Locus 4568

Sequence ID dm3.chr2R
Location 14,131,662 – 14,131,740
Length 78
Max. P 0.914800
window6259 window6260

overview

Window 9

Location 14,131,662 – 14,131,740
Length 78
Sequences 4
Columns 87
Reading direction forward
Mean pairwise identity 64.91
Shannon entropy 0.56764
G+C content 0.44620
Mean single sequence MFE -24.17
Consensus MFE -10.79
Energy contribution -10.85
Covariance contribution 0.06
Combinations/Pair 1.53
Mean z-score -1.43
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.56
SVM RNA-class probability 0.741309
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14131662 78 + 21146708
AAACUAUUUU-GCUUCGCAAACUCUCGGCCAAACUUUGAGCUUCAGUUUGAGACCGAGUUCGGGUUCGAGUUGGAGUUU--------
.......(((-((...)))))................((((((((..(((((.(((....))).)))))..))))))))-------- ( -19.80, z-score =  -0.22, R)
>droSim1.chr2R 12867240 84 + 19596830
CAACUAUUUU-GCUUCGCAAACUCUCAGCCAAACUUUGAGCUUCAAUUUGAGCCCGAGUUCGGGUUCGAGUUUGAGUUGGAGUUU--
..........-.......((((((.(((((((((.(((.....))).(((((((((....)))))))))))))).))))))))))-- ( -29.40, z-score =  -3.33, R)
>droEre2.scaffold_4845 8352768 85 + 22589142
CAACUAUUUUUGCCUCGCAAACUCUCGGCCAAACUUUGAGCUGCAGAUUGGGCCUGAGUUCGGGUUCGAGUUUGAGUUUGAGUUU--
.............(((((((((((.((((((.....)).))))......(((((((....))))))))))))))....))))...-- ( -23.40, z-score =  -0.38, R)
>droAna3.scaffold_13266 15490398 80 - 19884421
-AAGAGUAUC--CCCCAUUUACUCGCCUUAUAGUUUUGGG----AAACUGCAAGCUUGUUUGGCUUUGGCUGAGAUUUUGAGGCUUU
-..(((((..--.......)))))((((((.((((((((.----...))((.((((.....))))...)).)))))).))))))... ( -24.10, z-score =  -1.79, R)
>consensus
CAACUAUUUU_GCCUCGCAAACUCUCGGCCAAACUUUGAGCUUCAAAUUGAGACCGAGUUCGGGUUCGAGUUUGAGUUUGAGUUU__
.................(((((((...........(((.....)))...(((((((....))))))))))))))............. (-10.79 = -10.85 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 14,131,662 – 14,131,740
Length 78
Sequences 4
Columns 87
Reading direction reverse
Mean pairwise identity 64.91
Shannon entropy 0.56764
G+C content 0.44620
Mean single sequence MFE -19.97
Consensus MFE -10.74
Energy contribution -10.42
Covariance contribution -0.31
Combinations/Pair 1.53
Mean z-score -1.37
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.24
SVM RNA-class probability 0.914800
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14131662 78 - 21146708
--------AAACUCCAACUCGAACCCGAACUCGGUCUCAAACUGAAGCUCAAAGUUUGGCCGAGAGUUUGCGAAGC-AAAAUAGUUU
--------(((((.....(((....))).((((((..((((((.........))))))))))))..(((((...))-)))..))))) ( -17.80, z-score =  -0.88, R)
>droSim1.chr2R 12867240 84 - 19596830
--AAACUCCAACUCAAACUCGAACCCGAACUCGGGCUCAAAUUGAAGCUCAAAGUUUGGCUGAGAGUUUGCGAAGC-AAAAUAGUUG
--......((((((((((((..(.(((((((.((((((.....).)))))..))))))).)..)))))))......-.....))))) ( -23.60, z-score =  -2.36, R)
>droEre2.scaffold_4845 8352768 85 - 22589142
--AAACUCAAACUCAAACUCGAACCCGAACUCAGGCCCAAUCUGCAGCUCAAAGUUUGGCCGAGAGUUUGCGAGGCAAAAAUAGUUG
--.((((..........((((....(((((((.((((.((..(........)..)).))))..)))))))))))........)))). ( -19.97, z-score =  -0.99, R)
>droAna3.scaffold_13266 15490398 80 + 19884421
AAAGCCUCAAAAUCUCAGCCAAAGCCAAACAAGCUUGCAGUUU----CCCAAAACUAUAAGGCGAGUAAAUGGGG--GAUACUCUU-
....(((((....(((.(((.((((.......))))..(((((----....)))))....))))))....)))))--.........- ( -18.50, z-score =  -1.25, R)
>consensus
__AAACUCAAACUCAAACUCGAACCCGAACUCGGGCUCAAACUGAAGCUCAAAGUUUGGCCGAGAGUUUGCGAAGC_AAAAUAGUUG
..................(((....(((((((.((((.(((((........))))).))))..)))))))))).............. (-10.74 = -10.42 +  -0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:31:40 2011