Locus 4282

Sequence ID dm3.chr2R
Location 11,928,584 – 11,928,741
Length 157
Max. P 0.944867
window5867 window5868

overview

Window 7

Location 11,928,584 – 11,928,685
Length 101
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 82.92
Shannon entropy 0.29109
G+C content 0.55753
Mean single sequence MFE -28.42
Consensus MFE -22.70
Energy contribution -22.22
Covariance contribution -0.48
Combinations/Pair 1.35
Mean z-score -1.32
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.33
SVM RNA-class probability 0.645332
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11928584 101 + 21146708
GAGUCCGGAUCCGAGGGCGACAGCUACGAUUACGGCGAGCUGGAGGACAGCAACUCGGAGACACAGGAACAGAAGCAGAAAUCGCUGAAUCUUCAGCAGCA
...((((..(((((((((....))).............((((.....))))..))))))..)...)))......((.(....)(((((....))))).)). ( -30.60, z-score =  -1.36, R)
>droSim1.chr2R 10667209 93 + 19596830
GAGUCCGGAUCCGAGGGCGACAGCUACGAUUACGGCGAGCUGGAGGAUAGCAACUCGGAGACACAGGAACAGAAGCAGCAAUCGCUGAAUCUU--------
...((((..((((((.((..(((((.((....))...))))).......))..))))))..)...)))..(((..((((....))))..))).-------- ( -29.30, z-score =  -1.82, R)
>droSec1.super_1 9427546 95 + 14215200
GAGUCCGGAUCCGAGGGCGACAGCUACGAUUACGGCGAGCUGGAGGACAGCAACUCGGAGACACAGGAACAGAAGCAGCAAUUGCUGAAUCUUCA------
...((((..(((((((((....))).............((((.....))))..))))))..)...)))...((((((((....))))...)))).------ ( -30.80, z-score =  -2.13, R)
>droYak2.chr2R 4085181 95 - 21139217
GAGUCCGGAUCCGAGAGCGACAGCUACGAUUACGGCGAGCUGGAGGACAGCAAUUCGGAGACACAGGAGCAGAAGCAGCAAUCGCUGAAUCUUCA------
...((((..(((((((((....))).............((((.....))))..))))))..)...)))(.(((..((((....))))..))).).------ ( -28.30, z-score =  -0.93, R)
>droAna3.scaffold_13266 4417079 93 - 19884421
GACUCUGGCCCGGAGAGCGAGAGCUACGAUUACGAGGAAGCAGAUGACAGAAAUUUCGAGACACAGGAGCAACUGCAGCAAGCGCAGCAGUUG--------
...((((.((((..((((....))).).....)).))...)))).........((((........))))(((((((.((....)).)))))))-------- ( -23.10, z-score =  -0.33, R)
>consensus
GAGUCCGGAUCCGAGGGCGACAGCUACGAUUACGGCGAGCUGGAGGACAGCAACUCGGAGACACAGGAACAGAAGCAGCAAUCGCUGAAUCUUCA______
...(((...(((((((((....))).............((((.....))))..))))))......)))..(((..((((....))))..)))......... (-22.70 = -22.22 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,928,651 – 11,928,741
Length 90
Sequences 4
Columns 90
Reading direction reverse
Mean pairwise identity 92.53
Shannon entropy 0.11718
G+C content 0.42478
Mean single sequence MFE -22.32
Consensus MFE -19.98
Energy contribution -20.60
Covariance contribution 0.62
Combinations/Pair 1.07
Mean z-score -2.21
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.50
SVM RNA-class probability 0.944867
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11928651 90 - 21146708
UGCUCUCCGCUGAUAUGUAGUAAUCGUUUGAAUUGACUUUUUGUUGCUGUUGCUGCUGCUGCUGAAGAUUCAGCGAUUUCUGCUUCUGUU
........((.((...((((.(((((((.((((...((((..((.((.((....)).)).)).))))))))))))))).)))).)).)). ( -20.20, z-score =  -0.93, R)
>droSim1.chr2R 10667276 81 - 19596830
UGCUCUCCGCUGAUAUGUAGUAAUCGUUUGAAUUGACUUUCUGUUGCUGU---------UGCUGAAGAUUCAGCGAUUGCUGCUUCUGUU
........((.((...((((((((((((.((((((((.....)))((...---------.))....))))))))))))))))).)).)). ( -22.60, z-score =  -2.85, R)
>droSec1.super_1 9427613 84 - 14215200
UGCUCUCCGCUGAUAUGUAGUAAUCGUUUGAAUUGACUUUCUGUUGCUGU------UGCUGCUGAAGAUUCAGCAAUUGCUGCUUCUGUU
.((.....))......((((((((.((..(((......)))....)).))------))))))...(((..((((....))))..)))... ( -19.10, z-score =  -1.09, R)
>droYak2.chr2R 4085248 84 + 21139217
UGCUCUCCGCUGAUAUGUAGUAAUCGUUUGAAUUGACUUUCUGUUGCUGU------UGCUGCUGAAGAUUCAGCGAUUGCUGCUUCUGCU
........((.((...((((((((((((.(((((....(((.((.((...------.)).)).)))))))))))))))))))).)).)). ( -27.40, z-score =  -3.97, R)
>consensus
UGCUCUCCGCUGAUAUGUAGUAAUCGUUUGAAUUGACUUUCUGUUGCUGU______UGCUGCUGAAGAUUCAGCGAUUGCUGCUUCUGUU
........((.((...((((((((((((.(((((....(((.((.((..........)).)).)))))))))))))))))))).)).)). (-19.98 = -20.60 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:26:10 2011