Locus 42

Sequence ID sy_sapro.rRNA
Location 2,305,740 – 2,306,140
Length 400
Max. P 0.994136
window114 window115 window116 window117 window118 window119 window120

overview

Window 4

Location 2,305,740 – 2,305,860
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -38.97
Consensus MFE -39.63
Energy contribution -38.97
Covariance contribution -0.66
Combinations/Pair 1.07
Mean z-score -1.30
Structure conservation index 1.02
SVM decision value 0.02
SVM RNA-class probability 0.545607
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2305740 120 - 2516583
CUACGGGAGGCAGCAGUAGGGAAUCUUCCGCAAUGGGCGAAAGCCUGACGGAGCAACGCCGCGUGAGUGAUGAAGGGUUUCGGCUCGUAAAACUCUGUUAUUAGGGAAGAACAAACGUGU
((((...........))))....((((((.....((((....))))(((((((...((.(((....))).))..((((....))))......))))))).....)))))).......... ( -36.70)
>sy_haemo.rRNA 2543563 120 + 2685023
CUACGGGAGGCAGCAGUAGGGAAUCUUCCGCAAUGGGCGAAAGCCUGACGGAGCAACGCCGCGUGAGUGAUGAAGGUCUUCGGAUCGUAAAACUCUGUUAUUAGGGAAGAACAUACGUGU
((((...........))))....((((((.....((((....))))(((((((...((.(((....))).))..((((....))))......))))))).....)))))).......... ( -40.10)
>sy_aureus.rRNA 2279811 120 + 2809430
CUACGGGAGGCAGCAGUAGGGAAUCUUCCGCAAUGGGCGAAAGCCUGACGGAGCAACGCCGCGUGAGUGAUGAAGGUCUUCGGAUCGUAAAACUCUGUUAUUAGGGAAGAACAUAUGUGU
((((...........))))....((((((.....((((....))))(((((((...((.(((....))).))..((((....))))......))))))).....)))))).......... ( -40.10)
>consensus
CUACGGGAGGCAGCAGUAGGGAAUCUUCCGCAAUGGGCGAAAGCCUGACGGAGCAACGCCGCGUGAGUGAUGAAGGUCUUCGGAUCGUAAAACUCUGUUAUUAGGGAAGAACAUACGUGU
((((...........))))....((((((.....((((....))))(((((((...((.(((....))).))..((((....))))......))))))).....)))))).......... (-39.63 = -38.97 +  -0.66) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,305,860 – 2,305,980
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -43.21
Consensus MFE -42.37
Energy contribution -42.04
Covariance contribution -0.33
Combinations/Pair 1.06
Mean z-score -2.40
Structure conservation index 0.98
SVM decision value 1.64
SVM RNA-class probability 0.969532
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2305860 120 + 2516583
GAGUCUGGACCGUGUCUCAGUUCCAGUGUGGCCGAUCACCCUCUCAGGUCGGCUACGUAUCGUCGCCUUGGUAAGCCGUUACCUUACCAACUAGCUAAUACGGCGCGGGUCCAUCUAUAA
.....(((((((((((...........((((((((((.........))))))))))((((....((.((((((((.......))))))))...))..))))))))).))))))....... ( -43.90)
>sy_haemo.rRNA 2543683 120 - 2685023
GAGUCUGGACCGUGUCUCAGUUCCAGUGUGGCCGAUCACCCUCUCAGGUCGGCUACGUAUCGUCGCCUUGGUAAGCCGUUACCUUACCAACUAACUAAUACGGCGCGGGUCCAUCUAUAA
.....(((((((((((...........((((((((((.........))))))))))((((.......((((((((.......)))))))).......))))))))).))))))....... ( -43.34)
>sy_aureus.rRNA 2279931 120 - 2809430
GAGUCUGGACCGUGUCUCAGUUCCAGUGUGGCCGAUCACCCUCUCAGGUCGGCUAUGCAUCGUUGCCUUGGUAAGCCGUUACCUUACCAACUAGCUAAUGCAGCGCGGAUCCAUCUAUAA
.....((((((((((..((......((((((((((((.........))))))))))))...((((..((((((((.......)))))))).))))...))..)))))).))))....... ( -42.40)
>consensus
GAGUCUGGACCGUGUCUCAGUUCCAGUGUGGCCGAUCACCCUCUCAGGUCGGCUACGUAUCGUCGCCUUGGUAAGCCGUUACCUUACCAACUAGCUAAUACGGCGCGGGUCCAUCUAUAA
.....(((((((((((...........((((((((((.........))))))))))((((.......((((((((.......)))))))).......))))))))))).))))....... (-42.37 = -42.04 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,305,940 – 2,306,060
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.33
Mean single sequence MFE -30.30
Consensus MFE -28.23
Energy contribution -28.23
Covariance contribution 0.01
Combinations/Pair 1.09
Mean z-score -2.01
Structure conservation index 0.93
SVM decision value 0.78
SVM RNA-class probability 0.849511
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2305940 120 + 2516583
ACCUUACCAACUAGCUAAUACGGCGCGGGUCCAUCUAUAAGUGAUAGCAAAACCAUCUUUCACUUUAGAACCAUGCGGUUCCAAAUGUUAUCCGGUAUUAGCUCCGGUUUCCCGAAGUUA
