Locus 1048

Sequence ID dm3.chr2L
Location 7,870,953 – 7,871,081
Length 128
Max. P 0.991932
window1428 window1429 window1430

overview

Window 8

Location 7,870,953 – 7,871,051
Length 98
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 92.67
Shannon entropy 0.12474
G+C content 0.40292
Mean single sequence MFE -28.62
Consensus MFE -25.38
Energy contribution -25.94
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -2.96
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.51
SVM RNA-class probability 0.991932
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7870953 98 + 23011544
UUUCUUUUCAAGUGGCGCCUCCGAAAAAUUCAAUUUAAAUGUAAUUCGCGUUUUCUUGACUGCGCAGUAAUAAUAAAACUGCAGC----GGAGCCACUUGGU
.......(((((((((.............((((...((((((.....))))))..))))(((((((((.........))))).))----)).))))))))). ( -30.60, z-score =  -3.67, R)
>droEre2.scaffold_4929 16792771 98 + 26641161
UUCCUCUUGAAGUGGCGCCUUCAAAAAAUUCAAUUUAAAUGUAAUUCGCGUUUUCGUGGCUGCGCAGUAAUAAUAAAACUGCAAC----GGAGCCACUUGGU
.......(.(((((((.((.....................(((..(((((....))))).)))(((((.........)))))...----)).))))))).). ( -26.10, z-score =  -2.03, R)
>droYak2.chr2L 17299555 102 - 22324452
UUUCUUCUGAAGUGGCGCCUUUAAAAAAUUCAAUUUAAAUGUAAUUCGCGUUUUCCUGGCUGCGCAGUAAUAAUAAAACUGCAGUCACUGGAGCCACUUGGU
.........(((((((....................((((((.....))))))((((((((((..(((.........))))))))))..))))))))))... ( -25.20, z-score =  -1.59, R)
>droSec1.super_3 3384946 98 + 7220098
UUUCUCUUCAAGUGGCGCCUCCGAAAAAUUCAAUUUAAAUGUAAUUCGCGUUUUCUUGACUGCGCAGUAAUAAUAAAACUGCAGC----GGAGCCACUUGGU
.......(((((((((.............((((...((((((.....))))))..))))(((((((((.........))))).))----)).))))))))). ( -30.60, z-score =  -3.76, R)
>droSim1.chr2L 7668497 98 + 22036055
UUUCUCUUCAAGUGGCGCCUCCGAAAAAUUCAAUUUAAAUGUAAUUCGCGUUUUCUUGACUGCGCAGUAAUAAUAAAACUGCAGC----GGAGCCACUUGGU
.......(((((((((.............((((...((((((.....))))))..))))(((((((((.........))))).))----)).))))))))). ( -30.60, z-score =  -3.76, R)
>consensus
UUUCUCUUCAAGUGGCGCCUCCGAAAAAUUCAAUUUAAAUGUAAUUCGCGUUUUCUUGACUGCGCAGUAAUAAUAAAACUGCAGC____GGAGCCACUUGGU
.......(((((((((.((..........((((...((((((.....))))))..))))....(((((.........))))).......)).))))))))). (-25.38 = -25.94 +   0.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 7,870,953 – 7,871,051
Length 98
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 92.67
Shannon entropy 0.12474
G+C content 0.40292
Mean single sequence MFE -27.88
Consensus MFE -25.08
Energy contribution -25.04
Covariance contribution -0.04
Combinations/Pair 1.10
Mean z-score -2.57
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.11
SVM RNA-class probability 0.982696
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7870953 98 - 23011544
ACCAAGUGGCUCC----GCUGCAGUUUUAUUAUUACUGCGCAGUCAAGAAAACGCGAAUUACAUUUAAAUUGAAUUUUUCGGAGGCGCCACUUGAAAAGAAA
..((((((((.((----((.(((((.........)))))))..((..(((((..(((.(((....))).)))..)))))..)))).))))))))........ ( -29.90, z-score =  -3.26, R)
>droEre2.scaffold_4929 16792771 98 - 26641161
ACCAAGUGGCUCC----GUUGCAGUUUUAUUAUUACUGCGCAGCCACGAAAACGCGAAUUACAUUUAAAUUGAAUUUUUUGAAGGCGCCACUUCAAGAGGAA
.((..((((((..----((.(((((.........))))))))))))).............................((((((((......)))))))))).. ( -26.00, z-score =  -2.12, R)
>droYak2.chr2L 17299555 102 + 22324452
ACCAAGUGGCUCCAGUGACUGCAGUUUUAUUAUUACUGCGCAGCCAGGAAAACGCGAAUUACAUUUAAAUUGAAUUUUUUAAAGGCGCCACUUCAGAAGAAA
