,C40_G46CAUGCCG
HL_47787.2_Sequence_8 HL_47787.27A0S_C40_G46CAUGCCGtrue100000.00
HL_47787.2_Instance_9 HL_47787.2,HL_6AAY_001,C37_G44CAUUUUGG
HL_47787.2_Sequence_9 HL_47787.26AAY_C37_G44CAUUUUGGtrue29007.08
HL_47787.2_Instance_10 HL_47787.2,HL_7A0S_019,U622_A627UGAAAA
HL_47787.2_Sequence_10 HL_47787.27A0S_U622_A627UGAAAAtrue32006.73

Conserved interactions between motif group positions in HL_47787.2:
1 2 s35 
1 6 cWW 
2 3 s35 
2 6 s55 
4 5 s35 
3 6 6BPh
5 3 7BR
2 6 6BR
JAR3D SCFG/MRF model for HL_47787.2:
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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000083097415128] | Pair Probability [[0.008796437,0.015898754,0.010068450,0.184103077,0.000000000],[0.018965651,0.009017378,0.274483271,0.012533080,0.000000000],[0.010172994,0.187505233,0.001933553,0.021720751,0.000000000],[0.196096144,0.012050625,0.027283683,0.009370918,0.000000000],[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 [0.894854586,0.004971414,0.099652001,0.000497141,0.000024857] | Right Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair C37 - G43 cWW 
HairpinNode  | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A38:C42
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.682692308,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.009615385,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.298076923,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.009615385,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A38
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.104166667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.006944444,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.006944444,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.881944444,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U39
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.625000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.208333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C41
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.105769231,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.778846154,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.009615385,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.105769231,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C42
Insertion    | Location [2] | Length Distribution [0.399702455,0.597074138,0.003074634,0.000148773] | Letter Distribution [0.062500000,0.187500000,0.562500000,0.187500000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2
Sequences of instances from HL_47787.2:
> HL_47787.2  4V9F C   37 G   43
CAUCCCG
> HL_47787.2  9DFE C   38 G   44
CAUUCCG
> HL_47787.2  5J7L C   38 G   44
CAUGCCG
> HL_47787.2  1MJI C   38 G   44
CAUGCCG
> HL_47787.2  8OI5 C   36 G   41
CGUUCG
> HL_47787.2  4WF9 C   36 G   42
CAUGCCG
> HL_47787.2  8P9A C   36 G   41
CGUCCG
> HL_47787.2  7A0S C   40 G   46
CAUGCCG
> HL_47787.2  6AAY C   37 G   44
CAUUUUGG
> HL_47787.2  7A0S U  622 A  627
UGAAAA