Locus 7954

Sequence ID dm3.chr3L
Location 18,937,722 – 18,937,827
Length 105
Max. P 0.972629
window10951 window10952

overview

Window 1

Location 18,937,722 – 18,937,827
Length 105
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 91.41
Shannon entropy 0.13886
G+C content 0.52116
Mean single sequence MFE -21.90
Consensus MFE -19.33
Energy contribution -19.82
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.45
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.87
SVM RNA-class probability 0.972629
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 18937722 105 + 24543557
CUUUGCCAGCAGCUGGCAAAACAAUUUGCCCGCUGCCUUGUCUAUCUAGCAUCCAUUCAGCCCCAUUCCGCAUCGCCCAUCCUC--UUUUUCCCUGGCUCUUUUUCU
....(((((((((.((((((....)))))).))))).......................((........)).............--........))))......... ( -23.30, z-score =  -2.61, R)
>droSim1.chr3L 18243197 107 + 22553184
CUUUGCCAGCAGCUGGCAAAACAAUUCGCCCGCUGCCUUGUCUAUCUAGCAUCCAUUCAGCCCCAUUCCGCACCGCCCAUCCUCUCUUUUUUCCUGGCUCUUUUUCA
....(((((((((.(((..........))).))))).......................((........)).......................))))......... ( -19.70, z-score =  -1.39, R)
>droSec1.super_19 903175 107 + 1257711
CUUCGCCAGCAGCUGGCAAAACAAUUUGCCCGCUGCCUUGUCUAUCUAGCAUCCAUUCAGCCCCAUUCCGCACCGCCCAUCCUCUCUUUUUCCCUGGCUCUUUUUCA
....(((((((((.((((((....)))))).))))).......................((........)).......................))))......... ( -23.60, z-score =  -3.04, R)
>droYak2.chr3L 2517664 105 - 24197627
CUUUGCCAGCAGCUGGCAAAACAAUUUGCCCGCUGCCUUGUCUAUCUAGCAUCUAUUCGGCCCCAUUCCCUUCUGCUCAUCCUC--UACUUCCCUGCCUCUUUUUCG
....(((.(((((.((((((....)))))).)))))..(((.......))).......))).......................--..................... ( -21.00, z-score =  -2.78, R)
>consensus
CUUUGCCAGCAGCUGGCAAAACAAUUUGCCCGCUGCCUUGUCUAUCUAGCAUCCAUUCAGCCCCAUUCCGCACCGCCCAUCCUC__UUUUUCCCUGGCUCUUUUUCA
....(((((((((.((((((....)))))).)))))............((.........)).................................))))......... (-19.33 = -19.82 +   0.50)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 2

Location 18,937,722 – 18,937,827
Length 105
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 91.41
Shannon entropy 0.13886
G+C content 0.52116
Mean single sequence MFE -28.61
Consensus MFE -26.85
Energy contribution -26.60
Covariance contribution -0.25
Combinations/Pair 1.18
Mean z-score -1.59
Structure conservation index 0.94
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.11
SVM RNA-class probability 0.892539
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 18937722 105 - 24543557
AGAAAAAGAGCCAGGGAAAAA--GAGGAUGGGCGAUGCGGAAUGGGGCUGAAUGGAUGCUAGAUAGACAAGGCAGCGGGCAAAUUGUUUUGCCAGCUGCUGGCAAAG
.........(((.........--.......((((...(((.......)))......))))..........((((((.((((((....)))))).))))))))).... ( -27.90, z-score =  -1.15, R)
>droSim1.chr3L 18243197 107 - 22553184
UGAAAAAGAGCCAGGAAAAAAGAGAGGAUGGGCGGUGCGGAAUGGGGCUGAAUGGAUGCUAGAUAGACAAGGCAGCGGGCGAAUUGUUUUGCCAGCUGCUGGCAAAG
.........(((..........((....((..((((.(......).))))..))....))..........((((((.((((((....)))))).))))))))).... ( -30.00, z-score =  -1.80, R)
>droSec1.super_19 903175 107 - 1257711
UGAAAAAGAGCCAGGGAAAAAGAGAGGAUGGGCGGUGCGGAAUGGGGCUGAAUGGAUGCUAGAUAGACAAGGCAGCGGGCAAAUUGUUUUGCCAGCUGCUGGCGAAG
.........(((..........((....((..((((.(......).))))..))....))..........((((((.((((((....)))))).))))))))).... ( -30.30, z-score =  -1.83, R)
>droYak2.chr3L 2517664 105 + 24197627
CGAAAAAGAGGCAGGGAAGUA--GAGGAUGAGCAGAAGGGAAUGGGGCCGAAUAGAUGCUAGAUAGACAAGGCAGCGGGCAAAUUGUUUUGCCAGCUGCUGGCAAAG
..........((......((.--.......((((...((........)).......))))......))..((((((.((((((....)))))).)))))).)).... ( -26.24, z-score =  -1.60, R)
>consensus
UGAAAAAGAGCCAGGGAAAAA__GAGGAUGGGCGGUGCGGAAUGGGGCUGAAUGGAUGCUAGAUAGACAAGGCAGCGGGCAAAUUGUUUUGCCAGCUGCUGGCAAAG
.........(((..................((((...(((.......)))......))))..........((((((.((((((....)))))).))))))))).... (-26.85 = -26.60 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:36:41 2011