Locus 7059

Sequence ID dm3.chr3L
Location 11,857,600 – 11,857,705
Length 105
Max. P 0.999645
window9723 window9724

overview

Window 3

Location 11,857,600 – 11,857,705
Length 105
Sequences 4
Columns 131
Reading direction forward
Mean pairwise identity 77.54
Shannon entropy 0.34832
G+C content 0.46176
Mean single sequence MFE -38.08
Consensus MFE -24.01
Energy contribution -26.82
Covariance contribution 2.81
Combinations/Pair 1.03
Mean z-score -2.33
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.55
SVM RNA-class probability 0.949689
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11857600 105 + 24543557
GGUCAACAGCAACGGCACAAUGAUGAGCCACCAUGGCGGAUGAGUAAUGUUUAAUACU--------------------------CACUCAUCCGCAGUGAGGACCCCAGAAUGGAUGUGUGGCUUUGUUAU
....((((((....))........((((((((((.((((((((((...((.....)).--------------------------.))))))))))..........((.....))))).))))))))))).. ( -34.70, z-score =  -1.77, R)
>droSim1.chr3L 11227231 117 + 22553184
GGUCAACAGCAACGGUGCAAUG----GCCACCAUGGCGGAUGAGUAAUGUUUAAUACUUUUUCA--------UACUUGAAAUAUCACUCAUCCGCAGUGAGGACCC-AGAAAGGAUGUGUGGCUUUGUUA-
....(((((((....)))...(----((((((((.((((((((((.((((((............--------......)))))).)))))))))).........((-.....))))).)))))).)))).- ( -36.07, z-score =  -1.79, R)
>droSec1.super_0 4047782 117 + 21120651
GGUCAACAGCAACGGUGCAAUG----GCCACCAUGGCGGAUGAGUAAUGUUUAAUACUUUUUCA--------UACU-GAAAUAUCACUCAUCCGCAGUGAGGACCCCAGAAAGAGUAUGUGGCUUUGUUA-
....(((((((....)))...(----((((((((.((((((((((.((((((............--------....-.)))))).)))))))))).))).((...))...........)))))).)))).- ( -34.63, z-score =  -1.60, R)
>droYak2.chr3L 11900738 127 + 24197627
GCCGAACUGCAACGCUGCAAUG----GCCACCACUGCGGAUGAGUAAUGUUUUGUGCUUUUUCAAAAGCCGAUACUUCAAAAAUCACUCAUCCGCAGUGAUGACCGCAGCAUGGUCGUGUGACUUUGUUAU
((((...((((....)))).))----))(((((((((((((((((.((((.(((.(((((....)))))))).)).......)).))))))))))))))(((((((.....)))))))))).......... ( -46.91, z-score =  -4.18, R)
>consensus
GGUCAACAGCAACGGUGCAAUG____GCCACCAUGGCGGAUGAGUAAUGUUUAAUACUUUUUCA________UACU_GAAAUAUCACUCAUCCGCAGUGAGGACCCCAGAAAGGAUGUGUGGCUUUGUUA_
....(((((((....)))........((((((((.((((((((((.((((((..........................)))))).)))))))))).)))....((.......))....)))))..)))).. (-24.01 = -26.82 +   2.81)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,857,600 – 11,857,705
Length 105
Sequences 4
Columns 131
Reading direction reverse
Mean pairwise identity 77.54
Shannon entropy 0.34832
G+C content 0.46176
Mean single sequence MFE -43.41
Consensus MFE -27.67
Energy contribution -27.86
Covariance contribution 0.19
Combinations/Pair 1.19
Mean z-score -4.40
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.13
SVM RNA-class probability 0.999645
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11857600 105 - 24543557
AUAACAAAGCCACACAUCCAUUCUGGGGUCCUCACUGCGGAUGAGUG--------------------------AGUAUUAAACAUUACUCAUCCGCCAUGGUGGCUCAUCAUUGUGCCGUUGCUGUUGACC
.(((((.(((..((((.........(((((.(((..(((((((((((--------------------------(((.....)).))))))))))))..))).))))).....))))..)))..)))))... ( -36.54, z-score =  -2.89, R)
>droSim1.chr3L 11227231 117 - 22553184
-UAACAAAGCCACACAUCCUUUCU-GGGUCCUCACUGCGGAUGAGUGAUAUUUCAAGUA--------UGAAAAAGUAUUAAACAUUACUCAUCCGCCAUGGUGGC----CAUUGCACCGUUGCUGUUGACC
-(((((..(((((..((((.....-))))...((..(((((((((((((.(((((....--------)))))..((.....)))))))))))))))..)))))))----....(((....))))))))... ( -38.20, z-score =  -3.70, R)
>droSec1.super_0 4047782 117 - 21120651
-UAACAAAGCCACAUACUCUUUCUGGGGUCCUCACUGCGGAUGAGUGAUAUUUC-AGUA--------UGAAAAAGUAUUAAACAUUACUCAUCCGCCAUGGUGGC----CAUUGCACCGUUGCUGUUGACC
-(((((..(((((..(((((....)))))...((..(((((((((((((.(((.-((((--------(......)))))))).)))))))))))))..)))))))----....(((....))))))))... ( -39.80, z-score =  -3.84, R)
>droYak2.chr3L 11900738 127 - 24197627
AUAACAAAGUCACACGACCAUGCUGCGGUCAUCACUGCGGAUGAGUGAUUUUUGAAGUAUCGGCUUUUGAAAAAGCACAAAACAUUACUCAUCCGCAGUGGUGGC----CAUUGCAGCGUUGCAGUUCGGC
........(((..((..(.(((((((((((((((((((((((((((((((((((........(((((....))))).))))).))))))))))))))))))))))----)...))))))).)..))..))) ( -59.10, z-score =  -7.18, R)
>consensus
_UAACAAAGCCACACAUCCAUUCUGGGGUCCUCACUGCGGAUGAGUGAUAUUUC_AGUA________UGAAAAAGUAUUAAACAUUACUCAUCCGCCAUGGUGGC____CAUUGCACCGUUGCUGUUGACC
.((((...(((((..((((......))))...((..(((((((((((((..................................)))))))))))))..)))))))........(((....))).))))... (-27.67 = -27.86 +   0.19)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:19:45 2011