Locus 10960

Sequence ID dm3.chr3R
Location 17,810,530 – 17,810,620
Length 90
Max. P 0.938581
window15063 window15064

overview

Window 3

Location 17,810,530 – 17,810,620
Length 90
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 89.84
Shannon entropy 0.17324
G+C content 0.34989
Mean single sequence MFE -23.84
Consensus MFE -15.88
Energy contribution -16.08
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.96
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.45
SVM RNA-class probability 0.938581
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17810530 90 + 27905053
CUUGCAAGCCAUAAAAAAAGUGAUGUGAAAGUAUCAGGAAGCAAGCUUGUGCUUUUAUUAGAUGAUUUUU--AUGGCCUUUCCAAAACGUGA
.......((((((((((..((...(((((((((.((((.......)))))))))))))...))..)))))--)))))............... ( -22.50, z-score =  -2.07, R)
>droSim1.chr3R 17629037 88 + 27517382
CUUGUGAGCCAUAAAAAAAU--AUGUGAAAGUAUCAGGAAGCAAGCUUGUGCUUUUAUUAGAUGAUUUUU--AUGGCCUUUCCGAAACGUGA
.(((.((((((((((((.((--..(((((((((.((((.......)))))))))))))...))..)))))--)))))...)))))....... ( -22.50, z-score =  -2.76, R)
>droSec1.super_0 18181109 88 + 21120651
CUUGUGAGCCAUAAAAAAAU--AUGUGAAAGUAUCAGGAAGCAAGCUUGUGCUUUUAUUAGAUAAUUUUU--AUGGCCUUUCCGAAACGCGA
.(((((.((((((((((...--..(((((((((.((((.......))))))))))))).......)))))--)))))(.....)...))))) ( -21.50, z-score =  -2.17, R)
>droYak2.chr3R 18643846 89 + 28832112
CUUGUAGGCCAUAAAAAAU---AUGUGAAAGUAUCAGGAAGCAAGCUUGUGCUUUUAUUAGAUGUUUUUUUUAUGGCCUUUCCAAAACGUAG
.(((.(((((((((((((.---(((((((((((.((((.......))))))))))))).....)).)))))))))))))...)))....... ( -26.40, z-score =  -3.86, R)
>droEre2.scaffold_4820 199016 88 - 10470090
UUCGCUGGCCAUAAAAAAAU--AUGUGAAAGUAUCAGGAAGCAAGAUUGUGCUUUUAUUAGAUGUUUUUU--AUGGCCUUUCCGAAACGUAG
((((..((((((((((((..--..(((((((((.(((.........))))))))))))......))))))--))))))....))))...... ( -26.30, z-score =  -3.96, R)
>consensus
CUUGUAAGCCAUAAAAAAAU__AUGUGAAAGUAUCAGGAAGCAAGCUUGUGCUUUUAUUAGAUGAUUUUU__AUGGCCUUUCCGAAACGUGA
.......((((((((((.......(((((((((.((((.......))))))))))))).......)))))..)))))............... (-15.88 = -16.08 +   0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,810,530 – 17,810,620
Length 90
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 89.84
Shannon entropy 0.17324
G+C content 0.34989
Mean single sequence MFE -18.30
Consensus MFE -12.34
Energy contribution -12.30
Covariance contribution -0.04
Combinations/Pair 1.05
Mean z-score -2.80
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.17
SVM RNA-class probability 0.904124
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17810530 90 - 27905053
UCACGUUUUGGAAAGGCCAU--AAAAAUCAUCUAAUAAAAGCACAAGCUUGCUUCCUGAUACUUUCACAUCACUUUUUUUAUGGCUUGCAAG
.......(((...(((((((--(((((...........(((((......)))))..((((........))))...)))))))))))).))). ( -18.00, z-score =  -2.09, R)
>droSim1.chr3R 17629037 88 - 27517382
UCACGUUUCGGAAAGGCCAU--AAAAAUCAUCUAAUAAAAGCACAAGCUUGCUUCCUGAUACUUUCACAU--AUUUUUUUAUGGCUCACAAG
..............((((((--(((((...........(((((......)))))..(((.....)))...--...)))))))))))...... ( -15.80, z-score =  -2.45, R)
>droSec1.super_0 18181109 88 - 21120651
UCGCGUUUCGGAAAGGCCAU--AAAAAUUAUCUAAUAAAAGCACAAGCUUGCUUCCUGAUACUUUCACAU--AUUUUUUUAUGGCUCACAAG
..............((((((--(((((...........(((((......)))))..(((.....)))...--...)))))))))))...... ( -15.80, z-score =  -1.72, R)
>droYak2.chr3R 18643846 89 - 28832112
CUACGUUUUGGAAAGGCCAUAAAAAAAACAUCUAAUAAAAGCACAAGCUUGCUUCCUGAUACUUUCACAU---AUUUUUUAUGGCCUACAAG
.......(((...(((((((((((((............(((((......)))))..(((.....)))...---.))))))))))))).))). ( -21.60, z-score =  -4.14, R)
>droEre2.scaffold_4820 199016 88 + 10470090
CUACGUUUCGGAAAGGCCAU--AAAAAACAUCUAAUAAAAGCACAAUCUUGCUUCCUGAUACUUUCACAU--AUUUUUUUAUGGCCAGCGAA
......((((....((((((--((((((..........(((((......)))))..(((.....)))...--..))))))))))))..)))) ( -20.30, z-score =  -3.60, R)
>consensus
UCACGUUUCGGAAAGGCCAU__AAAAAUCAUCUAAUAAAAGCACAAGCUUGCUUCCUGAUACUUUCACAU__AUUUUUUUAUGGCUCACAAG
..............((((((..(((((...........(((((......)))))..(((.....)))......)))))..))))))...... (-12.34 = -12.30 +  -0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:33:47 2011