Locus 48

Sequence ID sy_sapro.rRNA
Location 2,352,816 – 2,352,976
Length 160
Max. P 0.997910
window143 window144 window145 window146

overview

Window 3

Location 2,352,816 – 2,352,936
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.56
Mean single sequence MFE -23.17
Consensus MFE -22.61
Energy contribution -22.40
Covariance contribution -0.21
Combinations/Pair 1.15
Mean z-score -1.40
Structure conservation index 0.98
SVM decision value 0.48
SVM RNA-class probability 0.753977
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2352816 120 + 2516583
AUUUCUCGUGUUCCGUCGUACUCAGGAUACACUCAAGAGUGAACAAACUUUCGACUACAGGAUUAUUACCUUCUUUGAUUCAUCUUUCCAGAUGAUUCGUCUAGUCUGUUCUUUUGUAAC
.......(((((((..........))).)))).(((((..(((((.(((...(((...(((.......))).....((.((((((....)))))).))))).))).)))))))))).... ( -25.80)
>sy_haemo.rRNA 2541704 120 - 2685023
AUUUCACGUGCUCCGUCGUACUCAGGAUCCACUCAAGAGAGAAUAUAUUUUCAACUACAGGAUUAUUACCUUCUUUGAUUCAACUUUCCAGAUGAUUCGUCUAAUAUAUUCCUUUGUAAC
.......(((.(((..........)))..)))...((((.(((((((((..........((((((..........))))))........(((((...))))))))))))))))))..... ( -18.60)
>sy_aureus.rRNA 2277923 120 - 2809430
AUUUCACGUGCUCCGUCGUACUCAGGAUCCACUCAAGAGAGACAACAUUUUCGACUACAGGAUUAUUACCUUCUUUGAUUCAUCUUUCCAGAUGAUUCGUCUAAUGUCGUCCUUUGUAAC
.......(((.(((..........)))..)))...((((.(((.(((((...(((...(((.......))).....((.((((((....)))))).))))).))))).)))))))..... ( -25.10)
>consensus
AUUUCACGUGCUCCGUCGUACUCAGGAUCCACUCAAGAGAGAAAAAAUUUUCGACUACAGGAUUAUUACCUUCUUUGAUUCAUCUUUCCAGAUGAUUCGUCUAAUAUAUUCCUUUGUAAC
.......(((.(((..........)))..)))...((((.(((((((((...(((...(((.......))).....((.((((((....)))))).))))).)))))))))))))..... (-22.61 = -22.40 +  -0.21)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,352,816 – 2,352,936
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 90.56
Mean single sequence MFE -31.00
Consensus MFE -30.61
Energy contribution -28.83
Covariance contribution -1.77
Combinations/Pair 1.21
Mean z-score -2.44
Structure conservation index 0.99
SVM decision value 2.18
SVM RNA-class probability 0.989807
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2352816 120 - 2516583
GUUACAAAAGAACAGACUAGACGAAUCAUCUGGAAAGAUGAAUCAAAGAAGGUAAUAAUCCUGUAGUCGAAAGUUUGUUCACUCUUGAGUGUAUCCUGAGUACGACGGAACACGAGAAAU
.........(((((((((.(((((.((((((....)))))).)).....(((.......)))...)))...)))))))))..((((..((((.(((..........)))))))))))... ( -34.00)
>sy_haemo.rRNA 2541704 120 + 2685023
GUUACAAAGGAAUAUAUUAGACGAAUCAUCUGGAAAGUUGAAUCAAAGAAGGUAAUAAUCCUGUAGUUGAAAAUAUAUUCUCUCUUGAGUGGAUCCUGAGUACGACGGAGCACGUGAAAU
.((((...((((((((((.(((((.(((.((....)).))).)).....(((.......)))...)))...)))))))))).......(((..(((..........))).)))))))... ( -24.60)
>sy_aureus.rRNA 2277923 120 + 2809430
GUUACAAAGGACGACAUUAGACGAAUCAUCUGGAAAGAUGAAUCAAAGAAGGUAAUAAUCCUGUAGUCGAAAAUGUUGUCUCUCUUGAGUGGAUCCUGAGUACGACGGAGCACGUGAAAU
.((((...((((((((((.(((((.((((((....)))))).)).....(((.......)))...)))...)))))))))).......(((..(((..........))).)))))))... ( -34.40)
>consensus
GUUACAAAGGAACACAUUAGACGAAUCAUCUGGAAAGAUGAAUCAAAGAAGGUAAUAAUCCUGUAGUCGAAAAUAUAUUCUCUCUUGAGUGGAUCCUGAGUACGACGGAGCACGUGAAAU
.((((....(((((((((.(((((.((((((....)))))).)).....(((.......)))...)))...)))))))))........(((..(((..........))).)))))))... (-30.61 = -28.83 +  -1.77) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,352,856 – 2,352,976
