Locus 2449

Sequence ID dm3.chr2L
Location 19,156,539 – 19,156,698
Length 159
Max. P 0.864465
window3370 window3371

overview

Window 0

Location 19,156,539 – 19,156,658
Length 119
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 78.29
Shannon entropy 0.29673
G+C content 0.30170
Mean single sequence MFE -23.97
Consensus MFE -17.77
Energy contribution -18.00
Covariance contribution 0.23
Combinations/Pair 1.18
Mean z-score -1.87
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.97
SVM RNA-class probability 0.864465
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19156539 119 + 23011544
UAUUUAUGAAAAACUCAAGUAUCUUCAUUUAAGUUAACUAACUGAGGUAUGAAAAUGCGGUGAGGGAAGAGAAAAUCUUUCACCUGUUCUUUCUAAGGAAGACUUAAAUGGUUUUUUAA
......((((((((..(((...)))((((((((((..((....(((((((....))))(((((((((........)))))))))....)))....))...)))))))))))))))))). ( -29.50, z-score =  -2.46, R)
>droSim1.chr2L 18846182 105 + 22036055
-------UAUAAACUCAAGUAUCUA-AUAACAAUCG------UGAGGUAUGAAAUUACGGAGAGGGAAGAGAAAAUCUCUCACCUGUUCAUCGUAAAGAAGACUUAAAUAGUUUUUAAA
-------...........((((((.-...((....)------).))))))....(((((((.(((..((((.....))))..))).))...))))).(((((((.....)))))))... ( -22.10, z-score =  -1.67, R)
>droSec1.super_7 2778972 111 + 3727775
UAUUUUUAAAAAACUCAAGUAUCUA-AUAACAAUCA------UGAUGUAUGAAAUUACGGAGAGGGAAGAGAAAAUCUCUCACCUGUUCAUCGCAAAGAAGACUUAAAUAGUUUUAAA-
.........((((((.((((.(((.-.......(((------((...)))))......(((.(((..((((.....))))..))).))).......)))..))))....))))))...- ( -20.30, z-score =  -1.47, R)
>consensus
UAUUU_UAAAAAACUCAAGUAUCUA_AUAACAAUCA______UGAGGUAUGAAAUUACGGAGAGGGAAGAGAAAAUCUCUCACCUGUUCAUCGUAAAGAAGACUUAAAUAGUUUUUAAA
.......((((((((.((((.(((......................(((......)))(((.(((..((((.....))))..))).))).......)))..))))....)))))))).. (-17.77 = -18.00 +   0.23)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 1

Location 19,156,579 – 19,156,698
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 88.06
Shannon entropy 0.16626
G+C content 0.31842
Mean single sequence MFE -24.65
Consensus MFE -19.54
Energy contribution -20.10
Covariance contribution 0.56
Combinations/Pair 1.08
Mean z-score -1.90
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.42
SVM RNA-class probability 0.689876
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19156579 119 + 23011544
-ACUGAGGUAUGAAAAUGCGGUGAGGGAAGAGAAAAUCUUUCACCUGUUCUUUCUAAGGAAGACUUAAAUGGUUUUUUAAAUCCCACAUGUCGCAUUAAUAUAAAAAUAACUAUGAAAUG
-......((((...(((((((((.((((..((((((((........((.((((.....))))))......))))))))...)))).)))..)))))).)))).................. ( -23.74, z-score =  -1.02, R)
>droSim1.chr2L 18846207 120 + 22036055
UCGUGAGGUAUGAAAUUACGGAGAGGGAAGAGAAAAUCUCUCACCUGUUCAUCGUAAAGAAGACUUAAAUAGUUUUUAAAACCCCAUAUGUCCCAUUAAUAUUAAAAUAACUAUGAAAUG
..(.((.(((((...(((((((.(((..((((.....))))..))).))...))))).(((((((.....))))))).......))))).)).).......................... ( -25.30, z-score =  -1.99, R)
>droSec1.super_7 2779004 119 + 3727775
UCAUGAUGUAUGAAAUUACGGAGAGGGAAGAGAAAAUCUCUCACCUGUUCAUCGCAAAGAAGACUUAAAUAGUUUU-AAAAUCCCAUAUAUCCCAUUAAUAUUAAAAUAACUAUGAAAUG
....((((((((.......(((.(((..((((.....))))..))).))).........((((((.....))))))-.......))))))))............................ ( -24.90, z-score =  -2.68, R)
>consensus
UCAUGAGGUAUGAAAUUACGGAGAGGGAAGAGAAAAUCUCUCACCUGUUCAUCGUAAAGAAGACUUAAAUAGUUUUUAAAAUCCCAUAUGUCCCAUUAAUAUUAAAAUAACUAUGAAAUG
....((.(((((.......(((.(((..((((.....))))..))).)))........(((((((.....))))))).......))))).))............................ (-19.54 = -20.10 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:51:27 2011