Locus 3939

Sequence ID dm3.chr2R
Location 9,192,499 – 9,192,634
Length 135
Max. P 0.623628
window5395 window5396

overview

Window 5

Location 9,192,499 – 9,192,595
Length 96
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 87.90
Shannon entropy 0.21871
G+C content 0.37452
Mean single sequence MFE -16.46
Consensus MFE -11.32
Energy contribution -11.92
Covariance contribution 0.60
Combinations/Pair 1.10
Mean z-score -2.01
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.22
SVM RNA-class probability 0.600916
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 9192499 96 + 21146708
AUUAAAUUCUUGUUGAACAACUCACAUAGAAAAUUUCUCCACCGAAUUGGCAACUUGUUCAUUAAUUAGCAGCCAAUAACCUGCUAAUUUCACACC
......(((((((.((.....))))).))))............((((.(....)..))))...(((((((((........)))))))))....... ( -15.80, z-score =  -2.48, R)
>droSim1.chr2R 7651560 96 + 19596830
AUUAAAUUCCGGUUGAACCACUGACAGAGAAAAUUUCUCCACCGAAUUGGCAACUUGUUCAUUAAUUAGCAGCCAAUAACCUGCUAAUUUCACACC
..........((((((..........((((.....))))....((((.(....)..))))...(((((((((........)))))))))))).))) ( -18.30, z-score =  -2.28, R)
>droSec1.super_1 6715543 96 + 14215200
AUUAAAUUCCGAUUGAACCACUCACAGCGAAAAUUUCUCCACCGAAUUGGCAACUUGUUCAUUAAUUAGCAACCAAUAACCUGCUAAUUUCACACC
.........((..(((.....)))...))..............((((.(....)..))))...((((((((..........))))))))....... ( -10.90, z-score =  -1.12, R)
>droYak2.chr2R 13372068 95 - 21139217
ACUAAAUUCCAGCUGAACAGCUUACAGA-AAAAUUUCUCCAACGAAUUGGCAACUUGUUCACUAAUUAGCAGCCAAUAAGCUGCUAAAUUCACACC
..........((((....))))....((-(.............((((.(....)..)))).....((((((((......)))))))).)))..... ( -19.80, z-score =  -2.94, R)
>droEre2.scaffold_4845 5967033 95 - 22589142
ACUGAAUUCCCGCUGAACAGGUCACAGU-AAAAUUUCUCUAGCGAAUUGAAAAGUUGUUCGUUAAUUAGCAGCCAAUAACCUGCUAAUUUCACACC
((((.....((........))...))))-..........((((((((.........))))))))((((((((........))))))))........ ( -17.50, z-score =  -1.22, R)
>consensus
AUUAAAUUCCGGUUGAACAACUCACAGAGAAAAUUUCUCCACCGAAUUGGCAACUUGUUCAUUAAUUAGCAGCCAAUAACCUGCUAAUUUCACACC
.............(((((((..............(((......)))..(....))))))))..(((((((((........)))))))))....... (-11.32 = -11.92 +   0.60)

alignment

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secondary structure

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dotplot

Postscript

Window 6

Location 9,192,530 – 9,192,634
Length 104
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 92.15
Shannon entropy 0.14086
G+C content 0.37193
Mean single sequence MFE -23.62
Consensus MFE -16.62
Energy contribution -17.02
Covariance contribution 0.40
Combinations/Pair 1.12
Mean z-score -2.33
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.27
SVM RNA-class probability 0.623628
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 9192530 104 + 21146708
AAUUUCUCCACCGAAUUGGCAACUUGUUCAUUAAUUAGCAGCCAAUAACCUGCUAAUUUCACACCAUAAACAGAAUGAUCAAAGAGCU-UGUGUGCCAAAAUGGC
..........(((..((((((((..((((...(((((((((........)))))))))......(((.......)))......)))).-.)).))))))..))). ( -25.10, z-score =  -2.70, R)
>droSim1.chr2R 7651591 104 + 19596830
AAUUUCUCCACCGAAUUGGCAACUUGUUCAUUAAUUAGCAGCCAAUAACCUGCUAAUUUCACACCAUAAACAGAAUGAUCAAAGAGCU-UGUGUGCCAAAAUGGC
..........(((..((((((((..((((...(((((((((........)))))))))......(((.......)))......)))).-.)).))))))..))). ( -25.10, z-score =  -2.70, R)
>droSec1.super_1 6715574 104 + 14215200
AAUUUCUCCACCGAAUUGGCAACUUGUUCAUUAAUUAGCAACCAAUAACCUGCUAAUUUCACACCAUAAACAGAAUGAUCAAAGAGCU-UGUGUGCCAAAAUGGC
..........(((..((((((((..((((...((((((((..........))))))))......(((.......)))......)))).-.)).))))))..))). ( -21.90, z-score =  -2.09, R)
>droYak2.chr2R 13372098 102 - 21139217
AAUUUCUCCAACGAAUUGGCAACUUGUUCACUAAUUAGCAGCCAAUAAGCUGCUAAAUUCACACCAUAAACUGAAUGAUCAAAGAA---UGUGUGCCAAUAUGGC
...........((.(((((((...(((((.....((((((((......))))))))(((((..........))))).......)))---))..))))))).)).. ( -26.40, z-score =  -3.24, R)
>droEre2.scaffold_4845 5967063 105 - 22589142
AAUUUCUCUAGCGAAUUGAAAAGUUGUUCGUUAAUUAGCAGCCAAUAACCUGCUAAUUUCACACCAUAAACUGAAUGAUCAAAGAGUUUUUUGUGCCAAUAAGGC
.....(((((((((((.........)))))))(((((((((........)))))))))........................))))........(((.....))) ( -19.60, z-score =  -0.94, R)
>consensus
AAUUUCUCCACCGAAUUGGCAACUUGUUCAUUAAUUAGCAGCCAAUAACCUGCUAAUUUCACACCAUAAACAGAAUGAUCAAAGAGCU_UGUGUGCCAAAAUGGC
...............((((((((..((((...(((((((((........)))))))))......(((.......)))......))))...)).))))))...... (-16.62 = -17.02 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:19:39 2011