........(((((((((((((.(.((((((...((((.((((((.((.........)).))))))))))))).)))(((..(....)..)))).))))))))).(((....))).)))). ( -29.70)
>sy_haemo.rRNA 2543763 120 - 2685023
ACCUUACCAACUAACUAAUACGGCGCGGGUCCAUCUAUAAGUGAUAGCAAAACCAUCUUUCACUAUCGAACCAUGCGGUUCGAAAUAUUAUCCGGUAUUAGCUCCGGUUUCCCGAAGUUA
........((((..(((((((....(((((.........(((((.((.........)).))))).(((((((....)))))))......))))))))))))...(((....))).)))). ( -28.20)
>sy_aureus.rRNA 2280011 120 - 2809430
ACCUUACCAACUAGCUAAUGCAGCGCGGAUCCAUCUAUAAGUGACAGCAAGACCGUCUUUCACUUUUGAACCAUGCGGUUCAAAAUAUUAUCCGGUAUUAGCUCCGGUUUCCCGAAGUUA
........(((((((((((((....(((((..........((((.(((......).)).))))(((((((((....)))))))))....)))))))))))))).(((....))).)))). ( -33.00)
>consensus
ACCUUACCAACUAGCUAAUACGGCGCGGGUCCAUCUAUAAGUGAUAGCAAAACCAUCUUUCACUUUAGAACCAUGCGGUUCAAAAUAUUAUCCGGUAUUAGCUCCGGUUUCCCGAAGUUA
........(((((((((((((....(((((.........(((((.((.........)).))))).(((((((....)))))))......)))))))))))))).(((....))).)))). (-28.23 = -28.23 +   0.01)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,305,940 – 2,306,060
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.33
Mean single sequence MFE -38.50
Consensus MFE -37.52
Energy contribution -36.63
Covariance contribution -0.88
Combinations/Pair 1.13
Mean z-score -2.50
Structure conservation index 0.97
SVM decision value 1.90
SVM RNA-class probability 0.981769
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2305940 120 - 2516583
UAACUUCGGGAAACCGGAGCUAAUACCGGAUAACAUUUGGAACCGCAUGGUUCUAAAGUGAAAGAUGGUUUUGCUAUCACUUAUAGAUGGACCCGCGCCGUAUUAGCUAGUUGGUAAGGU
(((((((((....))))(((((((((.((......(((((((((....)))))))))(((...(((((.....))))).((.......))...))).))))))))))))))))....... ( -38.90)
>sy_haemo.rRNA 2543763 120 + 2685023
UAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUCGAACCGCAUGGUUCGAUAGUGAAAGAUGGUUUUGCUAUCACUUAUAGAUGGACCCGCGCCGUAUUAGUUAGUUGGUAAGGU
(((((((((....))))(((((((((((((......))))...(((..((((((((((..(((.....)))..))))).(.....)..))))).)))..))))))))))))))....... ( -37.20)
>sy_aureus.rRNA 2280011 120 + 2809430
UAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUUGAACCGCAUGGUUCAAAAGUGAAAGACGGUCUUGCUGUCACUUAUAGAUGGAUCCGCGCUGCAUUAGCUAGUUGGUAAGGU
...((((((....))))))....((((((((....(((((((((....)))))))))((((..(((((.....)))))..))))......))))..(((((....)).))).)))).... ( -39.40)
>consensus
UAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUCGAACCGCAUGGUUCAAAAGUGAAAGAUGGUUUUGCUAUCACUUAUAGAUGGACCCGCGCCGUAUUAGCUAGUUGGUAAGGU
(((((((((....))))(((((((((.((......(((((((((....)))))))))(((...(((((.....))))).((.......))...))).))))))))))))))))....... (-37.52 = -36.63 +  -0.88) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,305,980 – 2,306,100
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -29.53
Consensus MFE -27.92
Energy contribution -28.70
Covariance contribution 0.78
Combinations/Pair 1.03
Mean z-score -1.50
Structure conservation index 0.95
SVM decision value -0.02
SVM RNA-class probability 0.521849
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2305980 120 + 2516583
GUGAUAGCAAAACCAUCUUUCACUUUAGAACCAUGCGGUUCCAAAUGUUAUCCGGUAUUAGCUCCGGUUUCCCGAAGUUAUCCCAGUCUUAUAGGUAGGUUACCCACGUGUUACUCACCC
(((((((((..(((.......(((((.(((((....))))).))).)).....((...(((((.(((....))).)))))..)).........))).((....))...))))).)))).. ( -26.40)
>sy_haemo.rRNA 2543803 120 - 2685023
GUGAUAGCAAAACCAUCUUUCACUAUCGAACCAUGCGGUUCGAAAUAUUAUCCGGUAUUAGCUCCGGUUUCCCGAAGUUAUCCCAGUCUUAUAGGUAGGUUACCCACGUGUUACUCACCC
(((((((((.((((((((...(((.(((((((....)))))))..........((...(((((.(((....))).)))))..))))).....)))).)))).......))))).)))).. ( -31.20)
>sy_aureus.rRNA 2280051 120 - 2809430
GUGACAGCAAGACCGUCUUUCACUUUUGAACCAUGCGGUUCAAAAUAUUAUCCGGUAUUAGCUCCGGUUUCCCGAAGUUAUCCCAGUCUUAUAGGUAGGUUAUCCACGUGUUACUCACCC