...(((((((.((.((((..(((((.........)))))((............))...)))).((((((........)))))))).)))))))......... ( -23.70, z-score =  -1.30, R)
>droSec1.super_3 3384946 98 - 7220098
ACCAAGUGGCUCC----GCUGCAGUUUUAUUAUUACUGCGCAGUCAAGAAAACGCGAAUUACAUUUAAAUUGAAUUUUUCGGAGGCGCCACUUGAAGAGAAA
..((((((((.((----((.(((((.........)))))))..((..(((((..(((.(((....))).)))..)))))..)))).))))))))........ ( -29.90, z-score =  -3.10, R)
>droSim1.chr2L 7668497 98 - 22036055
ACCAAGUGGCUCC----GCUGCAGUUUUAUUAUUACUGCGCAGUCAAGAAAACGCGAAUUACAUUUAAAUUGAAUUUUUCGGAGGCGCCACUUGAAGAGAAA
..((((((((.((----((.(((((.........)))))))..((..(((((..(((.(((....))).)))..)))))..)))).))))))))........ ( -29.90, z-score =  -3.10, R)
>consensus
ACCAAGUGGCUCC____GCUGCAGUUUUAUUAUUACUGCGCAGUCAAGAAAACGCGAAUUACAUUUAAAUUGAAUUUUUCGGAGGCGCCACUUGAAGAGAAA
..((((((((.......((.(((((.........))))))).(((..(((((..(((.(((....))).)))...)))))...)))))))))))........ (-25.08 = -25.04 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,870,991 – 7,871,081
Length 90
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 87.13
Shannon entropy 0.24180
G+C content 0.39598
Mean single sequence MFE -23.08
Consensus MFE -15.71
Energy contribution -16.60
Covariance contribution 0.89
Combinations/Pair 1.05
Mean z-score -1.85
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.03
SVM RNA-class probability 0.509419
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7870991 90 + 23011544
AUGUAAUUCGCGUUUUCUUGACUG-CGCAGUAAUAAUAAAACUGCAGC----GGAGCCACUUGGUUUGUUUACCCAAUCGAAAGAGGAUUACACA
.((((((((...(((((....(((-((((((.........))))).))----))((((....)))).............))))).)))))))).. ( -24.80, z-score =  -2.20, R)
>droAna3.scaffold_12943 3604719 85 - 5039921
AUUUAAUUCCUGUUGCUUUAAACGAUUCAAUAAUAA--AAAUUGCAGC--------ACUUUGUGUUUGUUUACCCAAUCGAAAGAGGAUUACACA
.......(((((((((....................--.....)))))--------.((((.((.(((......))).))))))))))....... ( -10.91, z-score =   0.14, R)
>droEre2.scaffold_4929 16792809 90 + 26641161
AUGUAAUUCGCGUUUUCGUGGCUG-CGCAGUAAUAAUAAAACUGCAAC----GGAGCCACUUGGUUUGUUUACUCAAUCGAAAGAGGAUUACACA
.((((((((...(((((((((((.-((((((.........)))))...----).))))))(((((......)).)))..))))).)))))))).. ( -28.30, z-score =  -3.12, R)
>droYak2.chr2L 17299593 94 - 22324452
AUGUAAUUCGCGUUUUCCUGGCUG-CGCAGUAAUAAUAAAACUGCAGUCACUGGAGCCACUUGGUUUGUUUACCCAAUCGAAAGAGGAUUACACA
.(((((((((.(((((..((((((-(..(((.........))))))))))..))))))....(((......)))...((....)))))))))).. ( -24.90, z-score =  -1.51, R)
>droSec1.super_3 3384984 90 + 7220098
AUGUAAUUCGCGUUUUCUUGACUG-CGCAGUAAUAAUAAAACUGCAGC----GGAGCCACUUGGUUUGUUUACCCAAUCGAAAGAGGAUUACACA
.((((((((...(((((....(((-((((((.........))))).))----))((((....)))).............))))).)))))))).. ( -24.80, z-score =  -2.20, R)
>droSim1.chr2L 7668535 90 + 22036055
AUGUAAUUCGCGUUUUCUUGACUG-CGCAGUAAUAAUAAAACUGCAGC----GGAGCCACUUGGUUUGUUUACCCAAUCGAAAGAGGAUUACACA
.((((((((...(((((....(((-((((((.........))))).))----))((((....)))).............))))).)))))))).. ( -24.80, z-score =  -2.20, R)
>consensus
AUGUAAUUCGCGUUUUCUUGACUG_CGCAGUAAUAAUAAAACUGCAGC____GGAGCCACUUGGUUUGUUUACCCAAUCGAAAGAGGAUUACACA
.((((((((.................(((((.........)))))........(((((....)))))..........((....)))))))))).. (-15.71 = -16.60 +   0.89)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:24:35 2011