Locus 46

Sequence ID sy_sapro.rRNA
Location 2,351,617 – 2,352,056
Length 439
Max. P 0.997464
window132 window133 window134 window135 window136 window137 window138 window139

overview

Window 2

Location 2,351,617 – 2,351,736
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 89.42
Mean single sequence MFE -28.37
Consensus MFE -26.31
Energy contribution -25.53
Covariance contribution -0.77
Combinations/Pair 1.11
Mean z-score -2.24
Structure conservation index 0.93
SVM decision value 1.34
SVM RNA-class probability 0.943568
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2351617 119 + 2516583
ACAAUUCUAGCUAGAGGCUUUUCUUGGCAGUGUGAAAUCAACGACUCGAGGAAACAAUUUCCUCUCCCCAUCACAGCUCAAUCUUAA-GAGUGCCGGAUUUGCCUAACACUCAAUCUCAC
..............((((...(((.(((..(((((..((...))...((((((.....))))))......)))))((((........-))))))))))...))))............... ( -27.00)
>sy_haemo.rRNA 2540506 119 - 2685023
UAUUAUCUAUCUAGAGGCUUUUCUCGGCAGUGUGAAAUCAACGACUCGAGGAAACAAUUUCCUCUCCCCAUCACAGCUCAAUCUUAA-GAGUGCCGGAUUUGCCUAACACUCAAUCUCAC
..............((((...((.((((..(((((..((...))...((((((.....))))))......)))))((((........-))))))))))...))))............... ( -29.20)
>sy_aureus.rRNA 2276724 120 - 2809430
UAUUUUCUAUCUAGAGGCUUUUCUCGGCAGUGUGAAAUCAACGACUCGAAGACACAAUGUCUUCUCCCCAUCACAGCUCAGCCUUAACGAGUACCGGAUUUGCCUAAUACUCAGCCUUAC
.............((((((......((((((((((..((...))...((((((.....))))))......))))).))..))).....(((((..((.....))...))))))))))).. ( -28.90)
>consensus
UAUUUUCUAUCUAGAGGCUUUUCUCGGCAGUGUGAAAUCAACGACUCGAGGAAACAAUUUCCUCUCCCCAUCACAGCUCAAUCUUAA_GAGUGCCGGAUUUGCCUAACACUCAAUCUCAC
..............((((...((.((((..(((((..((...))...((((((.....))))))......)))))((((.........))))))))))...))))............... (-26.31 = -25.53 +  -0.77)