((((((..(((((..........(((((((((....)))))))))........((...(((((.(((....))).)))))..)).)))))....((.((....)))).))))))...... ( -31.00)
>consensus
GUGAUAGCAAAACCAUCUUUCACUUUAGAACCAUGCGGUUCAAAAUAUUAUCCGGUAUUAGCUCCGGUUUCCCGAAGUUAUCCCAGUCUUAUAGGUAGGUUACCCACGUGUUACUCACCC
(((((((((..(((.........(((((((((....)))))))))........((...(((((.(((....))).)))))..)).........))).((....))...))))).)))).. (-27.92 = -28.70 +   0.78)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,305,980 – 2,306,100
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -39.63
Consensus MFE -39.44
Energy contribution -39.00
Covariance contribution -0.44
Combinations/Pair 1.08
Mean z-score -2.98
Structure conservation index 1.00
SVM decision value 2.45
SVM RNA-class probability 0.994136
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2305980 120 - 2516583
GGGUGAGUAACACGUGGGUAACCUACCUAUAAGACUGGGAUAACUUCGGGAAACCGGAGCUAAUACCGGAUAACAUUUGGAACCGCAUGGUUCUAAAGUGAAAGAUGGUUUUGCUAUCAC
..........((((((((((...)))))))....((((..((.((((((....)))))).))...))))......(((((((((....))))))))))))...(((((.....))))).. ( -40.40)
>sy_haemo.rRNA 2543803 120 + 2685023
GGGUGAGUAACACGUGGGUAACCUACCUAUAAGACUGGGAUAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUCGAACCGCAUGGUUCGAUAGUGAAAGAUGGUUUUGCUAUCAC
..........((((((((((...)))))))....((((..((.((((((....)))))).))...))))........(((((((....)))))))..)))...(((((.....))))).. ( -40.00)
>sy_aureus.rRNA 2280051 120 + 2809430
GGGUGAGUAACACGUGGAUAACCUACCUAUAAGACUGGGAUAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUUGAACCGCAUGGUUCAAAAGUGAAAGACGGUCUUGCUGUCAC
..........(((((((.....))))........((((..((.((((((....)))))).))...))))......(((((((((....))))))))))))...(((((.....))))).. ( -38.50)
>consensus
GGGUGAGUAACACGUGGGUAACCUACCUAUAAGACUGGGAUAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUCGAACCGCAUGGUUCAAAAGUGAAAGAUGGUUUUGCUAUCAC
..........((((((((((...)))))))....((((..((.((((((....)))))).))...))))......(((((((((....))))))))))))...(((((.....))))).. (-39.44 = -39.00 +  -0.44) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,306,020 – 2,306,140
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.17
Mean single sequence MFE -37.93
Consensus MFE -34.93
Energy contribution -34.60
Covariance contribution -0.33
Combinations/Pair 1.09
Mean z-score -1.69
Structure conservation index 0.92
SVM decision value 0.15
SVM RNA-class probability 0.607092
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2306020 120 - 2516583
AACAGAUAAGGAGCUUGCUCCUUUGACGUUAGCGGCGGACGGGUGAGUAACACGUGGGUAACCUACCUAUAAGACUGGGAUAACUUCGGGAAACCGGAGCUAAUACCGGAUAACAUUUGG
..(((((..(..(((..(((.((((.((....)).)))).)))..)))..)..(((((((...)))))))....((((..((.((((((....)))))).))...)))).....))))). ( -39.70)
>sy_haemo.rRNA 2543843 120 + 2685023
AACAGACAAGGAGCUUGCUCCUUUGACGUUAGCGGCGGACGGGUGAGUAACACGUGGGUAACCUACCUAUAAGACUGGGAUAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUCG
.........(..(((..(((.((((.((....)).)))).)))..)))..)..(((((((...)))))))....((((..((.((((((....)))))).))...))))........... ( -37.30)
>sy_aureus.rRNA 2280091 120 + 2809430
AACGGACGAGAAGCUUGCUUCUCUGAUGUUAGCGGCGGACGGGUGAGUAACACGUGGAUAACCUACCUAUAAGACUGGGAUAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUUG
..(((..((((((....))))))...(((((((((....((.(((.....))).)).....))..((((......)))).....(((((....)))))))))))))))............ ( -36.80)
>consensus
AACAGACAAGGAGCUUGCUCCUUUGACGUUAGCGGCGGACGGGUGAGUAACACGUGGGUAACCUACCUAUAAGACUGGGAUAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUCG
.........(..(((..(((.((((.((....)).)))).)))..)))..)..(((((((...)))))))....((((..((.((((((....)))))).))...))))........... (-34.93 = -34.60 +  -0.33) 
# 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 15:52:07 2006