Locus 44

Sequence ID sy_sapro.rRNA
Location 2,350,857 – 2,351,137
Length 280
Max. P 0.993672
window123 window124 window125 window126 window127 window128 window129

overview

Window 3

Location 2,350,857 – 2,350,977
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -33.70
Consensus MFE -34.36
Energy contribution -33.70
Covariance contribution -0.66
Combinations/Pair 1.06
Mean z-score -1.88
Structure conservation index 1.02
SVM decision value 1.10
SVM RNA-class probability 0.915513
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2350857 120 + 2516583
CUGCUCGACUUGUAAGUCUCGCAGUCAAGCUUCCUUAUGCCUUUACACUCUAUGAAUGAUUUCCAACCAUUCUGAGGAAACCUUUGAGCGCCUCCGUUACUCUUUAGGAGGCGACCGCCC
((((..((((....))))..))))(((((.(((((((((......))......(((((.........))))))))))))...))))).(((((((...........)))))))....... ( -31.90)
>sy_haemo.rRNA 2539746 120 - 2685023
CUGCUCGACUUGUAGGUCUCGCAGUCAAGCUCCCUUAUGCCUUUACACUCUAUGAAUGAUUUCCAACCAUUCUGAGGGAACCUUUGAGCGCCUCCGUUACCUUUUAGGAGGCGACCGCCC
((((..((((....))))..))))(((((.(((((((((......))......(((((.........))))))))))))...))))).(((((((...........)))))))....... ( -34.60)
>sy_aureus.rRNA 2275964 120 - 2809430
CUGCUCGACUUGUAGGUCUCGCAGUCAAGCUCCCUUAUGCCUUUACACUCUAUGAAUGAUUUCCAACCAUUCUGAGGGAACCUUUGAGCGCCUCCGUUACCUUUUAGGAGGCGACCGCCC
((((..((((....))))..))))(((((.(((((((((......))......(((((.........))))))))))))...))))).(((((((...........)))))))....... ( -34.60)
>consensus
CUGCUCGACUUGUAGGUCUCGCAGUCAAGCUCCCUUAUGCCUUUACACUCUAUGAAUGAUUUCCAACCAUUCUGAGGGAACCUUUGAGCGCCUCCGUUACCUUUUAGGAGGCGACCGCCC
((((..((((....))))..))))(((((.(((((((((......))......(((((.........))))))))))))...))))).(((((((...........)))))))....... (-34.36 = -33.70 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,350,857 – 2,350,977
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -43.50
Consensus MFE -43.78
Energy contribution -43.33
Covariance contribution -0.44
Combinations/Pair 1.03
Mean z-score -3.04
Structure conservation index 1.01
SVM decision value 2.42
SVM RNA-class probability 0.993672
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2350857 120 - 2516583
GGGCGGUCGCCUCCUAAAGAGUAACGGAGGCGCUCAAAGGUUUCCUCAGAAUGGUUGGAAAUCAUUCAUAGAGUGUAAAGGCAUAAGGAAGCUUGACUGCGAGACUUACAAGUCGAGCAG
..((((((((((((...........))))))......(((((((((..(((((((.....))))))).....((((....)))).)))))))))))))))..((((....))))...... ( -42.70)
>sy_haemo.rRNA 2539746 120 + 2685023
GGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCUCAAAGGUUCCCUCAGAAUGGUUGGAAAUCAUUCAUAGAGUGUAAAGGCAUAAGGGAGCUUGACUGCGAGACCUACAAGUCGAGCAG
..((((((((((((...........))))))......(((((((((..(((((((.....))))))).....((((....)))).)))))))))))))))..(((......)))...... ( -43.90)
>sy_aureus.rRNA 2275964 120 + 2809430
GGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCUCAAAGGUUCCCUCAGAAUGGUUGGAAAUCAUUCAUAGAGUGUAAAGGCAUAAGGGAGCUUGACUGCGAGACCUACAAGUCGAGCAG
..((((((((((((...........))))))......(((((((((..(((((((.....))))))).....((((....)))).)))))))))))))))..(((......)))...... ( -43.90)
>consensus
GGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCUCAAAGGUUCCCUCAGAAUGGUUGGAAAUCAUUCAUAGAGUGUAAAGGCAUAAGGGAGCUUGACUGCGAGACCUACAAGUCGAGCAG
..((((((((((((...........))))))......(((((((((..(((((((.....))))))).....((((....)))).)))))))))))))))..(((......)))...... (-43.78 = -43.33 +  -0.44) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,350,937 – 2,351,057
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -42.27
Consensus MFE -41.11
Energy contribution -40.67
Covariance contribution -0.44
Combinations/Pair 1.03
Mean z-score -2.13
Structure conservation index 0.97
SVM decision value 1.22
SVM RNA-class probability 0.932215
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2350937 120 + 2516583
