Locus 5307

Sequence ID dm3.chr2R
Location 19,369,341 – 19,369,453
Length 112
Max. P 0.959346
window7271 window7272 window7273

overview

Window 1

Location 19,369,341 – 19,369,445
Length 104
Sequences 3
Columns 104
Reading direction reverse
Mean pairwise identity 91.00
Shannon entropy 0.12362
G+C content 0.36137
Mean single sequence MFE -24.48
Consensus MFE -22.31
Energy contribution -23.20
Covariance contribution 0.89
Combinations/Pair 1.05
Mean z-score -1.76
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.02
SVM RNA-class probability 0.875934
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19369341 104 - 21146708
AAUAAAAUUAUGUCUCAGGCACUUAAGUGUCUGAGCCGAUUUUUCUUGGAAAUUGUCUGCGCACAAAUUGUAACAAAAUUUAUUAACCAUUUCUGCAAAAAGCC
.............(((((((((....))))))))).(((((((.....))))))).....(((.((((.((..............)).)))).)))........ ( -19.84, z-score =  -1.17, R)
>droSim1.chr2R 17950737 103 - 19596830
AAUAAAAUUAUGUCUCAGGCACUUAAGUGUCUGAGUUGACUUUUCUUGGAACUUCUUUGCGCAGAAAUUGUAGCAAAG-UUGUUAACCAUUUCUGCAAAAAGCC
.............(((((((((....)))))))))...................((((..((((((((..(((((...-.)))))...))))))))..)))).. ( -28.40, z-score =  -2.77, R)
>droSec1.super_9 2658078 103 - 3197100
AAUAAAAUUAUGUCUCAGGCACUGAAGUGUCUGAGCUGUCUUUUCUUGGAACUUCUCUGCGCAGAAAUUGUAGCAAAG-UUGAUAACCAUUUCUGCAAAAAGCC
...........(.(((((((((....))))))))))..(((......)))..........((((((((.((..((...-.))...)).))))))))........ ( -25.20, z-score =  -1.34, R)
>consensus
AAUAAAAUUAUGUCUCAGGCACUUAAGUGUCUGAGCUGACUUUUCUUGGAACUUCUCUGCGCAGAAAUUGUAGCAAAG_UUGUUAACCAUUUCUGCAAAAAGCC
.............(((((((((....))))))))).........................((((((((..(((((.....)))))...))))))))........ (-22.31 = -23.20 +   0.89)

alignment

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secondary structure

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dotplot

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Window 2

Location 19,369,349 – 19,369,453
Length 104
Sequences 3
Columns 104
Reading direction forward
Mean pairwise identity 90.35
Shannon entropy 0.13245
G+C content 0.37752
Mean single sequence MFE -24.27
Consensus MFE -21.61
Energy contribution -22.17
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -1.54
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.50
SVM RNA-class probability 0.721823
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19369349 104 + 21146708
GCAGAAAUGGUUAAUAAAUUUUGUUACAAUUUGUGCGCAGACAAUUUCCAAGAAAAAUCGGCUCAGACACUUAAGUGCCUGAGACAUAAUUUUAUUGCGACAAA
(((.((((...(((((.....)))))..)))).)))((((....((((...))))....(.(((((.(((....))).))))).).........))))...... ( -20.70, z-score =  -0.92, R)
>droSim1.chr2R 17950745 103 + 19596830
GCAGAAAUGGUUAACAA-CUUUGCUACAAUUUCUGCGCAAAGAAGUUCCAAGAAAAGUCAACUCAGACACUUAAGUGCCUGAGACAUAAUUUUAUUGCGGCAAA
((((((((.((...((.-...))..)).))))))))((((.((((((....((....))..(((((.(((....))).)))))....)))))).))))...... ( -26.50, z-score =  -2.40, R)
>droSec1.super_9 2658086 103 + 3197100
GCAGAAAUGGUUAUCAA-CUUUGCUACAAUUUCUGCGCAGAGAAGUUCCAAGAAAAGACAGCUCAGACACUUCAGUGCCUGAGACAUAAUUUUAUUGCGGCAAA
((((((((.((...((.-...))..)).))))))))........((..(((.((((.....(((((.(((....))).)))))......)))).)))..))... ( -25.60, z-score =  -1.31, R)
>consensus
GCAGAAAUGGUUAACAA_CUUUGCUACAAUUUCUGCGCAGAGAAGUUCCAAGAAAAGUCAGCUCAGACACUUAAGUGCCUGAGACAUAAUUUUAUUGCGGCAAA
((((((((.((...((.....))..)).))))))))((((.((((((....(......)..(((((.(((....))).)))))....)))))).))))...... (-21.61 = -22.17 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 19,369,349 – 19,369,453
Length 104
Sequences 3
Columns 104
Reading direction reverse
Mean pairwise identity 90.35
Shannon entropy 0.13245
G+C content 0.37752
Mean single sequence MFE -27.03
Consensus MFE -24.02
Energy contribution -23.13
Covariance contribution -0.89
Combinations/Pair 1.09
Mean z-score -2.27
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.67
SVM RNA-class probability 0.959346
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19369349 104 - 21146708
UUUGUCGCAAUAAAAUUAUGUCUCAGGCACUUAAGUGUCUGAGCCGAUUUUUCUUGGAAAUUGUCUGCGCACAAAUUGUAACAAAAUUUAUUAACCAUUUCUGC
(((((((((((((........(((((((((....)))))))))((((......))))...)))).)))).)))))............................. ( -24.90, z-score =  -2.64, R)
>droSim1.chr2R 17950745 103 - 19596830
UUUGCCGCAAUAAAAUUAUGUCUCAGGCACUUAAGUGUCUGAGUUGACUUUUCUUGGAACUUCUUUGCGCAGAAAUUGUAGCAAAG-UUGUUAACCAUUUCUGC
......((((...........(((((((((....)))))))))..((..(((....)))..)).))))((((((((..(((((...-.)))))...)))))))) ( -29.40, z-score =  -2.72, R)
>droSec1.super_9 2658086 103 - 3197100
UUUGCCGCAAUAAAAUUAUGUCUCAGGCACUGAAGUGUCUGAGCUGUCUUUUCUUGGAACUUCUCUGCGCAGAAAUUGUAGCAAAG-UUGAUAACCAUUUCUGC
......(((..........(.(((((((((....))))))))))..(((......))).......)))((((((((.((..((...-.))...)).)))))))) ( -26.80, z-score =  -1.45, R)
>consensus
UUUGCCGCAAUAAAAUUAUGUCUCAGGCACUUAAGUGUCUGAGCUGACUUUUCUUGGAACUUCUCUGCGCAGAAAUUGUAGCAAAG_UUGUUAACCAUUUCUGC
(((((..((((..........(((((((((....))))))))).................((((......))))))))..)))))................... (-24.02 = -23.13 +  -0.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:45:42 2011