Locus 12000

Sequence ID dm3.chr3R
Location 25,013,629 – 25,013,726
Length 97
Max. P 0.998213
window16491 window16492

overview

Window 1

Location 25,013,629 – 25,013,726
Length 97
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 93.24
Shannon entropy 0.11738
G+C content 0.37445
Mean single sequence MFE -22.32
Consensus MFE -17.34
Energy contribution -17.54
Covariance contribution 0.20
Combinations/Pair 1.08
Mean z-score -2.14
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.43
SVM RNA-class probability 0.691561
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25013629 97 + 27905053
AUUAAAGCAACGUCAGAUAUGAAAAUCUGAUGCUGAGGGGAAAAAU-GCUGAGAGCAAUGAAAUUUACUAAUUGGAUUGCCCUCAACUCGUGCAACUC
......(((.((((((((......)))))))).((((((......(-((.....)))....((((((.....)))))).)))))).....)))..... ( -24.80, z-score =  -2.48, R)
>droEre2.scaffold_4820 7453429 95 - 10470090
AUUAAAGCAACGUCAGAUAUGAAAAUACGACGCUGAAGGUAAAAAU-GCUGAGAGCAAUGAAAUUUGCUAAUUGGAUUGCCCUCAACUCUUGCAAA--
......((((((((.(.(((....)))))))).(((.(((((....-.(..(.(((((......)))))..)..).))))).)))....))))...-- ( -20.80, z-score =  -1.72, R)
>droYak2.chr3R 7346617 96 - 28832112
AUUAAAGCAACAUCAGAUAUGAAAAUAUGAUGCUGAAGGGAAAAAUUGCUGAGAGCAAUGAAAUUUGCUAAUUGGAUUGCCCUCAACUCUUGCAAG--
......(((((((((..(((....)))))))).(((.(((...((((......(((((......))))).....)))).))))))....))))...-- ( -21.00, z-score =  -1.28, R)
>droSec1.super_4 3876696 95 + 6179234
AUUAAAGCCACGUCAGAUAUGAAAAUAUGACGCUGAGGUGAAAAAU-GCUGAGAGCAAUGAAAUUUACUAAUUGGAUUGCCCUCAACUCUUGCAAC--
......(((((.((((((((....))))....)))).)))......-..((((.(((((..((((....))))..))))).))))......))...-- ( -22.70, z-score =  -2.80, R)
>droSim1.chr3R 24684572 95 + 27517382
AUUAAAGCAACGUCAGAUAUGAAAAUAUGACGCUGAGGGGAAAAAU-GCUGAGAGCAAUGAAAUUUACUAAUUGGAUUGCCCUCAACUCUUGCAAC--
......(((((((((..(((....)))))))).((((((......(-((.....)))....((((((.....)))))).))))))....))))...-- ( -22.30, z-score =  -2.43, R)
>consensus
AUUAAAGCAACGUCAGAUAUGAAAAUAUGACGCUGAGGGGAAAAAU_GCUGAGAGCAAUGAAAUUUACUAAUUGGAUUGCCCUCAACUCUUGCAAC__
......(((((((((.((......)).))))).................((((.(((((..((((....))))..))))).))))....))))..... (-17.34 = -17.54 +   0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 25,013,629 – 25,013,726
Length 97
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 93.24
Shannon entropy 0.11738
G+C content 0.37445
Mean single sequence MFE -26.82
Consensus MFE -24.06
Energy contribution -24.06
Covariance contribution 0.00
Combinations/Pair 1.08
Mean z-score -3.87
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.29
SVM RNA-class probability 0.998213
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25013629 97 - 27905053
GAGUUGCACGAGUUGAGGGCAAUCCAAUUAGUAAAUUUCAUUGCUCUCAGC-AUUUUUCCCCUCAGCAUCAGAUUUUCAUAUCUGACGUUGCUUUAAU
.....(((((.((((((((((((..((((....))))..))))))))))))-................((((((......)))))))).)))...... ( -28.00, z-score =  -3.94, R)
>droEre2.scaffold_4820 7453429 95 + 10470090
--UUUGCAAGAGUUGAGGGCAAUCCAAUUAGCAAAUUUCAUUGCUCUCAGC-AUUUUUACCUUCAGCGUCGUAUUUUCAUAUCUGACGUUGCUUUAAU
--.........((((((((((((..((((....))))..))))))))))))-...........((((((((.((......)).))))))))....... ( -26.60, z-score =  -3.91, R)
>droYak2.chr3R 7346617 96 + 28832112
--CUUGCAAGAGUUGAGGGCAAUCCAAUUAGCAAAUUUCAUUGCUCUCAGCAAUUUUUCCCUUCAGCAUCAUAUUUUCAUAUCUGAUGUUGCUUUAAU
--.........((((((((((((..((((....))))..))))))))))))............((((((((.((......)).))))))))....... ( -25.90, z-score =  -3.21, R)
>droSec1.super_4 3876696 95 - 6179234
--GUUGCAAGAGUUGAGGGCAAUCCAAUUAGUAAAUUUCAUUGCUCUCAGC-AUUUUUCACCUCAGCGUCAUAUUUUCAUAUCUGACGUGGCUUUAAU
--...((....((((((((((((..((((....))))..))))))))))))-.............((((((.((......)).)))))).))...... ( -26.30, z-score =  -3.71, R)
>droSim1.chr3R 24684572 95 - 27517382
--GUUGCAAGAGUUGAGGGCAAUCCAAUUAGUAAAUUUCAUUGCUCUCAGC-AUUUUUCCCCUCAGCGUCAUAUUUUCAUAUCUGACGUUGCUUUAAU
--.........((((((((((((..((((....))))..))))))))))))-...........((((((((.((......)).))))))))....... ( -27.30, z-score =  -4.60, R)
>consensus
__GUUGCAAGAGUUGAGGGCAAUCCAAUUAGUAAAUUUCAUUGCUCUCAGC_AUUUUUCCCCUCAGCGUCAUAUUUUCAUAUCUGACGUUGCUUUAAU
...........((((((((((((..((((....))))..))))))))))))............((((((((.((......)).))))))))....... (-24.06 = -24.06 +   0.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:53:44 2011