Locus 13227

Sequence ID dm3.chrX
Location 5,171,442 – 5,171,508
Length 66
Max. P 0.998594
window18193 window18194

overview

Window 3

Location 5,171,442 – 5,171,508
Length 66
Sequences 4
Columns 66
Reading direction forward
Mean pairwise identity 95.45
Shannon entropy 0.07375
G+C content 0.49242
Mean single sequence MFE -22.75
Consensus MFE -22.75
Energy contribution -22.38
Covariance contribution -0.38
Combinations/Pair 1.11
Mean z-score -3.63
Structure conservation index 1.00
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.41
SVM RNA-class probability 0.998594
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5171442 66 + 22422827
AAGUCAUAAGCCGAAAAGGUCAACAGGAGUUGACCUAUGGCCGAAAGGAGCGCCGUGACAUGUCAA
..(((((..((.....((((((((....))))))))....((....)).))...)))))....... ( -23.70, z-score =  -3.68, R)
>droSim1.chrX 3989427 66 + 17042790
AAGUCAUAAGCCGAAAAGGUCGACAGGAGUUGACCUAUGGCCGAAAGGAGCGCAGUGACAUGUCAA
..(((((..((.....((((((((....))))))))....((....)).))...)))))....... ( -23.40, z-score =  -3.71, R)
>droSec1.super_4 4592653 66 - 6179234
AAGUCAUAAGCCGAAAAGGUCGACAGGAGUUGACCUAUGGCCGAAAGGAGCGCAGUGACAUGUCAA
..(((((..((.....((((((((....))))))))....((....)).))...)))))....... ( -23.40, z-score =  -3.71, R)
>droYak2.chrX 18475727 66 - 21770863
UAGUUAUAAGCCGAAAAGGUCGACACGAGUUGACCUAUGGCCGAAAGAAGCGCAGUGACAUGUCAA
..(((((..((((...((((((((....)))))))).))))(....).......)))))....... ( -20.50, z-score =  -3.43, R)
>consensus
AAGUCAUAAGCCGAAAAGGUCGACAGGAGUUGACCUAUGGCCGAAAGGAGCGCAGUGACAUGUCAA
..(((((..((((...((((((((....)))))))).))))(....).......)))))....... (-22.75 = -22.38 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 5,171,442 – 5,171,508
Length 66
Sequences 4
Columns 66
Reading direction reverse
Mean pairwise identity 95.45
Shannon entropy 0.07375
G+C content 0.49242
Mean single sequence MFE -15.95
Consensus MFE -13.80
Energy contribution -13.80
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.64
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.14
SVM RNA-class probability 0.561637
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5171442 66 - 22422827
UUGACAUGUCACGGCGCUCCUUUCGGCCAUAGGUCAACUCCUGUUGACCUUUUCGGCUUAUGACUU
.......((((.((....))....((((..((((((((....))))))))....))))..)))).. ( -20.60, z-score =  -3.04, R)
>droSim1.chrX 3989427 66 - 17042790
UUGACAUGUCACUGCGCUCCUUUCGGCCAUAGGUCAACUCCUGUCGACCUUUUCGGCUUAUGACUU
.......((((..(((((......)))...(((((.((....)).))))).....))...)))).. ( -14.70, z-score =  -1.24, R)
>droSec1.super_4 4592653 66 + 6179234
UUGACAUGUCACUGCGCUCCUUUCGGCCAUAGGUCAACUCCUGUCGACCUUUUCGGCUUAUGACUU
.......((((..(((((......)))...(((((.((....)).))))).....))...)))).. ( -14.70, z-score =  -1.24, R)
>droYak2.chrX 18475727 66 + 21770863
UUGACAUGUCACUGCGCUUCUUUCGGCCAUAGGUCAACUCGUGUCGACCUUUUCGGCUUAUAACUA
.(((....))).............((((..(((((.((....)).)))))....))))........ ( -13.80, z-score =  -1.04, R)
>consensus
UUGACAUGUCACUGCGCUCCUUUCGGCCAUAGGUCAACUCCUGUCGACCUUUUCGGCUUAUGACUU
.(((....))).............((((..(((((.((....)).)))))....))))........ (-13.80 = -13.80 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:17:11 2011