Locus 10392

Sequence ID dm3.chr3R
Location 13,552,204 – 13,552,351
Length 147
Max. P 0.997461
window14294 window14295

overview

Window 4

Location 13,552,204 – 13,552,313
Length 109
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 77.44
Shannon entropy 0.40150
G+C content 0.35907
Mean single sequence MFE -31.34
Consensus MFE -14.68
Energy contribution -16.36
Covariance contribution 1.68
Combinations/Pair 1.23
Mean z-score -3.37
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.71
SVM RNA-class probability 0.994518
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13552204 109 - 27905053
GCCAACAAAGUGCAUUUUAAUUUGUUUUAAAAUUGUAUUUUGUGCGUUUAGAAAGCGCAUGGCCGU--UUCUAUCUAUCCAGUCAAAG--------AAAUCUCUCUGAUUUUUGAAGUC
((((((((((((((((((((......)))))).))))))))))(((((.....))))).))))...--..............(((..(--------(((((.....))))))))).... ( -27.20, z-score =  -3.31, R)
>droEre2.scaffold_4770 9667871 102 + 17746568
---------GUGCAUUUUAAUUUGUUUU-AAAUUGUAUUUUGUGUGUUUAGACAGCGCAGUGC-------CUGUGCAUACAGUCAAAGACACAAAGAAAUCUCUCUGAAUUUCAGAGUC
---------(((((.(((((......))-))).)))))(((((((.(((.(((.((((((...-------)))))).....)))))).))))))).......(((((.....))))).. ( -28.80, z-score =  -2.78, R)
>droYak2.chr3R 2129898 112 - 28832112
GCCAACAGAGUGCAUUUUAAUUGGUUUU-AAAUUGUAUUUUGUGCGCUUAGAAAGCUCAUUGUC------UUGUUUAUUGAGUCAAAGACACAAUGAAAUUUCUCUGAAUUUUUAGGUC
((..((((((((((.(((((......))-))).))))))))))))(((((((((..(((..(..------...(((((((.(((...))).)))))))....)..))).))))))))). ( -29.70, z-score =  -2.86, R)
>droSec1.super_12 1513005 119 + 2123299
GCCAACAAAGUGCAUUUUAAUUUGUUUUAAAAUUGCACUUUGUGCGUUUAGAAAGCGCAUUGCUGUGCGUCUAUCUAUCCGGACAAAGAUGCCCAGAAAUCUCUCCGAUUUUUGAAGUC
.((.((((((((((((((((......)))))).))))))))))..(..((((.(((((((....))))).)).))))..))).....(((...((((((((.....))))))))..))) ( -38.10, z-score =  -4.66, R)
>droSim1.chr3R 19577134 119 + 27517382
GCCAACAAAGUGCAUUUUAAUUUGUUUUAAAAUUGCAUUUUGUGCGUUUAGAAAGCGCAUUGCUGUGCGUCUAUCUAUCCGGACAAAGAUGCCCACAAAUCUCUCCGAUUUUUGAAGUC
((..((((((((((((((((......)))))).))))))))))))(..((((.(((((((....))))).)).))))..)(((...((((........)))).)))............. ( -32.90, z-score =  -3.25, R)
>consensus
GCCAACAAAGUGCAUUUUAAUUUGUUUUAAAAUUGUAUUUUGUGCGUUUAGAAAGCGCAUUGCCGU___UCUAUCUAUCCAGUCAAAGACACAAAGAAAUCUCUCUGAUUUUUGAAGUC
....((((((((((((((((......)))))).))))))))))(((((.....))))).............................(((.....((((((.....))))))....))) (-14.68 = -16.36 +   1.68)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,552,236 – 13,552,351
Length 115
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 77.82
Shannon entropy 0.37770
G+C content 0.39569
Mean single sequence MFE -34.08
Consensus MFE -20.08
Energy contribution -20.72
Covariance contribution 0.64
Combinations/Pair 1.26
Mean z-score -3.31
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.11
SVM RNA-class probability 0.997461
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13552236 115 - 27905053
UUGGCUGACCGCAAAAACUC--GUGUGUGUGUGUCUCCAAGCCAACAAAGUGCAUUUUAAUUUGUUUUAAAAUUGUAUUUUGUGCGUUUAGAAAGCGCAUGGCCGUU--UCUAUCUAUC
((((..(((((((...((..--..)).)))).))).))))((((((((((((((((((((......)))))).))))))))))(((((.....))))).))))....--.......... ( -35.10, z-score =  -3.94, R)
>droEre2.scaffold_4770 9667911 92 + 17746568
--GGCUGGCCGCAAAAACUC--UUGUGU---------------UGCUAAGUGCAUUUUAAUUUGUUUU-AAAUUGUAUUUUGUGUGUUUAGACAGCGCAGUGCC-UGUGCAUA------
--((....))(((.......--((((((---------------(((((((..(((..(((((((...)-))))))......)))..))))).))))))))....-..)))...------ ( -24.32, z-score =  -0.74, R)
>droYak2.chr3R 2129938 102 - 28832112
--GGCUGGCCGCAAACACUC--GUGUGU------UUCUAAGCCAACAGAGUGCAUUUUAAUUGGUUUU-AAAUUGUAUUUUGUGCGCUUAGAAAGCUCAUUGUCUUGUUUAUU------
--((....))(((((((...--(((.((------((((((((((.(((((((((.(((((......))-))).))))))))))).)))))).)))).)))))).)))).....------ ( -30.70, z-score =  -2.90, R)
>droSec1.super_12 1513045 119 + 2123299
UUGGCUGACCGCAAAAACUCGAGUGUGUGUGUGUCUCCAAGCCAACAAAGUGCAUUUUAAUUUGUUUUAAAAUUGCACUUUGUGCGUUUAGAAAGCGCAUUGCUGUGCGUCUAUCUAUC
.((((((((((((...((....))...)))).)))....)))))((((((((((((((((......)))))).)))))))))).....((((.(((((((....))))).)).)))).. ( -41.50, z-score =  -4.64, R)
>droSim1.chr3R 19577174 117 + 27517382
UUGGCUGACCGCAAAAACUC--GUGUGUGUGUGUCUCCAAGCCAACAAAGUGCAUUUUAAUUUGUUUUAAAAUUGCAUUUUGUGCGUUUAGAAAGCGCAUUGCUGUGCGUCUAUCUAUC
.((((((((((((...((..--..)).)))).)))....)))))((((((((((((((((......)))))).)))))))))).....((((.(((((((....))))).)).)))).. ( -38.80, z-score =  -4.34, R)
>consensus
UUGGCUGACCGCAAAAACUC__GUGUGUGUGUGUCUCCAAGCCAACAAAGUGCAUUUUAAUUUGUUUUAAAAUUGUAUUUUGUGCGUUUAGAAAGCGCAUUGCCGUGCGUCUAUCUAUC
....((((.(((....((......))..................((((((((((((((((......)))))).))))))))))))).))))...((((((....))))))......... (-20.08 = -20.72 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:23:08 2011