CCUUUGAGCGCCUCCGUUACUCUUUAGGAGGCGACCGCCCCAGUCAAACUGCCCAUCUGACACUGUCUCCCACCAUGAUAAAUGGUGCGGGUUAGAAAUCCAACACAGCGAGGGUAGUAU
.....(..(((((((...........)))))))..)...........(((((((.((((((.(((.....((((((.....)))))))))))))))..(((......).))))))))).. ( -40.40)
>sy_haemo.rRNA 2539826 120 - 2685023
CCUUUGAGCGCCUCCGUUACCUUUUAGGAGGCGACCGCCCCAGUCAAACUGCCCGCCUGACACUGUCUCCCACCACGAUAAGUGGUGCGGGUUAGAAAGCCAACACAGCUAGGGUAGUAU
.....(..(((((((...........)))))))..)...........(((((((..(((((.(((.....((((((.....))))))))))))))..(((.......))).))))))).. ( -43.20)
>sy_aureus.rRNA 2276044 120 - 2809430
CCUUUGAGCGCCUCCGUUACCUUUUAGGAGGCGACCGCCCCAGUCAAACUGCCCGCCUGACACUGUCUCCCACCACGAUAAGUGGUGCGGGUUAGAAAGCCAACACAGCUAGGGUAGUAU
.....(..(((((((...........)))))))..)...........(((((((..(((((.(((.....((((((.....))))))))))))))..(((.......))).))))))).. ( -43.20)
>consensus
CCUUUGAGCGCCUCCGUUACCUUUUAGGAGGCGACCGCCCCAGUCAAACUGCCCGCCUGACACUGUCUCCCACCACGAUAAGUGGUGCGGGUUAGAAAGCCAACACAGCUAGGGUAGUAU
.....(..(((((((...........)))))))..)...........(((((((..(((.........((((((((.....)))))).))(((.(....).))).)))...))))))).. (-41.11 = -40.67 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,350,937 – 2,351,057
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.56
Mean single sequence MFE -47.23
Consensus MFE -47.68
Energy contribution -47.13
Covariance contribution -0.55
Combinations/Pair 1.08
Mean z-score -1.92
Structure conservation index 1.01
SVM decision value 1.20
SVM RNA-class probability 0.929149
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2350937 120 - 2516583
AUACUACCCUCGCUGUGUUGGAUUUCUAACCCGCACCAUUUAUCAUGGUGGGAGACAGUGUCAGAUGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAGAGUAACGGAGGCGCUCAAAGG
..((..((((.((((((((((....)))))((.((((((.....))))))))..)))))(((((((.....))))))).))))..))(((((((...........)))))))........ ( -44.50)
>sy_haemo.rRNA 2539826 120 + 2685023
AUACUACCCUAGCUGUGUUGGCUUUCUAACCCGCACCACUUAUCGUGGUGGGAGACAGUGUCAGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCUCAAAGG
..((..(((((((((((((((....)))))((.((((((.....))))))))..)))))(((((((.....))))))))))))..))(((((((...........)))))))........ ( -48.60)
>sy_aureus.rRNA 2276044 120 + 2809430
AUACUACCCUAGCUGUGUUGGCUUUCUAACCCGCACCACUUAUCGUGGUGGGAGACAGUGUCAGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCUCAAAGG
..((..(((((((((((((((....)))))((.((((((.....))))))))..)))))(((((((.....))))))))))))..))(((((((...........)))))))........ ( -48.60)
>consensus
AUACUACCCUAGCUGUGUUGGCUUUCUAACCCGCACCACUUAUCGUGGUGGGAGACAGUGUCAGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCUCAAAGG
..((..(((((((((((((((....)))))((.((((((.....))))))))..)))))(((((((.....))))))))))))..))(((((((...........)))))))........ (-47.68 = -47.13 +  -0.55) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,350,977 – 2,351,097
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 94.44
Mean single sequence MFE -34.50
Consensus MFE -33.21
Energy contribution -32.77
Covariance contribution -0.44
Combinations/Pair 1.03
Mean z-score -1.48
Structure conservation index 0.96
SVM decision value 0.11
SVM RNA-class probability 0.587640
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2350977 120 + 2516583
CAGUCAAACUGCCCAUCUGACACUGUCUCCCACCAUGAUAAAUGGUGCGGGUUAGAAAUCCAACACAGCGAGGGUAGUAUCCCACCAACGCCUCCACGUAAGCUAGCGCUCACGUAUCUC
.......(((((((.((((((.(((.....((((((.....)))))))))))))))..(((......).))))))))).................((((.(((....))).))))..... ( -32.90)
>sy_haemo.rRNA 2539866 120 - 2685023
CAGUCAAACUGCCCGCCUGACACUGUCUCCCACCACGAUAAGUGGUGCGGGUUAGAAAGCCAACACAGCUAGGGUAGUAUCCCACCAGCGCCUCCACGUAAGCUAGCGCUCACGUUUCAA
.......(((((((..(((((.(((.....((((((.....))))))))))))))..(((.......))).)))))))........(((((.....(....)...))))).......... ( -35.30)
>sy_aureus.rRNA 2276084 120 - 2809430