alignment

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secondary structure

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Window 3

Location 2,351,657 – 2,351,776
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 91.64
Mean single sequence MFE -24.10
Consensus MFE -24.79
Energy contribution -22.80
Covariance contribution -1.99
Combinations/Pair 1.23
Mean z-score -1.96
Structure conservation index 1.03
SVM decision value 1.89
SVM RNA-class probability 0.981416
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2351657 119 + 2516583
ACGACUCGAGGAAACAAUUUCCUCUCCCCAUCACAGCUCAAUCUUAA-GAGUGCCGGAUUUGCCUAACACUCAAUCUCACUGCUUGGACGUACAAUCCAAUCGUACGCUUCGCCUAUCCU
.......((((((.....)))))).......................-(((((..((.....))...))))).........((..((.(((((.........)))))))..))....... ( -22.60)
>sy_haemo.rRNA 2540546 119 - 2685023
ACGACUCGAGGAAACAAUUUCCUCUCCCCAUCACAGCUCAAUCUUAA-GAGUGCCGGAUUUGCCUAACACUCAAUCUCACUGCUUAGACGUACAAUCCAAUCGUACGCUUCGCCUAUCCU
.......((((((.....)))))).......................-(((((..((.....))...))))).........((..((.(((((.........)))))))..))....... ( -22.60)
>sy_aureus.rRNA 2276764 120 - 2809430
ACGACUCGAAGACACAAUGUCUUCUCCCCAUCACAGCUCAGCCUUAACGAGUACCGGAUUUGCCUAAUACUCAGCCUUACUGCUUAGACGUGCAAUCCAAUCGCACGCUUCGCCUAUCCU
...((((((((((.....))))))...........((...))......))))...((((..((......((.(((......))).)).(((((.........)))))....))..)))). ( -27.10)
>consensus
ACGACUCGAGGAAACAAUUUCCUCUCCCCAUCACAGCUCAAUCUUAA_GAGUGCCGGAUUUGCCUAACACUCAAUCUCACUGCUUAGACGUACAAUCCAAUCGUACGCUUCGCCUAUCCU
.......((((((.....))))))........................(((((..((.....))...))))).........((..((.(((((.........)))))))..))....... (-24.79 = -22.80 +  -1.99)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,351,657 – 2,351,776
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 91.64
Mean single sequence MFE -38.67
Consensus MFE -41.28
Energy contribution -38.40
Covariance contribution -2.88
Combinations/Pair 1.18
Mean z-score -2.33
Structure conservation index 1.07
SVM decision value 2.86
SVM RNA-class probability 0.997464
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2351657 119 - 2516583
AGGAUAGGCGAAGCGUACGAUUGGAUUGUACGUCCAAGCAGUGAGAUUGAGUGUUAGGCAAAUCCGGCACUC-UUAAGAUUGAGCUGUGAUGGGGAGAGGAAAUUGUUUCCUCGAGUCGU
......(((...(((((((((...)))))))))(((.(((((..((((((((((..((....))..))))))-....))))..)))))..)))...((((((.....))))))..))).. ( -39.20)
>sy_haemo.rRNA 2540546 119 + 2685023
AGGAUAGGCGAAGCGUACGAUUGGAUUGUACGUCUAAGCAGUGAGAUUGAGUGUUAGGCAAAUCCGGCACUC-UUAAGAUUGAGCUGUGAUGGGGAGAGGAAAUUGUUUCCUCGAGUCGU
......(((...(((((((((...)))))))))(((.(((((..((((((((((..((....))..))))))-....))))..)))))..)))...((((((.....))))))..))).. ( -36.90)
>sy_aureus.rRNA 2276764 120 + 2809430
AGGAUAGGCGAAGCGUGCGAUUGGAUUGCACGUCUAAGCAGUAAGGCUGAGUAUUAGGCAAAUCCGGUACUCGUUAAGGCUGAGCUGUGAUGGGGAGAAGACAUUGUGUCUUCGAGUCGU
......(((...(((((((((...)))))))))(((.(((((..((((((((((..((....))..)))))).....))))..)))))..)))...((((((.....))))))..))).. ( -39.90)
>consensus
AGGAUAGGCGAAGCGUACGAUUGGAUUGUACGUCUAAGCAGUGAGAUUGAGUGUUAGGCAAAUCCGGCACUC_UUAAGAUUGAGCUGUGAUGGGGAGAGGAAAUUGUUUCCUCGAGUCGU
......(((...(((((((((...)))))))))(((.(((((..((((((((((..((....))..)))))).....))))..)))))..)))...((((((.....))))))..))).. (-41.28 = -38.40 +  -2.88) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,351,776 – 2,351,896
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -44.73
Consensus MFE -41.97
Energy contribution -42.30
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.61
Structure conservation index 0.94
SVM decision value 0.07
SVM RNA-class probability 0.568756
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2351776 120 - 2516583
