Locus 9937

Sequence ID dm3.chr3R
Location 9,946,215 – 9,946,310
Length 95
Max. P 0.977502
window13656 window13657

overview

Window 6

Location 9,946,215 – 9,946,310
Length 95
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 75.18
Shannon entropy 0.42214
G+C content 0.30522
Mean single sequence MFE -22.37
Consensus MFE -13.12
Energy contribution -14.32
Covariance contribution 1.20
Combinations/Pair 1.00
Mean z-score -2.33
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.97
SVM RNA-class probability 0.977502
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9946215 95 + 27905053
AUAUACAAGAUAACAUAUGAAUUUCAUGGAGUUAUACACAGUACAAACACGAAAACCUAGUAUAACUUUU--------------------UUUAGCUGAGUAUAACCCUAUGAUA
.......................((((((.(((((((.((((............................--------------------....)))).))))))).)))))).. ( -16.75, z-score =  -2.30, R)
>droEre2.scaffold_4770 9495033 115 + 17746568
AUAUAGAAGAUAACAUGUGUAUUUCUUGGGGUUAUACGCAGUACAAUUACGAAAACCUAAUAUGAAUUUAAUAAAAAACUACUUUUCAUGUUUAUCUGAGUAUAACCCUCUGGUA
...(((((((..((....))...))))((((((((((.(((.................((((((((..................))))))))...))).)))))))))))))... ( -21.72, z-score =  -1.26, R)
>droYak2.chr3R 12349501 115 - 28832112
AUAUACAAUAUAAGAUGUGUAGUUCAUGGGGUUAUACGCAGUACGAUUACGAAAACCUAAUAUAAUUUUGAUAAAACACAACUUUUUGUGUUCAGCUGAGUAUAACCCUCUGAUA
.((((((........))))))..(((.((((((((((.((((.......(((((...........)))))....(((((((....)))))))..)))).)))))))))).))).. ( -31.50, z-score =  -3.84, R)
>droSec1.super_0 9050532 92 - 21120651
AUAUACAAGAUAACAUGUGUAU--CAUGUGGUUAUACGCAGUACAAUCACGAAAACCUAGUAU-AACUUA-------------------GUUUAGCUGAGUAUAACCCUCAAUU-
(((((((........)))))))--..((.((((((((.((((.(......).((((..((...-..))..-------------------)))).)))).))))))))..))...- ( -19.40, z-score =  -1.80, R)
>droSim1.chr3R 16034323 95 - 27517382
AUAUACAAGAUAACAUGUGUAUUUAAUGGGGUUAUACGCAGUACAAUCACGAAAACCUAUUAUAACUUUGUUAA--------------------GCUGAGUAUAACCCUCUGAUA
(((((((........))))))).....((((((((((.((((((((.....................))))...--------------------)))).))))))))))...... ( -22.50, z-score =  -2.46, R)
>consensus
AUAUACAAGAUAACAUGUGUAUUUCAUGGGGUUAUACGCAGUACAAUCACGAAAACCUAAUAUAAAUUUA_UAA_______________GUUUAGCUGAGUAUAACCCUCUGAUA
.((((((........))))))......((((((((((.((((....................................................)))).))))))))))...... (-13.12 = -14.32 +   1.20)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,946,215 – 9,946,310
Length 95
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 75.18
Shannon entropy 0.42214
G+C content 0.30522
Mean single sequence MFE -21.03
Consensus MFE -12.04
Energy contribution -12.08
Covariance contribution 0.04
Combinations/Pair 1.08
Mean z-score -1.57
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.681570
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9946215 95 - 27905053
UAUCAUAGGGUUAUACUCAGCUAAA--------------------AAAAGUUAUACUAGGUUUUCGUGUUUGUACUGUGUAUAACUCCAUGAAAUUCAUAUGUUAUCUUGUAUAU
..((((.(((((((((.(((...((--------------------(...(..(........)..)...)))...))).))))))))).))))....................... ( -17.10, z-score =  -1.03, R)
>droEre2.scaffold_4770 9495033 115 - 17746568
UACCAGAGGGUUAUACUCAGAUAAACAUGAAAAGUAGUUUUUUAUUAAAUUCAUAUUAGGUUUUCGUAAUUGUACUGCGUAUAACCCCAAGAAAUACACAUGUUAUCUUCUAUAU
.....(.(((((((((.(((((((..(((((((.((((((......))))).......).)))))))..)))).))).))))))))))((((...((....))..))))...... ( -22.91, z-score =  -2.10, R)
>droYak2.chr3R 12349501 115 + 28832112
UAUCAGAGGGUUAUACUCAGCUGAACACAAAAAGUUGUGUUUUAUCAAAAUUAUAUUAGGUUUUCGUAAUCGUACUGCGUAUAACCCCAUGAACUACACAUCUUAUAUUGUAUAU
..(((..(((((((((.(((..((((((((....))))))))(((.((((((......)))))).)))......))).)))))))))..))).....(((........))).... ( -28.20, z-score =  -3.29, R)
>droSec1.super_0 9050532 92 + 21120651
-AAUUGAGGGUUAUACUCAGCUAAAC-------------------UAAGUU-AUACUAGGUUUUCGUGAUUGUACUGCGUAUAACCACAUG--AUACACAUGUUAUCUUGUAUAU
-....(((((((((((.(((..((((-------------------(.((..-...)).)))))...........))).))))))))(((((--.....)))))...)))...... ( -18.72, z-score =  -0.56, R)
>droSim1.chr3R 16034323 95 + 27517382
UAUCAGAGGGUUAUACUCAGC--------------------UUAACAAAGUUAUAAUAGGUUUUCGUGAUUGUACUGCGUAUAACCCCAUUAAAUACACAUGUUAUCUUGUAUAU
.....(.(((((((((.(((.--------------------.(((((..(..((.....))..)..)).)))..))).)))))))))).....(((((..........))))).. ( -18.20, z-score =  -0.88, R)
>consensus
UAUCAGAGGGUUAUACUCAGCUAAAC_______________UUA_CAAAGUUAUACUAGGUUUUCGUGAUUGUACUGCGUAUAACCCCAUGAAAUACACAUGUUAUCUUGUAUAU
.......(((((((((.(((......................................................))).)))))))))............................ (-12.04 = -12.08 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:14:17 2011