Locus 13325

Sequence ID dm3.chrX
Location 5,828,307 – 5,828,368
Length 61
Max. P 0.967113
window18341 window18342

overview

Window 1

Location 5,828,307 – 5,828,368
Length 61
Sequences 5
Columns 61
Reading direction forward
Mean pairwise identity 93.11
Shannon entropy 0.12412
G+C content 0.39672
Mean single sequence MFE -14.66
Consensus MFE -13.14
Energy contribution -14.14
Covariance contribution 1.00
Combinations/Pair 1.11
Mean z-score -2.32
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.78
SVM RNA-class probability 0.967113
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5828307 61 + 22422827
CUGUCUAGCCACGAAAUUCGUCGAGUUCAAAAUCCAUUUGAUCUCAAUCGAGAAUUGGCAU
.......((((.....((((..(((.(((((.....))))).)))...))))...)))).. ( -14.30, z-score =  -1.82, R)
>droEre2.scaffold_4690 3170460 61 + 18748788
UUUUCUACCCACGAAACUCGUUGAGCUCGAAAUCCAUUUGAUCUCAAUCGAAAAUUGGCAU
........(((......((((((((.(((((.....))))).))))).)))....)))... ( -11.50, z-score =  -1.68, R)
>droYak2.chrX 14684965 61 + 21770863
UUUUCUAACCACGAAACUCGUUGAGUUCGAAAUCCAUUUGAUCUCAAUCGAAAAUUGGCAU
........(((......((((((((.(((((.....))))).))))).)))....)))... ( -11.80, z-score =  -1.48, R)
>droSec1.super_4 5242931 61 - 6179234
CUUUCUAGCCACGAAACUCGUUGAGUUCCAAAUCCAUUUGAUCUCAAUCGAGAAUUGGCAU
.......((((.....(((((((((...((((....))))..))))).))))...)))).. ( -16.50, z-score =  -3.08, R)
>droSim1.chrX 4553774 61 + 17042790
CUUUCUAGCCACGAAACUCGUUGAGUUCGAAAUCCAUUUGAUCUCAAUCGAGAAUUGGCAU
.......((((.....(((((((((.(((((.....))))).))))).))))...)))).. ( -19.20, z-score =  -3.53, R)
>consensus
CUUUCUAGCCACGAAACUCGUUGAGUUCGAAAUCCAUUUGAUCUCAAUCGAGAAUUGGCAU
.......((((.....(((((((((.(((((.....))))).))))).))))...)))).. (-13.14 = -14.14 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 5,828,307 – 5,828,368
Length 61
Sequences 5
Columns 61
Reading direction reverse
Mean pairwise identity 93.11
Shannon entropy 0.12412
G+C content 0.39672
Mean single sequence MFE -15.96
Consensus MFE -14.22
Energy contribution -14.18
Covariance contribution -0.04
Combinations/Pair 1.18
Mean z-score -1.73
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.78
SVM RNA-class probability 0.816500
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5828307 61 - 22422827
AUGCCAAUUCUCGAUUGAGAUCAAAUGGAUUUUGAACUCGACGAAUUUCGUGGCUAGACAG
..((((....(((.(((((.(((((.....))))).))))))))......))))....... ( -17.30, z-score =  -2.41, R)
>droEre2.scaffold_4690 3170460 61 - 18748788
AUGCCAAUUUUCGAUUGAGAUCAAAUGGAUUUCGAGCUCAACGAGUUUCGUGGGUAGAAAA
.......(((((..((((((((.....))))))))(((((.((.....))))))).))))) ( -15.10, z-score =  -1.21, R)
>droYak2.chrX 14684965 61 - 21770863
AUGCCAAUUUUCGAUUGAGAUCAAAUGGAUUUCGAACUCAACGAGUUUCGUGGUUAGAAAA
..((((...((((.(((((.((.((.....)).)).))))))))).....))))....... ( -12.70, z-score =  -0.51, R)
>droSec1.super_4 5242931 61 + 6179234
AUGCCAAUUCUCGAUUGAGAUCAAAUGGAUUUGGAACUCAACGAGUUUCGUGGCUAGAAAG
..((((...((((.(((((.(((((....)))))..))))))))).....))))....... ( -17.50, z-score =  -2.34, R)
>droSim1.chrX 4553774 61 - 17042790
AUGCCAAUUCUCGAUUGAGAUCAAAUGGAUUUCGAACUCAACGAGUUUCGUGGCUAGAAAG
..((((...((((.(((((.((.((.....)).)).))))))))).....))))....... ( -17.20, z-score =  -2.17, R)
>consensus
AUGCCAAUUCUCGAUUGAGAUCAAAUGGAUUUCGAACUCAACGAGUUUCGUGGCUAGAAAG
..((((...((((.(((((.((.((.....)).)).))))))))).....))))....... (-14.22 = -14.18 +  -0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:19:11 2011