AAGGCUCGUCCGCUCUGGGUUAGUCGGGUCCUAAGCUGAGGCCGAUAGGCGUAGGCGAUGGAUAACAGGUUGAUAUUCCUGUACCACCAUUAUUCGUUUUAAGCGAUGGGGGGACGCAGU
...((((((((.(((..(((.....((((((...(((.(.(((....))).).)))...)))).(((((........))))).))))).....((((.....)))).))).))))).))) ( -42.80)
>sy_haemo.rRNA 2540665 120 + 2685023
AAGGCUCGUCCGCUCUGGGUUAGUCGGGUCCUAAGCUGAGGCCGACAGGCGUAGGCGAUGGAUAACAGGUUGAUAUUCCUGUACCACCUAGCAUCGUUUUAAUCGAUGGGGGGACGCAGU
...((((((((.(((...(((((..((((((...(((.(.(((....))).).)))...)))).(((((........))))).))..)))))((((.......))))))).))))).))) ( -47.20)
>sy_aureus.rRNA 2276884 120 + 2809430
AAGGCUCGUCCGCUCUGGGUUAGUCGGGUCCUAAGCUGAGGCCGACAGGCGUAGGCGAUGGAUAACAGGUUGAUAUUCCUGUACCACCUAUAAUCGUUUUAAUCGAUGGGGGGACGCAGU
...((((((((((.(((.((..(((((..(((......))))))))..)).)))))..(((...(((((........))))).)))(((...((((.......)))).)))))))).))) ( -44.20)
>consensus
AAGGCUCGUCCGCUCUGGGUUAGUCGGGUCCUAAGCUGAGGCCGACAGGCGUAGGCGAUGGAUAACAGGUUGAUAUUCCUGUACCACCUAUAAUCGUUUUAAUCGAUGGGGGGACGCAGU
...((((((((.((((.((((((.(((((((...(((.(.(((....))).).)))...)))).(((((........)))))...........)))..)))))).).))).))))).))) (-41.97 = -42.30 +   0.33) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,351,856 – 2,351,976
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 100.00
Mean single sequence MFE -39.50
Consensus MFE -39.50
Energy contribution -39.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.09
Structure conservation index 1.00
SVM decision value 2.12
SVM RNA-class probability 0.988451
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2351856 120 + 2516583
CUCAGCUUAGGACCCGACUAACCCAGAGCGGACGAGCCUUCCUCUGGAAACCUUAGUCAAUCGGUGGACGGGAUUCUCACCCGUCUUUCGCUACUCACACCGGCAUUCUCACUUCUAAGC
....((((((((...((((((.((((((.(((......))))))))).....))))))..((((((((((((.......))))))....(.....).)))))).........)))))))) ( -39.50)
>sy_haemo.rRNA 2540745 120 - 2685023
CUCAGCUUAGGACCCGACUAACCCAGAGCGGACGAGCCUUCCUCUGGAAACCUUAGUCAAUCGGUGGACGGGAUUCUCACCCGUCUUUCGCUACUCACACCGGCAUUCUCACUUCUAAGC
....((((((((...((((((.((((((.(((......))))))))).....))))))..((((((((((((.......))))))....(.....).)))))).........)))))))) ( -39.50)
>sy_aureus.rRNA 2276964 120 - 2809430
CUCAGCUUAGGACCCGACUAACCCAGAGCGGACGAGCCUUCCUCUGGAAACCUUAGUCAAUCGGUGGACGGGAUUCUCACCCGUCUUUCGCUACUCACACCGGCAUUCUCACUUCUAAGC
....((((((((...((((((.((((((.(((......))))))))).....))))))..((((((((((((.......))))))....(.....).)))))).........)))))))) ( -39.50)
>consensus
CUCAGCUUAGGACCCGACUAACCCAGAGCGGACGAGCCUUCCUCUGGAAACCUUAGUCAAUCGGUGGACGGGAUUCUCACCCGUCUUUCGCUACUCACACCGGCAUUCUCACUUCUAAGC
....((((((((...((((((.((((((.(((......))))))))).....))))))..((((((((((((.......))))))....(.....).)))))).........)))))))) (-39.50 = -39.50 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,351,896 – 2,352,016
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 99.44
Mean single sequence MFE -37.97
Consensus MFE -37.97
Energy contribution -37.97
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.38
Structure conservation index 1.00
SVM decision value 0.07
SVM RNA-class probability 0.568939
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2351896 120 - 2516583
UCUAAGGGCGUUGAAGCAUGAUCGCAAGGACAUGUGGAGCGCUUAGAAGUGAGAAUGCCGGUGUGAGUAGCGAAAGACGGGUGAGAAUCCCGUCCACCGAUUGACUAAGGUUUCCAGAGG
((((((.((......(((((.((....)).)))))...)).))))))..((.(((.(((...((.(((..((...((((((.......))))))...))))).))...)))))))).... ( -38.30)
>sy_haemo.rRNA 2540785 120 + 2685023
UCUAAGGGCGUUGAAGCAUGAUCGCAAGGACAUGUGGAGCGCUUAGAAGUGAGAAUGCCGGUGUGAGUAGCGAAAGACGGGUGAGAAUCCCGUCCACCGAUUGACUAAGGUUUCCAGAGG
((((((.((......(((((.((....)).)))))...)).))))))..((.(((.(((...((.(((..((...((((((.......))))))...))))).))...)))))))).... ( -38.30)
>sy_aureus.rRNA 2277004 120 + 2809430
