Locus 11

Sequence ID	sy_aureus.rRNA
Location	582,351 – 582,511
Length	160
Max. P	0.868291

overview

Window 4

Location	582,351 – 582,471
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	99.17
Mean single sequence MFE	-56.30
Consensus MFE	-56.38
Energy contribution	-56.00
Covariance contribution	-0.38
Combinations/Pair	1.02
Mean z-score	-2.23
Structure conservation index	1.00
SVM decision value	0.86
SVM RNA-class probability	0.868291
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_aureus.rRNA 582351 120 + 2809430
ACAUCGACGGGGAGGUUUGGCACCUCGAUGUCGGCUCAUCGCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGUACGCGAGCUGGGUUCAGAACGUCG
....(((((..(((((.....)))))((..((((((((((((((((((((((((....))))))).)))))(((((.....))))).....)))))....)))))))..))....))))) ( -54.80)
>sp_agal.rRNA 20716 120 + 2160275
ACAUCGACGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCG
....(((((..(((((.....)))))((..((((((((((((((((((((((((....))))))).)))))(((((.....))))).....)))....)))))))))..))....))))) ( -56.80)
>sp_mutans.rRNA 21295 120 + 2030929
ACAUCGACGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCG
....(((((..(((((.....)))))((..((((((((((((((((((((((((....))))))).)))))(((((.....))))).....)))....)))))))))..))....))))) ( -56.80)
>sp_pneumo.rRNA 19426 120 + 2038623
ACAUCGACGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCG
....(((((..(((((.....)))))((..((((((((((((((((((((((((....))))))).)))))(((((.....))))).....)))....)))))))))..))....))))) ( -56.80)
>consensus
ACAUCGACGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCG
....(((((..(((((.....)))))((..((((((((((((((((((((((((....))))))).)))))(((((.....))))).....)))))....)))))))..))....))))) (-56.38 = -56.00 +  -0.38)

alignment

secondary structure

dotplot

Window 5

Location	582,391 – 582,511
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	98.75
Mean single sequence MFE	-52.25
Consensus MFE	-49.50
Energy contribution	-52.12
Covariance contribution	2.62
Combinations/Pair	1.05
Mean z-score	-1.75
Structure conservation index	0.95
SVM decision value	0.05
SVM RNA-class probability	0.561142
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_aureus.rRNA 582391 120 + 2809430
GCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGUACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCCCUAUCCGUCGUGGGCGUAGGAAAU
((((((((((((((....))))))).)))))(((((.....))))).....)).(..((((((.((((..(.(((((((....))).)))).)..))))..).)))))..)......... ( -50.00)
>sp_agal.rRNA 20756 120 + 2160275
GCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCCCUAUCCGUCGCGGGCGUAGGAAAU
((((((((((((((....))))))).)))))(((((.....))))).....)).((.((((((.((((..(.(((((((....))).)))).)..))))..).))))).))......... ( -53.00)
>sp_mutans.rRNA 21335 120 + 2030929
GCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCCCUAUCCGUCGCGGGCGAAGGAAAU
((((((((((((((....))))))).)))))(((((.....))))).....)).((.((((((.((((..(.(((((((....))).)))).)..))))..).))))).))......... ( -53.00)
>sp_pneumo.rRNA 19466 120 + 2038623
GCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCCCUAUCCGUCGCGGGCGUAGGAAAU
((((((((((((((....))))))).)))))(((((.....))))).....)).((.((((((.((((..(.(((((((....))).)))).)..))))..).))))).))......... ( -53.00)
>consensus
GCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCCCUAUCCGUCGCGGGCGUAGGAAAU
((((((((((((((....))))))).)))))(((((.....))))).....)).((.((((((.((((..(.(((((((....))).)))).)..))))..).))))).))......... (-49.50 = -52.12 +   2.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Fri Apr 7 15:51:05 2006