Locus 1050

Sequence ID dm3.chr2L
Location 7,899,603 – 7,899,693
Length 90
Max. P 0.957952
window1433 window1434

overview

Window 3

Location 7,899,603 – 7,899,693
Length 90
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 88.82
Shannon entropy 0.18577
G+C content 0.54431
Mean single sequence MFE -30.38
Consensus MFE -25.16
Energy contribution -25.28
Covariance contribution 0.12
Combinations/Pair 1.12
Mean z-score -2.37
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.65
SVM RNA-class probability 0.957952
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7899603 90 + 23011544
------------GGAGUUGGAUGUGAAUGUGGAUGCAGAGAUGCCGAUGGAGACGGCAAACGGCAAUGGCAAACGGCGUUGACAAUGAAGUCCGACCGAGUC
------------.(.(((((((.....(((.(((((.....(((((.((....))((.....))..)))))....))))).))).....))))))))..... ( -29.00, z-score =  -2.40, R)
>droSim1.chr2L 7696029 90 + 22036055
------------GGAGUUGGAUGUGAAUGUGGAUGCAGAGAUGCCGAUGGAGACGGCAAACGGCAAUGGCAAACGGCGUUGACAAUGAAGUCCGACCGAGUC
------------.(.(((((((.....(((.(((((.....(((((.((....))((.....))..)))))....))))).))).....))))))))..... ( -29.00, z-score =  -2.40, R)
>droSec1.super_3 3414276 90 + 7220098
------------GGAGUUGGAUGUGAAUGUGGAUGCAGAGAUGCCGAUGGAGACGGCAAACGGCAAUGGCAAACGGCGUUGACAAUGAAGUCCGACCGAGUC
------------.(.(((((((.....(((.(((((.....(((((.((....))((.....))..)))))....))))).))).....))))))))..... ( -29.00, z-score =  -2.40, R)
>droYak2.chr2L 17328836 102 - 22324452
GGAGUUGGAUGUGAAUGUGAAUGUGGACGGGGAUGCAGAGAUGCCGAUGGAGACGGCAAACGGCAAUGGCAAACGGCGUUGACAAUGAAGUCCAACCGAGUC
.(.(((((((.....(((.(((((...((....(((...(.(((((.((....)).....))))).).)))..))))))).))).....))))))))..... ( -29.10, z-score =  -1.44, R)
>droEre2.scaffold_4929 16821718 102 + 26641161
GGAGUUGGAGUUGGAGUUGGAUGUGAAUGUGGAUGCAGAGAUGCCGAUGGAGACGGCAAACGGCACUGGCAAACGGCGUUGACAAUGAAGUCCGACCGAGUC
.((.((((..(((((.((.(.(((.(((((.(.(((..((.(((((.((....)).....))))))).)))..).))))).))).).)).))))))))).)) ( -35.80, z-score =  -3.23, R)
>consensus
____________GGAGUUGGAUGUGAAUGUGGAUGCAGAGAUGCCGAUGGAGACGGCAAACGGCAAUGGCAAACGGCGUUGACAAUGAAGUCCGACCGAGUC
............(((.((.(.(((.(((((.(.(((...(.(((((.((....)).....))))).).)))..).))))).))).).)).)))......... (-25.16 = -25.28 +   0.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,899,603 – 7,899,693
Length 90
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 88.82
Shannon entropy 0.18577
G+C content 0.54431
Mean single sequence MFE -19.78
Consensus MFE -19.12
Energy contribution -18.96
Covariance contribution -0.16
Combinations/Pair 1.06
Mean z-score -1.30
Structure conservation index 0.97
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.10
SVM RNA-class probability 0.891418
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7899603 90 - 23011544
GACUCGGUCGGACUUCAUUGUCAACGCCGUUUGCCAUUGCCGUUUGCCGUCUCCAUCGGCAUCUCUGCAUCCACAUUCACAUCCAACUCC------------
.....(((..(((......)))...)))(..((....(((.(..(((((.......)))))...).)))....))..)............------------ ( -19.20, z-score =  -1.27, R)
>droSim1.chr2L 7696029 90 - 22036055
GACUCGGUCGGACUUCAUUGUCAACGCCGUUUGCCAUUGCCGUUUGCCGUCUCCAUCGGCAUCUCUGCAUCCACAUUCACAUCCAACUCC------------
.....(((..(((......)))...)))(..((....(((.(..(((((.......)))))...).)))....))..)............------------ ( -19.20, z-score =  -1.27, R)
>droSec1.super_3 3414276 90 - 7220098
GACUCGGUCGGACUUCAUUGUCAACGCCGUUUGCCAUUGCCGUUUGCCGUCUCCAUCGGCAUCUCUGCAUCCACAUUCACAUCCAACUCC------------
.....(((..(((......)))...)))(..((....(((.(..(((((.......)))))...).)))....))..)............------------ ( -19.20, z-score =  -1.27, R)
>droYak2.chr2L 17328836 102 + 22324452
GACUCGGUUGGACUUCAUUGUCAACGCCGUUUGCCAUUGCCGUUUGCCGUCUCCAUCGGCAUCUCUGCAUCCCCGUCCACAUUCACAUUCACAUCCAACUCC
(((.((((..(((......)))...))))........(((.(..(((((.......)))))...).))).....)))......................... ( -21.10, z-score =  -1.46, R)
>droEre2.scaffold_4929 16821718 102 - 26641161
GACUCGGUCGGACUUCAUUGUCAACGCCGUUUGCCAGUGCCGUUUGCCGUCUCCAUCGGCAUCUCUGCAUCCACAUUCACAUCCAACUCCAACUCCAACUCC
.....(((..(((......)))...)))(..((...((((.(..(((((.......)))))...).))))...))..)........................ ( -20.20, z-score =  -1.22, R)
>consensus
GACUCGGUCGGACUUCAUUGUCAACGCCGUUUGCCAUUGCCGUUUGCCGUCUCCAUCGGCAUCUCUGCAUCCACAUUCACAUCCAACUCC____________
.....(((..(((......)))...)))(..((....(((.(..(((((.......)))))...).)))....))..)........................ (-19.12 = -18.96 +  -0.16)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:24:38 2011