Locus 11123

Sequence ID dm3.chr3R
Location 18,781,309 – 18,781,425
Length 116
Max. P 0.997922
window15284 window15285

overview

Window 4

Location 18,781,309 – 18,781,425
Length 116
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 94.04
Shannon entropy 0.11626
G+C content 0.41090
Mean single sequence MFE -28.50
Consensus MFE -23.62
Energy contribution -25.12
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -1.75
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.18
SVM RNA-class probability 0.581800
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18781309 116 + 27905053
AUUUGUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUUUUAGCCGGGGCCAAAAGAUGUCGGCGAUUGAUUCAAUUUGUUGCCA-CUCUGUUUACAAAGCGUUACAAAAU
...((((....))))..(((.....)))(..((((((((.((.((((.((....)).)))))).))))))))..)......(((((.((..-((.((....)).)).)).))))).. ( -30.70, z-score =  -2.29, R)
>droSim1.chr3R 18594101 116 + 27517382
AUUUCUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUUUUAGCCGGGGCCAAAAGAUGUCGGCGAUUGAUUCAAUUUGUUGCCA-CUCUGUUUACAAAGCGUUACAAAAU
.........((((....(((.....)))(..((((((((.((.((((.((....)).)))))).))))))))..)..))))(((((.((..-((.((....)).)).)).))))).. ( -28.60, z-score =  -1.98, R)
>droSec1.super_0 19145423 116 + 21120651
AUUUGUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUUUUAGCCGGGGCCAAAAGAUGUCGGCGAUUGAUUCAAUUUGUUGCCA-CUCUGUUUACAAAGCGUUACAAAAU
...((((....))))..(((.....)))(..((((((((.((.((((.((....)).)))))).))))))))..)......(((((.((..-((.((....)).)).)).))))).. ( -30.70, z-score =  -2.29, R)
>droYak2.chr3R 19639319 116 + 28832112
AUUUGUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUUUUAGCCGGGGCCAAAAGAUGUCGGCGAUUGAUUCAAUUUGUUGCCA-CUCUGUUUACAAAGCGUUACAAAAU
...((((....))))..(((.....)))(..((((((((.((.((((.((....)).)))))).))))))))..)......(((((.((..-((.((....)).)).)).))))).. ( -30.70, z-score =  -2.29, R)
>droEre2.scaffold_4820 1182165 115 - 10470090
AUUUGUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUUUUAGCCGGG-CCAAAAGACGUCGGCGAUUGAUUCAAUUUGUUGCCA-CUCUGUUUACAAAGCGUUACAAAAU
...((((....))))..(((.....)))(..((((((((.((.((((.((...)-).)))))).))))))))..)......(((((.((..-((.((....)).)).)).))))).. ( -27.70, z-score =  -1.67, R)
>droAna3.scaffold_13340 11157355 112 - 23697760
AUUUGUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUUUUUAGCAAGAGCAA--GAUGUCGGCGCUUGAUUCAAUUUGUUCCAAACUCUGUUUGCAAAGUGUUACAA---
...((((....))))..(((.....))).((.(((((((.....((((.((....))))--)).)))))))...))......((((.....(((.((....)).)))...))))--- ( -22.60, z-score =   0.03, R)
>consensus
AUUUGUCUUUUGACAUUUGCUACUUGCACUCUCGCCGACUUCAUUUUAGCCGGGGCCAAAAGAUGUCGGCGAUUGAUUCAAUUUGUUGCCA_CUCUGUUUACAAAGCGUUACAAAAU
...((((....))))..(((.....)))(..((((((((.((.((((.((....)).)))))).))))))))..)......(((((.((...((.((....)).)).)).))))).. (-23.62 = -25.12 +   1.50)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,781,309 – 18,781,425
Length 116
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 94.04
Shannon entropy 0.11626
G+C content 0.41090
Mean single sequence MFE -38.17
Consensus MFE -30.72
Energy contribution -32.22
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -4.21
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.21
SVM RNA-class probability 0.997922
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18781309 116 - 27905053
AUUUUGUAACGCUUUGUAAACAGAG-UGGCAACAAAUUGAAUCAAUCGCCGACAUCUUUUGGCCCCGGCUAAAAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGACAAAU
..(((((..(((((((....)))))-))...))))).........((((((((.(((((((((....))))))).)).))))))))...(((.....)))..((((....))))... ( -41.10, z-score =  -5.09, R)
>droSim1.chr3R 18594101 116 - 27517382
AUUUUGUAACGCUUUGUAAACAGAG-UGGCAACAAAUUGAAUCAAUCGCCGACAUCUUUUGGCCCCGGCUAAAAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGAGAAAU
..(((((..(((((((....)))))-))...)))))((((.....((((((((.(((((((((....))))))).)).))))))))...(((.....)))....))))......... ( -39.80, z-score =  -4.69, R)
>droSec1.super_0 19145423 116 - 21120651
AUUUUGUAACGCUUUGUAAACAGAG-UGGCAACAAAUUGAAUCAAUCGCCGACAUCUUUUGGCCCCGGCUAAAAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGACAAAU
..(((((..(((((((....)))))-))...))))).........((((((((.(((((((((....))))))).)).))))))))...(((.....)))..((((....))))... ( -41.10, z-score =  -5.09, R)
>droYak2.chr3R 19639319 116 - 28832112
AUUUUGUAACGCUUUGUAAACAGAG-UGGCAACAAAUUGAAUCAAUCGCCGACAUCUUUUGGCCCCGGCUAAAAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGACAAAU
..(((((..(((((((....)))))-))...))))).........((((((((.(((((((((....))))))).)).))))))))...(((.....)))..((((....))))... ( -41.10, z-score =  -5.09, R)
>droEre2.scaffold_4820 1182165 115 + 10470090
AUUUUGUAACGCUUUGUAAACAGAG-UGGCAACAAAUUGAAUCAAUCGCCGACGUCUUUUGG-CCCGGCUAAAAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGACAAAU
..(((((..(((((((....)))))-))...))))).........((((((((.((((((((-(...))))))).)).))))))))...(((.....)))..((((....))))... ( -38.10, z-score =  -3.94, R)
>droAna3.scaffold_13340 11157355 112 + 23697760
---UUGUAACACUUUGCAAACAGAGUUUGGAACAAAUUGAAUCAAGCGCCGACAUC--UUGCUCUUGCUAAAAAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGACAAAU
---((((.((((((((....))))))..........(((..((...(((((((.((--..((....)).......)).))))))).))...))))).)))).((((....))))... ( -27.80, z-score =  -1.34, R)
>consensus
AUUUUGUAACGCUUUGUAAACAGAG_UGGCAACAAAUUGAAUCAAUCGCCGACAUCUUUUGGCCCCGGCUAAAAUGAAGUCGGCGAGAGUGCAAGUAGCAAAUGUCAAAAGACAAAU
..(((((.((.(((((....)))))...........(((......((((((((.(((((((((....))))))).)).)))))))).....))))).)))))((((....))))... (-30.72 = -32.22 +   1.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:36:50 2011