Locus 11544

Sequence ID dm3.chr3R
Location 21,980,661 – 21,980,733
Length 72
Max. P 0.983353
window15862 window15863

overview

Window 2

Location 21,980,661 – 21,980,733
Length 72
Sequences 5
Columns 73
Reading direction forward
Mean pairwise identity 88.67
Shannon entropy 0.19614
G+C content 0.37698
Mean single sequence MFE -19.80
Consensus MFE -14.12
Energy contribution -14.72
Covariance contribution 0.60
Combinations/Pair 1.08
Mean z-score -3.14
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.13
SVM RNA-class probability 0.983353
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 21980661 72 + 27905053
CAAGUGAUUGAGUAAUUGG-CCUGAAAGUGACAGGUCGAAUACAGUCGAUUACUCAAAUCGAUUGUAAAAUGA
(((....))).....((((-((((.......)))))))).(((((((((((.....)))))))))))...... ( -23.40, z-score =  -4.45, R)
>droEre2.scaffold_4820 4401203 72 - 10470090
CAAGUGAUUGAGUAAUUGG-CCUGAAAAUGAAAGGUCGGAUGCAGUCGAUUACUCAACUUGAUUGUAAAAUUA
(((((...(((((((((((-(.((....(((....)))....)))))))))))))))))))............ ( -21.10, z-score =  -3.92, R)
>droYak2.chr3R 4331945 70 - 28832112
CAAGUGAUUGAGUAAUUGG-CCUGAAAAUGAAAGGUCGGAUGCAAUUGAUUACUCAACGUGAUUG--AAAUAA
(((....))).(((.((((-(((.........))))))).)))..(..(((((.....)))))..--)..... ( -16.00, z-score =  -2.59, R)
>droSec1.super_13 766577 72 + 2104621
CAUGUGAUUGAGUAAUUGGGCCUGAAAGUGACAGGUCGAAUACAGUCGAUUACUCA-CUCGAUUGUAGAAUAA
....(((.((((((((((((((((.......))))))(....)...))))))))))-.)))............ ( -20.10, z-score =  -2.32, R)
>droSim1.chr3R 21836971 72 + 27517382
CAAGUGAUUGAGUAAUUGG-CCUGAAAGUGACAGGACGAAUACAGUCGAUUACUCAACUCGAUUGUAAAAUGA
(((.(((((((((((((((-(.((...((......)).....))))))))))))))).))).)))........ ( -18.40, z-score =  -2.44, R)
>consensus
CAAGUGAUUGAGUAAUUGG_CCUGAAAGUGACAGGUCGAAUACAGUCGAUUACUCAACUCGAUUGUAAAAUAA
(((.(((((((((((((((..(((....(((....)))....))))))))))))))).))).)))........ (-14.12 = -14.72 +   0.60)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 3

Location 21,980,661 – 21,980,733
Length 72
Sequences 5
Columns 73
Reading direction reverse
Mean pairwise identity 88.67
Shannon entropy 0.19614
G+C content 0.37698
Mean single sequence MFE -13.30
Consensus MFE -9.08
Energy contribution -10.28
Covariance contribution 1.20
Combinations/Pair 1.00
Mean z-score -2.50
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.89
SVM RNA-class probability 0.845292
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 21980661 72 - 27905053
UCAUUUUACAAUCGAUUUGAGUAAUCGACUGUAUUCGACCUGUCACUUUCAGG-CCAAUUACUCAAUCACUUG
.............((((.((((((((((......))))((((.......))))-....))))))))))..... ( -15.70, z-score =  -3.29, R)
>droEre2.scaffold_4820 4401203 72 + 10470090
UAAUUUUACAAUCAAGUUGAGUAAUCGACUGCAUCCGACCUUUCAUUUUCAGG-CCAAUUACUCAAUCACUUG
............(((((((((((((.(.(((.....((....)).....))).-.).))))))))...))))) ( -12.30, z-score =  -2.74, R)
>droYak2.chr3R 4331945 70 + 28832112
UUAUUU--CAAUCACGUUGAGUAAUCAAUUGCAUCCGACCUUUCAUUUUCAGG-CCAAUUACUCAAUCACUUG
......--.......((((((((((...(((.....((....)).....))).-...))))))))))...... (  -8.50, z-score =  -1.63, R)
>droSec1.super_13 766577 72 - 2104621
UUAUUCUACAAUCGAG-UGAGUAAUCGACUGUAUUCGACCUGUCACUUUCAGGCCCAAUUACUCAAUCACAUG
.............((.-(((((((((((......))))((((.......)))).....))))))).))..... ( -15.80, z-score =  -2.62, R)
>droSim1.chr3R 21836971 72 - 27517382
UCAUUUUACAAUCGAGUUGAGUAAUCGACUGUAUUCGUCCUGUCACUUUCAGG-CCAAUUACUCAAUCACUUG
............(((((((((((((.((......))(.((((.......))))-.).))))))))...))))) ( -14.20, z-score =  -2.21, R)
>consensus
UCAUUUUACAAUCGAGUUGAGUAAUCGACUGUAUUCGACCUGUCACUUUCAGG_CCAAUUACUCAAUCACUUG
...............((((((((((((........)))((((.......)))).....)))))))))...... ( -9.08 = -10.28 +   1.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:44:56 2011