Locus 9231

Sequence ID dm3.chr3R
Location 5,057,623 – 5,057,714
Length 91
Max. P 0.942181
window12652 window12653

overview

Window 2

Location 5,057,623 – 5,057,714
Length 91
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 73.87
Shannon entropy 0.40826
G+C content 0.36772
Mean single sequence MFE -18.02
Consensus MFE -9.56
Energy contribution -10.30
Covariance contribution 0.75
Combinations/Pair 1.05
Mean z-score -2.35
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.48
SVM RNA-class probability 0.942181
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 5057623 91 + 27905053
CCGAGCCUUAUCAAUUGAAUUAAA--GACUACUACUUAUGCUACUGAUAAGUGGUAGUAUUCCUAAGCAAAUCAAUUGCAACAUAUUCCCCUC-----------------------
..(((...................--.((((((((((((.(....)))))))))))))........((((.....))))...........)))----------------------- ( -18.00, z-score =  -2.67, R)
>droEre2.scaffold_4770 1203452 113 - 17746568
CCGAGCGUUAUCAAUUGAAUUAAA--GAAUACUACUCAUGCUACUGAUAAGUAA-AGUAUUCCUAAACAAAUCAAUUGCAACAUAUCCCACAUGUGUAUGUGCGUUCCCUCCCUUC
..((((((...(((((((......--(((((((.(....).((((....)))).-))))))).........)))))))..(((((..(.....)..)))))))))))......... ( -19.46, z-score =  -2.30, R)
>droYak2.chr3R 9109434 115 + 28832112
CCGGGCCUUAUCAAUUGAAUUAAAAUGAAUACUACUCGUGCUACUGAUAAGUAA-AGUAUUCCCAACCAAAUCAAUUGCAACAUAUCGCAGAUAUGUGUAUGCCCUCUCCCUUUAA
..((((.....(((((((........(((((((.....((((.......)))).-))))))).........)))))))..(((((((...)))))))....))))........... ( -24.33, z-score =  -3.11, R)
>droSim1.chr3R 11264259 91 - 27517382
CCCAGCCUUAUCAAUUGAAUUAAA--GAAUACUACUCAUGCUUCUGAUAAGUGAUAGUAUCCCUAACCAAAUCAAUUGCAACAUAUUCCCCUC-----------------------
...........(((((((.....(--(.((((((.((((.(....)....))))))))))..)).......)))))))...............----------------------- ( -10.30, z-score =  -1.31, R)
>consensus
CCGAGCCUUAUCAAUUGAAUUAAA__GAAUACUACUCAUGCUACUGAUAAGUAA_AGUAUUCCUAACCAAAUCAAUUGCAACAUAUCCCACAC_______________________
...........(((((((........((((((((....((((.......)))).)))))))).........)))))))...................................... ( -9.56 = -10.30 +   0.75)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,057,623 – 5,057,714
Length 91
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 73.87
Shannon entropy 0.40826
G+C content 0.36772
Mean single sequence MFE -23.79
Consensus MFE -16.00
Energy contribution -16.88
Covariance contribution 0.88
Combinations/Pair 1.07
Mean z-score -1.57
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.95
SVM RNA-class probability 0.860174
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 5057623 91 - 27905053
-----------------------GAGGGGAAUAUGUUGCAAUUGAUUUGCUUAGGAAUACUACCACUUAUCAGUAGCAUAAGUAGUAGUC--UUUAAUUCAAUUGAUAAGGCUCGG
-----------------------...(((.........(((((((.(((...((((...((((.(((((((....).)))))).))))))--))))).)))))))......))).. ( -17.06, z-score =   0.05, R)
>droEre2.scaffold_4770 1203452 113 + 17746568
GAAGGGAGGGAACGCACAUACACAUGUGGGAUAUGUUGCAAUUGAUUUGUUUAGGAAUACU-UUACUUAUCAGUAGCAUGAGUAGUAUUC--UUUAAUUCAAUUGAUAACGCUCGG
.....(((....(.(((((....))))).)....(((((((((((.(((...(((((((((-..(((((((....).)))))))))))))--))))).))))))).)))).))).. ( -30.20, z-score =  -3.18, R)
>droYak2.chr3R 9109434 115 - 28832112
UUAAAGGGAGAGGGCAUACACAUAUCUGCGAUAUGUUGCAAUUGAUUUGGUUGGGAAUACU-UUACUUAUCAGUAGCACGAGUAGUAUUCAUUUUAAUUCAAUUGAUAAGGCCCGG
...........((((....(((((((...)))))))..(((((((.((((....(((((((-..((((...........)))))))))))...)))).))))))).....)))).. ( -29.30, z-score =  -2.34, R)
>droSim1.chr3R 11264259 91 + 27517382
-----------------------GAGGGGAAUAUGUUGCAAUUGAUUUGGUUAGGGAUACUAUCACUUAUCAGAAGCAUGAGUAGUAUUC--UUUAAUUCAAUUGAUAAGGCUGGG
-----------------------...........(((.(((((((.(((...(((((((((...(((((((....).)))))))))))))--))))).)))))))....))).... ( -18.60, z-score =  -0.80, R)
>consensus
_______________________AAGGGGAAUAUGUUGCAAUUGAUUUGGUUAGGAAUACU_UCACUUAUCAGUAGCAUGAGUAGUAUUC__UUUAAUUCAAUUGAUAAGGCUCGG
..................................(((.(((((((.((((....(((((((...(((((((....).)))))))))))))...)))).)))))))....))).... (-16.00 = -16.88 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:00:22 2011