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 91.11
Mean single sequence MFE -21.87
Consensus MFE -23.20
Energy contribution -23.10
Covariance contribution -0.10
Combinations/Pair 1.14
Mean z-score -1.42
Structure conservation index 1.06
SVM decision value 1.42
SVM RNA-class probability 0.952463
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2352856 120 + 2516583
GAACAAACUUUCGACUACAGGAUUAUUACCUUCUUUGAUUCAUCUUUCCAGAUGAUUCGUCUAGUCUGUUCUUUUGUAACUCCGUAUAGAGUGUCCUACAACCCCAACAAGCAAGCUCGU
(((((.(((...(((...(((.......))).....((.((((((....)))))).))))).))).)))))..(((((((((......))))....)))))................... ( -22.60)
>sy_haemo.rRNA 2541744 120 - 2685023
GAAUAUAUUUUCAACUACAGGAUUAUUACCUUCUUUGAUUCAACUUUCCAGAUGAUUCGUCUAAUAUAUUCCUUUGUAACUCCGUAUAGAGUGUCCUACAACCCCAAUAAGCAAGCUUAU
(((((((((..........((((((..........))))))........(((((...))))))))))))))..(((((((((......))))....))))).....(((((....))))) ( -17.30)
>sy_aureus.rRNA 2277963 120 - 2809430
GACAACAUUUUCGACUACAGGAUUAUUACCUUCUUUGAUUCAUCUUUCCAGAUGAUUCGUCUAAUGUCGUCCUUUGUAACUCCGUAUAGAGUGUCCUACAACCCCAACAAGCAAGCUUGU
(((.(((((...(((...(((.......))).....((.((((((....)))))).))))).))))).)))..(((((((((......))))....))))).....(((((....))))) ( -25.70)
>consensus
GAAAAAAUUUUCGACUACAGGAUUAUUACCUUCUUUGAUUCAUCUUUCCAGAUGAUUCGUCUAAUAUAUUCCUUUGUAACUCCGUAUAGAGUGUCCUACAACCCCAACAAGCAAGCUUGU
(((((((((...(((...(((.......))).....((.((((((....)))))).))))).)))))))))..(((((((((......))))....))))).....(((((....))))) (-23.20 = -23.10 +  -0.10)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,352,856 – 2,352,976
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 91.11
Mean single sequence MFE -30.53
Consensus MFE -33.64
Energy contribution -30.87
Covariance contribution -2.77
Combinations/Pair 1.24
Mean z-score -2.06
Structure conservation index 1.10
SVM decision value 2.96
SVM RNA-class probability 0.997910
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2352856 120 - 2516583
ACGAGCUUGCUUGUUGGGGUUGUAGGACACUCUAUACGGAGUUACAAAAGAACAGACUAGACGAAUCAUCUGGAAAGAUGAAUCAAAGAAGGUAAUAAUCCUGUAGUCGAAAGUUUGUUC
(((((....))))).....(((((....(((((....))))))))))..(((((((((.(((((.((((((....)))))).)).....(((.......)))...)))...))))))))) ( -34.50)
>sy_haemo.rRNA 2541744 120 + 2685023
AUAAGCUUGCUUAUUGGGGUUGUAGGACACUCUAUACGGAGUUACAAAGGAAUAUAUUAGACGAAUCAUCUGGAAAGUUGAAUCAAAGAAGGUAAUAAUCCUGUAGUUGAAAAUAUAUUC
(((((....))))).....(((((....(((((....))))))))))..(((((((((.(((((.(((.((....)).))).)).....(((.......)))...)))...))))))))) ( -22.70)
>sy_aureus.rRNA 2277963 120 + 2809430
ACAAGCUUGCUUGUUGGGGUUGUAGGACACUCUAUACGGAGUUACAAAGGACGACAUUAGACGAAUCAUCUGGAAAGAUGAAUCAAAGAAGGUAAUAAUCCUGUAGUCGAAAAUGUUGUC
(((((....))))).....(((((....(((((....))))))))))..(((((((((.(((((.((((((....)))))).)).....(((.......)))...)))...))))))))) ( -34.40)
>consensus
ACAAGCUUGCUUGUUGGGGUUGUAGGACACUCUAUACGGAGUUACAAAGGAACACAUUAGACGAAUCAUCUGGAAAGAUGAAUCAAAGAAGGUAAUAAUCCUGUAGUCGAAAAUAUAUUC
(((((....))))).....(((((....(((((....))))))))))..(((((((((.(((((.((((((....)))))).)).....(((.......)))...)))...))))))))) (-33.64 = -30.87 +  -2.77) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Fri Apr 7 15:52:31 2006