Locus 10781

Sequence ID dm3.chr3R
Location 16,398,838 – 16,398,918
Length 80
Max. P 0.997266
window14811 window14812

overview

Window 1

Location 16,398,838 – 16,398,918
Length 80
Sequences 5
Columns 84
Reading direction forward
Mean pairwise identity 89.26
Shannon entropy 0.18677
G+C content 0.51656
Mean single sequence MFE -24.18
Consensus MFE -20.20
Energy contribution -20.40
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.14
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.37
SVM RNA-class probability 0.932246
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 16398838 80 + 27905053
----AGAAUCGGAGUCCGCGCUAGUGCUUGGAAAUUGGGCCCACCUGAGCGGUGGACCCGAAGACAUAGUGAAACAAGUAUUAG
----.....(((...)))..((((((((((....(((((.(((((.....))))).)))))...(.....)...)))))))))) ( -25.90, z-score =  -2.13, R)
>droEre2.scaffold_4770 12472513 76 - 17746568
------ACUACGAGUCCGCG--AGUGCUUUGAAAUUGGGCCCACCUGAGCGGUGGACCCGAAGACAAAGUGAAACAAGUAUUAG
------(((.((......))--)))((((((...(((((.(((((.....))))).)))))...)))))).............. ( -23.20, z-score =  -2.43, R)
>droYak2.chr3R 5184641 81 + 28832112
ACUCCGACUCCAAGUCCGCG--AGUACUU-AAAAUUGGGCCCACCUGAGUGGUGGACCCGAAGACAAAGUAAAACAAGUAUUAG
.(((((((.....)).)).)--))(((((-....(((((.(((((.....))))).))))).....)))))............. ( -23.30, z-score =  -2.60, R)
>droSec1.super_27 461730 80 - 799419
----AGAAUCGGAGUCCGCGCGAGUGCUUGGAAAUUGGGCCCACCUGAGCGGUGGACCCGAAGACAAAGUGAAACAAGUAUUAG
----....((.((((..((....)))))).))..(((((.(((((.....))))).)))))....................... ( -23.90, z-score =  -1.40, R)
>droSim1.chr3R 22447155 78 - 27517382
----AGAAUCGGAGUCCGCG--AGUGCUUGGAAAUUGGGCCCACCUGAGCGGUGGACCCGAAGACAAAGUGAAACAAGUAUUAG
----....((.(((..(...--.)..))).))..(((((.(((((.....))))).)))))....................... ( -24.60, z-score =  -2.15, R)
>consensus
____AGAAUCGGAGUCCGCG__AGUGCUUGGAAAUUGGGCCCACCUGAGCGGUGGACCCGAAGACAAAGUGAAACAAGUAUUAG
.............((((((....)))........(((((.(((((.....))))).))))).)))................... (-20.20 = -20.40 +   0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,398,838 – 16,398,918
Length 80
Sequences 5
Columns 84
Reading direction reverse
Mean pairwise identity 89.26
Shannon entropy 0.18677
G+C content 0.51656
Mean single sequence MFE -26.18
Consensus MFE -24.30
Energy contribution -24.14
Covariance contribution -0.16
Combinations/Pair 1.07
Mean z-score -3.13
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.07
SVM RNA-class probability 0.997266
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 16398838 80 - 27905053
CUAAUACUUGUUUCACUAUGUCUUCGGGUCCACCGCUCAGGUGGGCCCAAUUUCCAAGCACUAGCGCGGACUCCGAUUCU----
.........(..((...........(((((((((.....)))))))))....(((..((....))..)))....))..).---- ( -25.70, z-score =  -2.88, R)
>droEre2.scaffold_4770 12472513 76 + 17746568
CUAAUACUUGUUUCACUUUGUCUUCGGGUCCACCGCUCAGGUGGGCCCAAUUUCAAAGCACU--CGCGGACUCGUAGU------
..............(((..((((..(((((((((.....))))))))).........((...--.))))))....)))------ ( -25.10, z-score =  -3.38, R)
>droYak2.chr3R 5184641 81 - 28832112
CUAAUACUUGUUUUACUUUGUCUUCGGGUCCACCACUCAGGUGGGCCCAAUUUU-AAGUACU--CGCGGACUUGGAGUCGGAGU
..............((((((.(((((((((((((.....)))))))))......-((((...--.....)))))))).)))))) ( -29.90, z-score =  -3.43, R)
>droSec1.super_27 461730 80 + 799419
CUAAUACUUGUUUCACUUUGUCUUCGGGUCCACCGCUCAGGUGGGCCCAAUUUCCAAGCACUCGCGCGGACUCCGAUUCU----
.........(..((...........(((((((((.....)))))))))....(((..((....))..)))....))..).---- ( -25.70, z-score =  -2.95, R)
>droSim1.chr3R 22447155 78 + 27517382
CUAAUACUUGUUUCACUUUGUCUUCGGGUCCACCGCUCAGGUGGGCCCAAUUUCCAAGCACU--CGCGGACUCCGAUUCU----
...................((((..(((((((((.....))))))))).........((...--.)))))).........---- ( -24.50, z-score =  -2.99, R)
>consensus
CUAAUACUUGUUUCACUUUGUCUUCGGGUCCACCGCUCAGGUGGGCCCAAUUUCCAAGCACU__CGCGGACUCCGAUUCU____
...................((((..(((((((((.....))))))))).........((......))))))............. (-24.30 = -24.14 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:30:17 2011