CAGUCAAACUGCCCGCCUGACACUGUCUCCCACCACGAUAAGUGGUGCGGGUUAGAAAGCCAACACAGCUAGGGUAGUAUCCCACCAGCGCCUCCACGUAAGCUAGCGCUCACGUUUCAA
.......(((((((..(((((.(((.....((((((.....))))))))))))))..(((.......))).)))))))........(((((.....(....)...))))).......... ( -35.30)
>consensus
CAGUCAAACUGCCCGCCUGACACUGUCUCCCACCACGAUAAGUGGUGCGGGUUAGAAAGCCAACACAGCUAGGGUAGUAUCCCACCAGCGCCUCCACGUAAGCUAGCGCUCACGUUUCAA
.......(((((((..(((.........((((((((.....)))))).))(((.(....).))).)))...))))))).................((((.(((....))).))))..... (-33.21 = -32.77 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,350,977 – 2,351,097
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.44
Mean single sequence MFE -46.20
Consensus MFE -45.22
Energy contribution -44.33
Covariance contribution -0.88
Combinations/Pair 1.08
Mean z-score -1.69
Structure conservation index 0.98
SVM decision value 0.61
SVM RNA-class probability 0.799581
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2350977 120 - 2516583
GAGAUACGUGAGCGCUAGCUUACGUGGAGGCGUUGGUGGGAUACUACCCUCGCUGUGUUGGAUUUCUAACCCGCACCAUUUAUCAUGGUGGGAGACAGUGUCAGAUGGGCAGUUUGACUG
(((.(((((((((....)))))))))........(((((....))))))))((((((((((....)))))((.((((((.....))))))))..)))))(((((((.....))))))).. ( -46.80)
>sy_haemo.rRNA 2539866 120 + 2685023
UUGAAACGUGAGCGCUAGCUUACGUGGAGGCGCUGGUGGGAUACUACCCUAGCUGUGUUGGCUUUCUAACCCGCACCACUUAUCGUGGUGGGAGACAGUGUCAGGCGGGCAGUUUGACUG
.....((((((((....)))))))).((.(((((((.((.......))))))).)).)).(((.(((...((.((((((.....))))))))))).)))(((((((.....))))))).. ( -45.90)
>sy_aureus.rRNA 2276084 120 + 2809430
UUGAAACGUGAGCGCUAGCUUACGUGGAGGCGCUGGUGGGAUACUACCCUAGCUGUGUUGGCUUUCUAACCCGCACCACUUAUCGUGGUGGGAGACAGUGUCAGGCGGGCAGUUUGACUG
.....((((((((....)))))))).((.(((((((.((.......))))))).)).)).(((.(((...((.((((((.....))))))))))).)))(((((((.....))))))).. ( -45.90)
>consensus
UUGAAACGUGAGCGCUAGCUUACGUGGAGGCGCUGGUGGGAUACUACCCUAGCUGUGUUGGCUUUCUAACCCGCACCACUUAUCGUGGUGGGAGACAGUGUCAGGCGGGCAGUUUGACUG
.....((((((((....)))))))).........(((((....)))))...((((((((((....)))))((.((((((.....))))))))..)))))(((((((.....))))))).. (-45.22 = -44.33 +  -0.88) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,351,017 – 2,351,137
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -46.90
Consensus MFE -43.63
Energy contribution -43.97
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.64
Structure conservation index 0.93
SVM decision value 1.44
SVM RNA-class probability 0.954387
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2351017 120 - 2516583
UUGAAAUUCGGCACAGCUUGUACAGGAUAGGUAGGAGCCUGAGAUACGUGAGCGCUAGCUUACGUGGAGGCGUUGGUGGGAUACUACCCUCGCUGUGUUGGAUUUCUAACCCGCACCAUU
..(((((((((((((((((.(((.......))).))((((....(((((((((....))))))))).))))(..(((((....)))))..)))))))))))))))).............. ( -49.70)
>sy_haemo.rRNA 2539906 120 + 2685023
UUGAAAUUCGGCACAGCUUGUACAGGAUAGGUAGGAGCCUUUGAAACGUGAGCGCUAGCUUACGUGGAGGCGCUGGUGGGAUACUACCCUAGCUGUGUUGGCUUUCUAACCCGCACCACU
..((((..((((((((((.(.............((.(((((....((((((((....)))))))).))))).))(((((....)))))).))))))))))..)))).............. ( -45.50)
>sy_aureus.rRNA 2276124 120 + 2809430
UUGAAAUUCGGCACAGCUUGUACAGGAUAGGUAGGAGCCUUUGAAACGUGAGCGCUAGCUUACGUGGAGGCGCUGGUGGGAUACUACCCUAGCUGUGUUGGCUUUCUAACCCGCACCACU
..((((..((((((((((.(.............((.(((((....((((((((....)))))))).))))).))(((((....)))))).))))))))))..)))).............. ( -45.50)
>consensus
UUGAAAUUCGGCACAGCUUGUACAGGAUAGGUAGGAGCCUUUGAAACGUGAGCGCUAGCUUACGUGGAGGCGCUGGUGGGAUACUACCCUAGCUGUGUUGGCUUUCUAACCCGCACCACU
..((((.((((((((((((.(((.......))).))(((((....((((((((....)))))))).)))))...(((((....)))))...)))))))))).)))).............. (-43.63 = -43.97 +   0.33) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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