Locus 11132

Sequence ID dm3.chr3R
Location 18,848,228 – 18,848,287
Length 59
Max. P 0.953134
window15300 window15301

overview

Window 0

Location 18,848,228 – 18,848,287
Length 59
Sequences 6
Columns 66
Reading direction forward
Mean pairwise identity 76.19
Shannon entropy 0.43090
G+C content 0.48603
Mean single sequence MFE -17.60
Consensus MFE -12.70
Energy contribution -14.03
Covariance contribution 1.34
Combinations/Pair 1.25
Mean z-score -1.67
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.59
SVM RNA-class probability 0.953134
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18848228 59 + 27905053
GAGCGUUGCGUUAGUACUG------UAGUAUUUGCCUCAGAUGCGAGUUCGCAUCA-AACCGCAGC
....(((((((.(((((..------..))))).))....((((((....)))))).-....))))) ( -19.60, z-score =  -2.28, R)
>droSim1.chr3R 18662300 59 + 27517382
GAGCGUUGCGUUAGUACUG------UAGUAUUUGCCUCAGAUGCGAGUUCGCAUCA-AACCGCAGC
....(((((((.(((((..------..))))).))....((((((....)))))).-....))))) ( -19.60, z-score =  -2.28, R)
>droSec1.super_0 19211881 65 + 21120651
GAGCGUUGCGUUAGUACUAGUGCGUUAGUAUUUGCCUCAGAUGCGAGUUCGCAUCA-AACCGCAGC
....(((((((.((((((((....)))))))).))....((((((....)))))).-....))))) ( -22.30, z-score =  -2.36, R)
>droYak2.chr3R 19710255 59 + 28832112
GAGCGUUGCGUUAGUACUG------UAGUAUUUGCCUCAGAUGCGAAUUCGCAUCA-AACCGCAGC
....(((((((.(((((..------..))))).))....((((((....)))))).-....))))) ( -19.60, z-score =  -2.59, R)
>droEre2.scaffold_4820 1248724 60 - 10470090
GAGCGUUGCGUUAGUACUG------UAGUAUUUGCCUCACAUGCGAAUUCGCAUCGCAACCGCAGA
..(((((((((.(((((..------..))))).)).....(((((....))))).)))).)))... ( -18.80, z-score =  -1.69, R)
>droMoj3.scaffold_6540 1411153 50 - 34148556
---------GAGAAU-CUG-----UUAUUAUUUGAUCUAUUUGUGUGGCUGCUAUA-GACGCCAGC
---------..((((-..(-----(((.....))))..))))...((((..(....-)..)))).. (  -5.70, z-score =   1.18, R)
>consensus
GAGCGUUGCGUUAGUACUG______UAGUAUUUGCCUCAGAUGCGAGUUCGCAUCA_AACCGCAGC
....(((((((.(((((((......))))))).))....((((((....))))))......))))) (-12.70 = -14.03 +   1.34)

alignment

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secondary structure

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dotplot

Postscript

Window 1

Location 18,848,228 – 18,848,287
Length 59
Sequences 6
Columns 66
Reading direction reverse
Mean pairwise identity 76.19
Shannon entropy 0.43090
G+C content 0.48603
Mean single sequence MFE -14.85
Consensus MFE -8.88
Energy contribution -10.77
Covariance contribution 1.89
Combinations/Pair 1.06
Mean z-score -1.32
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.22
SVM RNA-class probability 0.597295
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18848228 59 - 27905053
GCUGCGGUU-UGAUGCGAACUCGCAUCUGAGGCAAAUACUA------CAGUACUAACGCAACGCUC
(((((((((-(((((((....))))))..))))...(((..------..)))....))))..)).. ( -16.20, z-score =  -1.63, R)
>droSim1.chr3R 18662300 59 - 27517382
GCUGCGGUU-UGAUGCGAACUCGCAUCUGAGGCAAAUACUA------CAGUACUAACGCAACGCUC
(((((((((-(((((((....))))))..))))...(((..------..)))....))))..)).. ( -16.20, z-score =  -1.63, R)
>droSec1.super_0 19211881 65 - 21120651
GCUGCGGUU-UGAUGCGAACUCGCAUCUGAGGCAAAUACUAACGCACUAGUACUAACGCAACGCUC
(((((((((-(((((((....))))))..))))...(((((......)))))....))))..)).. ( -18.60, z-score =  -1.97, R)
>droYak2.chr3R 19710255 59 - 28832112
GCUGCGGUU-UGAUGCGAAUUCGCAUCUGAGGCAAAUACUA------CAGUACUAACGCAACGCUC
(((((((((-(((((((....))))))..))))...(((..------..)))....))))..)).. ( -16.20, z-score =  -1.59, R)
>droEre2.scaffold_4820 1248724 60 + 10470090
UCUGCGGUUGCGAUGCGAAUUCGCAUGUGAGGCAAAUACUA------CAGUACUAACGCAACGCUC
...(((.((((((((((....)))))((.((.......)))------)........)))))))).. ( -17.30, z-score =  -1.23, R)
>droMoj3.scaffold_6540 1411153 50 + 34148556
GCUGGCGUC-UAUAGCAGCCACACAAAUAGAUCAAAUAAUAA-----CAG-AUUCUC---------
..((((...-.......)))).....................-----...-......--------- (  -4.60, z-score =   0.11, R)
>consensus
GCUGCGGUU_UGAUGCGAACUCGCAUCUGAGGCAAAUACUA______CAGUACUAACGCAACGCUC
..(((((((..((((((....))))))...)))...((((........))))....))))...... ( -8.88 = -10.77 +   1.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:37:03 2011