Locus 1341

Sequence ID dm3.chr2L
Location 10,440,828 – 10,440,953
Length 125
Max. P 0.618455
window1829 window1830

overview

Window 9

Location 10,440,828 – 10,440,953
Length 125
Sequences 5
Columns 136
Reading direction forward
Mean pairwise identity 82.94
Shannon entropy 0.27931
G+C content 0.38119
Mean single sequence MFE -25.76
Consensus MFE -19.62
Energy contribution -19.82
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.49
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.26
SVM RNA-class probability 0.618455
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 10440828 125 + 23011544
CCCCCAAUAUUUUACUACGAAUCCGCCCCUGCCAUUAUGUCAAUUUUUAUGACCGCCUACAAAUUGUGAAAUAUGUAGAAGGGGCACUUGUGAAGUUAUAGCAAUAUAAAAU---------GUAUGUAUGUUAU--
........(((((((...(....)((((((((..(((((........)))))..))(((((.(((....))).))))).))))))....))))))).(((((((((((....---------.))))).))))))-- ( -26.20, z-score =  -1.47, R)
>droSim1.chr2L 10234967 134 + 22036055
CCCCCAAUAUUUUACUACGAAUCCGCCCCUGCCAUUAUGUCAAUUUUUAUGACCGCCUACAAAUUGUGAAAUAUGUUGAAGGGGCACUUGUGAAGUUAUAGCAAUAUAAAAUAGUUAACUCGGUUGUAUGGUAU--
......((((..(((..(((....((((((..((.(((((((((((.((........)).))))))....))))).)).))))))..((((....(((((....))))).)))).....)))...)))..))))-- ( -25.80, z-score =   0.22, R)
>droSec1.super_3 5868718 136 + 7220098
CCCCCAAUAUUUUACUACGAAUCCGCCCCUGCCAUUAUGUCAAUUUUUAUGACCGCCUACAAAUUGUGAAAUAUGUAGAAGGGGCACUUAUGAAGUUAUAGCGACAUGAAAUAGUUAACUCGCUUGUAUGCUAUAU
........................((((((((..(((((........)))))..))(((((.(((....))).))))).))))))...........((((((((((.(....((....))..).))).))))))). ( -28.00, z-score =  -1.39, R)
>droYak2.chr2L 6845862 105 + 22324452
CCCCCAAUAUUUUACUACGAAUCCGCCCCUGCCAUUAUGUCAAUUUUUAUGACCGCCUACAAAUUGUGAAAUAUGUAGUAGGGGCACUUUUGAAGUUAUAGCAAU-------------------------------
.......(((...(((.((((...((((((((......((((.......))))....((((.(((....))).))))))))))))...)))).))).))).....------------------------------- ( -24.40, z-score =  -2.51, R)
>droEre2.scaffold_4929 11649780 105 - 26641161
CCCCCAAUAUUUUACUACGAAUCCGCCCCUGCCAUUAUGUCAAUUUUUAUGACCGCCUACAGAUUGUGAAAUAUGUAGUAGGGGCACUUUUGAAGUUAUAGCAAU-------------------------------
.......(((...(((.((((...((((((((......((((.......))))....((((.(((....))).))))))))))))...)))).))).))).....------------------------------- ( -24.40, z-score =  -2.30, R)
>consensus
CCCCCAAUAUUUUACUACGAAUCCGCCCCUGCCAUUAUGUCAAUUUUUAUGACCGCCUACAAAUUGUGAAAUAUGUAGAAGGGGCACUUGUGAAGUUAUAGCAAUAU_AAAU_________G__UGUAUG_UAU__
.......(((...(((.((.....((((((((..(((((........)))))..))(((((.(((....))).))))).)))))).....)).))).))).................................... (-19.62 = -19.82 +   0.20)

alignment

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secondary structure

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dotplot

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Window 0

Location 10,440,828 – 10,440,953
Length 125
Sequences 5
Columns 136
Reading direction reverse
Mean pairwise identity 82.94
Shannon entropy 0.27931
G+C content 0.38119
Mean single sequence MFE -26.72
Consensus MFE -24.18
Energy contribution -24.58
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -0.89
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.21
SVM RNA-class probability 0.596021
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 10440828 125 - 23011544
--AUAACAUACAUAC---------AUUUUAUAUUGCUAUAACUUCACAAGUGCCCCUUCUACAUAUUUCACAAUUUGUAGGCGGUCAUAAAAAUUGACAUAAUGGCAGGGGCGGAUUCGUAGUAAAAUAUUGGGGG
--............(---------(...(((.(((((((.(((.....)))((((((((((((.(((....))).))))))..((((.......))))........))))))......))))))).))).)).... ( -26.90, z-score =  -1.38, R)
>droSim1.chr2L 10234967 134 - 22036055
--AUACCAUACAACCGAGUUAACUAUUUUAUAUUGCUAUAACUUCACAAGUGCCCCUUCAACAUAUUUCACAAUUUGUAGGCGGUCAUAAAAAUUGACAUAAUGGCAGGGGCGGAUUCGUAGUAAAAUAUUGGGGG
--...((...(((...((....))....(((.(((((((.(((.....)))((((((((((((.(((....))).))).....((((.......))))....))).))))))......))))))).)))))).)). ( -25.50, z-score =   0.34, R)
>droSec1.super_3 5868718 136 - 7220098
AUAUAGCAUACAAGCGAGUUAACUAUUUCAUGUCGCUAUAACUUCAUAAGUGCCCCUUCUACAUAUUUCACAAUUUGUAGGCGGUCAUAAAAAUUGACAUAAUGGCAGGGGCGGAUUCGUAGUAAAAUAUUGGGGG
.((((((..(((.(.((((.....))))).))).)))))).(((((....(((((((((((((.(((....))).))))))..((((.......))))........))))))).....(((......)))))))). ( -28.80, z-score =  -0.34, R)
>droYak2.chr2L 6845862 105 - 22324452
-------------------------------AUUGCUAUAACUUCAAAAGUGCCCCUACUACAUAUUUCACAAUUUGUAGGCGGUCAUAAAAAUUGACAUAAUGGCAGGGGCGGAUUCGUAGUAAAAUAUUGGGGG
-------------------------------.(((((((.(((.....)))((((((.(((((.(((....))).)))))...((((.......))))........))))))......)))))))........... ( -26.30, z-score =  -1.64, R)
>droEre2.scaffold_4929 11649780 105 + 26641161
-------------------------------AUUGCUAUAACUUCAAAAGUGCCCCUACUACAUAUUUCACAAUCUGUAGGCGGUCAUAAAAAUUGACAUAAUGGCAGGGGCGGAUUCGUAGUAAAAUAUUGGGGG
-------------------------------.(((((((.(((.....)))((((((.(((((.(((....))).)))))...((((.......))))........))))))......)))))))........... ( -26.10, z-score =  -1.44, R)
>consensus
__AUA_CAUACA__C_________AUUU_AUAUUGCUAUAACUUCAAAAGUGCCCCUUCUACAUAUUUCACAAUUUGUAGGCGGUCAUAAAAAUUGACAUAAUGGCAGGGGCGGAUUCGUAGUAAAAUAUUGGGGG
................................(((((((.(((.....)))((((((.(((((.(((....))).)))))...((((.......))))........))))))......)))))))........... (-24.18 = -24.58 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:30:07 2011