Locus 5705

Sequence ID dm3.chr3L
Location 585,750 – 585,827
Length 77
Max. P 0.998008
window7835 window7836

overview

Window 5

Location 585,750 – 585,827
Length 77
Sequences 7
Columns 77
Reading direction forward
Mean pairwise identity 67.41
Shannon entropy 0.67846
G+C content 0.52286
Mean single sequence MFE -16.36
Consensus MFE -9.30
Energy contribution -10.24
Covariance contribution 0.94
Combinations/Pair 1.44
Mean z-score -1.87
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.23
SVM RNA-class probability 0.998008
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 585750 77 + 24543557
GCAUAAGAAACCCCCAGCGGAUCGCACAUCCAUGGUGCGAUCGCCGCCAUCUAUCAUCCCACCUAUCAUAGAUCUUU
....((((........(((((((((((.......)))))))..))))..(((((.((.......)).))))))))). ( -17.90, z-score =  -2.25, R)
>droSim1.chr3L 234740 77 + 22553184
GCAUAAGAAACCCCCAGCGGAUCGCACAUCCAUGGUGCGAUCGCCGCCAUCUAUCAUCCCACCUAUCAUAGAUCUUU
....((((........(((((((((((.......)))))))..))))..(((((.((.......)).))))))))). ( -17.90, z-score =  -2.25, R)
>droSec1.super_2 605834 77 + 7591821
GCAUAAGAAACCCCCAGCGGAUCGCACAUCCAUGGUGCGAUCGCCGCCAUCUAUCAUCCCACCUAUCAUAGAUCUUU
....((((........(((((((((((.......)))))))..))))..(((((.((.......)).))))))))). ( -17.90, z-score =  -2.25, R)
>droYak2.chr3L 568243 77 + 24197627
GCAUAAGAAAGCCCCAUGGGAUCGCGCACUCAAAGUGCGAUCGUCGCCAUCUAUCAUCCCACCUAUCAUAGAUCUUU
((.........((....))((((((((.......))))))))...)).((((((.((.......)).)))))).... ( -15.90, z-score =  -1.11, R)
>droEre2.scaffold_4784 588177 76 + 25762168
GCAUAAGAAA-CCCCACCGGAUCGCACACUCAAAGUGCGAUCGUCGCCAUCUAUCAUCCCACCUAUCAUAGAUCUUU
....((((..-........((((((((.......)))))))).......(((((.((.......)).))))))))). ( -15.30, z-score =  -3.25, R)
>droAna3.scaffold_13337 21177299 58 - 23293914
----ACGAAACCCCUUUCGAAACGCACAGU---------------GCCAUCUAUCAUGCCACCUAUCGUAGAUCUUU
----.(((((....)))))..(((....((---------------(.(((.....))).)))....)))........ (  -7.20, z-score =  -1.29, R)
>droVir3.scaffold_13049 3430190 61 + 25233164
-------GCAUUUUGGUUGCCCUGCCCAGCUGCCGGGCA--UAACGCUGCCCGA-GCACAGCCUGUCGCAG------
-------(((.......))).((((.(((((((((((((--......)))))).-))..)).)))..))))------ ( -22.40, z-score =  -0.71, R)
>consensus
GCAUAAGAAACCCCCAGCGGAUCGCACAUCCAUGGUGCGAUCGCCGCCAUCUAUCAUCCCACCUAUCAUAGAUCUUU
...................((((((((.......))))))))......((((((.((.......)).)))))).... ( -9.30 = -10.24 +   0.94)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 585,750 – 585,827
Length 77
Sequences 7
Columns 77
Reading direction reverse
Mean pairwise identity 67.41
Shannon entropy 0.67846
G+C content 0.52286
Mean single sequence MFE -21.19
Consensus MFE -10.12
Energy contribution -11.57
Covariance contribution 1.45
Combinations/Pair 1.31
Mean z-score -0.79
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.736158
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 585750 77 - 24543557
AAAGAUCUAUGAUAGGUGGGAUGAUAGAUGGCGGCGAUCGCACCAUGGAUGUGCGAUCCGCUGGGGGUUUCUUAUGC
.(((((((((.((.......)).)))))...((((((((((((.......))))))).)))))......)))).... ( -23.00, z-score =  -0.87, R)
>droSim1.chr3L 234740 77 - 22553184
AAAGAUCUAUGAUAGGUGGGAUGAUAGAUGGCGGCGAUCGCACCAUGGAUGUGCGAUCCGCUGGGGGUUUCUUAUGC
.(((((((((.((.......)).)))))...((((((((((((.......))))))).)))))......)))).... ( -23.00, z-score =  -0.87, R)
>droSec1.super_2 605834 77 - 7591821
AAAGAUCUAUGAUAGGUGGGAUGAUAGAUGGCGGCGAUCGCACCAUGGAUGUGCGAUCCGCUGGGGGUUUCUUAUGC
.(((((((((.((.......)).)))))...((((((((((((.......))))))).)))))......)))).... ( -23.00, z-score =  -0.87, R)
>droYak2.chr3L 568243 77 - 24197627
AAAGAUCUAUGAUAGGUGGGAUGAUAGAUGGCGACGAUCGCACUUUGAGUGCGCGAUCCCAUGGGGCUUUCUUAUGC
.((((.......(..(((((((....((((....).)))((((.....))))...)))))))..)....)))).... ( -18.50, z-score =   0.29, R)
>droEre2.scaffold_4784 588177 76 - 25762168
AAAGAUCUAUGAUAGGUGGGAUGAUAGAUGGCGACGAUCGCACUUUGAGUGUGCGAUCCGGUGGGG-UUUCUUAUGC
....((((((.((.......)).)))))).((...((((((((.......))))))))..(((((.-...))))))) ( -19.70, z-score =  -0.79, R)
>droAna3.scaffold_13337 21177299 58 + 23293914
AAAGAUCUACGAUAGGUGGCAUGAUAGAUGGC---------------ACUGUGCGUUUCGAAAGGGGUUUCGU----
..(((((((((...((((.(((.....))).)---------------)))...)))..(....)))))))...---- ( -14.50, z-score =  -1.38, R)
>droVir3.scaffold_13049 3430190 61 - 25233164
------CUGCGACAGGCUGUGC-UCGGGCAGCGUUA--UGCCCGGCAGCUGGGCAGGGCAACCAAAAUGC-------
------.(((..(((.((((..-.((((((......--))))))))))))).)))((....)).......------- ( -26.60, z-score =  -1.05, R)
>consensus
AAAGAUCUAUGAUAGGUGGGAUGAUAGAUGGCGGCGAUCGCACCAUGGAUGUGCGAUCCGAUGGGGGUUUCUUAUGC
....((((((.((.......)).))))))......((((((((.......))))))))................... (-10.12 = -11.57 +   1.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:53:30 2011