Alignment of HL_77600.2 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
3
I

12
3

6
13
2
I

14
2

7
15
1
I


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HL_77600.2_Instance_1 HL_77600.2,HL_8CRE_009,G303_C312GGUAAAUUCC
HL_77600.2_Sequence_1 HL_77600.28CRE_G303_C312GGUAAAUUCCtrue93000.74
HL_77600.2_Instance_2 HL_77600.2,HL_8P9A_121,G303_C312GGUAAAUUCC
HL_77600.2_Sequence_2 HL_77600.28P9A_G303_C312GGUAAAUUCCtrue93000.74
HL_77600.2_Instance_3 HL_77600.2,HL_4ENC_001,G5_C14GAUGAGGCCC
HL_77600.2_Sequence_3 HL_77600.24ENC_G5_C14GAUGAGGCCCtrue79002.17
HL_77600.2_Instance_4 HL_77600.2,HL_4QLM_002,U72_G81UACUCCUUCG
HL_77600.2_Sequence_4 HL_77600.24QLM_U72_G81UACUCCUUCGtrue73002.80
HL_77600.2_Instance_5 HL_77600.2,HL_7JRR_001,G12_C20GAACCAUCC
HL_77600.2_Sequence_5 HL_77600.27JRR_G12_C20GAACCAUCCtrue100000.00
HL_77600.2_Instance_6 HL_77600.2,HL_7JRR_002,G39_C47GGAUGGUUC
HL_77600.2_Sequence_6 HL_77600.27JRR_G39_C47GGAUGGUUCtrue85001.54
HL_77600.2_Instance_7 HL_77600.2,HL_5X6B_004,A30_U38ACUGCAGAU
HL_77600.2_Sequence_7 HL_77600.25X6B_A30_U38ACUGCAGAUtrue64003.65
HL_77600.2_Instance_8 HL_77600.2,HL_4WF9_002,U87_A95UGUAAGUAA
HL_77600.2_Sequence_8 HL_77600.24WF9_U87_A95UGUAAGUAAtrue99000.06
HL_77600.2_Instance_9 HL_77600.2,HL_9DFE_002,C87_G95CGGUAGCGG
HL_77600.2_Sequence_9 HL_77600.29DFE_C87_G95CGGUAGCGGtrue76002.49
HL_77600.2_Instance_10 HL_77600.2,HL_7KGA_003,U22_G31UCAAGCCUAG
HL_77600.2_Sequence_10 HL_77600.27KGA_U22_G31UCAAGCCUAGtrue64003.72

Conserved interactions between motif group positions in HL_77600.2:
1 7 cWW 
2 3 s35 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35
JAR3D SCFG/MRF model for HL_77600.2:
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 [0.0000000000436092] | Pair Probability [[0.009181353,0.017245752,0.010641707,0.164907837,0.000000000],[0.069582759,0.012309588,0.166723983,0.012396028,0.000000000],[0.010654023,0.204306309,0.002154412,0.024377760,0.000000000],[0.173025483,0.012331391,0.099931327,0.010230288,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.000000000,0.002474635,0.497401633,0.497401633,0.002598367,0.000123732] | Left Letter Distribution [0.351851852,0.129629630,0.277777778,0.240740741,0.000000000] | 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 [7] // Basepair G303 - C312 cWW 
HairpinNode  | Num Bases [5] | Left Index [2] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node A307:C311
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.208333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.208333333,0.000000000,0.000000000],[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 A307
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.208333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A308
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.208333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.291666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U309
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.041666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.208333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[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 U310
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.291666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.458333333,0.000000000,0.000000000,0.000000000],[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 C311
Sequences of instances from HL_77600.2:
> HL_77600.2  8CRE G  303 C  312
GGUAAAUUCC
> HL_77600.2  8P9A G  303 C  312
GGUAAAUUCC
> HL_77600.2  4ENC G    5 C   14
GAUGAGGCCC
> HL_77600.2  4QLM U   72 G   81
UACUCCUUCG
> HL_77600.2  7JRR G   12 C   20
GAACCAUCC
> HL_77600.2  7JRR G   39 C   47
GGAUGGUUC
> HL_77600.2  5X6B A   30 U   38
ACUGCAGAU
> HL_77600.2  4WF9 U   87 A   95
UGUAAGUAA
> HL_77600.2  9DFE C   87 G   95
CGGUAGCGG
> HL_77600.2  7KGA U   22 G   31
UCAAGCCUAG