UCUAAGGGCGUUGAAGCAUGAUCGUAAGGACAUGUGGAGCGCUUAGAAGUGAGAAUGCCGGUGUGAGUAGCGAAAGACGGGUGAGAAUCCCGUCCACCGAUUGACUAAGGUUUCCAGAGG
((((((.((......(((((.((....)).)))))...)).))))))..((.(((.(((...((.(((..((...((((((.......))))))...))))).))...)))))))).... ( -37.30)
>consensus
UCUAAGGGCGUUGAAGCAUGAUCGCAAGGACAUGUGGAGCGCUUAGAAGUGAGAAUGCCGGUGUGAGUAGCGAAAGACGGGUGAGAAUCCCGUCCACCGAUUGACUAAGGUUUCCAGAGG
((((((.((......(((((.((....)).)))))...)).))))))..((.(((.(((...((.(((..((...((((((.......))))))...))))).))...)))))))).... (-37.97 = -37.97 +  -0.00) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,351,936 – 2,352,056
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.77
Mean single sequence MFE -20.41
Consensus MFE -21.44
Energy contribution -21.44
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.51
Structure conservation index 1.05
SVM decision value 0.61
SVM RNA-class probability 0.799716
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2351936 120 + 2516583
CCGUCUUUCGCUACUCACACCGGCAUUCUCACUUCUAAGCGCUCCACAUGUCCUUGCGAUCAUGCUUCAACGCCCUUAGAACGCUCUCCUACCAUUGUCCUUACGGACAAUCCACAGCUU
.........(((.........((.........(((((((.((....((((((.....)).)))).......)).)))))))..........))(((((((....)))))))....))).. ( -21.41)
>sy_haemo.rRNA 2540825 119 - 2685023
CCGUCUUUCGCUACUCACACCGGCAUUCUCACUUCUAAGCGCUCCACAUGUCCUUGCGAUCAUGCUUCAACGCCCUUAGAACGCUCUCCUACCAUUGUCCU-ACGGACAAUCCACAGCUU
.........(((.........((.........(((((((.((....((((((.....)).)))).......)).)))))))..........))(((((((.-..)))))))....))).. ( -19.91)
>sy_aureus.rRNA 2277044 119 - 2809430
CCGUCUUUCGCUACUCACACCGGCAUUCUCACUUCUAAGCGCUCCACAUGUCCUUACGAUCAUGCUUCAACGCCCUUAGAACGCUCUCCUACCAUUGUCCA-AAGGACAAUCCACAGCUU
.........(((.........((.........(((((((.((....((((((.....)).)))).......)).)))))))..........))(((((((.-..)))))))....))).. ( -19.91)
>consensus
CCGUCUUUCGCUACUCACACCGGCAUUCUCACUUCUAAGCGCUCCACAUGUCCUUGCGAUCAUGCUUCAACGCCCUUAGAACGCUCUCCUACCAUUGUCCU_ACGGACAAUCCACAGCUU
.........(((.........((.........(((((((.((....((((((.....)).)))).......)).)))))))..........))(((((((....)))))))....))).. (-21.44 = -21.44 +   0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,351,936 – 2,352,056
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.77
Mean single sequence MFE -39.90
Consensus MFE -41.37
Energy contribution -41.37
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.60
Structure conservation index 1.04
SVM decision value 2.74
SVM RNA-class probability 0.996718
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2351936 120 - 2516583
AAGCUGUGGAUUGUCCGUAAGGACAAUGGUAGGAGAGCGUUCUAAGGGCGUUGAAGCAUGAUCGCAAGGACAUGUGGAGCGCUUAGAAGUGAGAAUGCCGGUGUGAGUAGCGAAAGACGG
..((((...(((((((....)))))))((((.....((.(((((((.((......(((((.((....)).)))))...)).))))))))).....))))........))))......... ( -43.10)
>sy_haemo.rRNA 2540825 119 + 2685023
AAGCUGUGGAUUGUCCGU-AGGACAAUGGUAGGAGAGCGUUCUAAGGGCGUUGAAGCAUGAUCGCAAGGACAUGUGGAGCGCUUAGAAGUGAGAAUGCCGGUGUGAGUAGCGAAAGACGG
..((((...(((((((..-.)))))))((((.....((.(((((((.((......(((((.((....)).)))))...)).))))))))).....))))........))))......... ( -38.80)
>sy_aureus.rRNA 2277044 119 + 2809430
AAGCUGUGGAUUGUCCUU-UGGACAAUGGUAGGAGAGCGUUCUAAGGGCGUUGAAGCAUGAUCGUAAGGACAUGUGGAGCGCUUAGAAGUGAGAAUGCCGGUGUGAGUAGCGAAAGACGG
..((((...(((((((..-.)))))))((((.....((.(((((((.((......(((((.((....)).)))))...)).))))))))).....))))........))))......... ( -37.80)
>consensus
AAGCUGUGGAUUGUCCGU_AGGACAAUGGUAGGAGAGCGUUCUAAGGGCGUUGAAGCAUGAUCGCAAGGACAUGUGGAGCGCUUAGAAGUGAGAAUGCCGGUGUGAGUAGCGAAAGACGG
..((((...(((((((....)))))))((((.....((.(((((((.((......(((((.((....)).)))))...)).))))))))).....))))........))))......... (-41.37 = -41.37 +   0.00) 
# 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 15:52:24 2006