Locus 3

Sequence ID	sy_aureus.rRNA
Location	576,942 – 577,085
Length	143
Max. P	0.942494

overview

Window 8

Location	576,942 – 577,050
Length	108
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	63.88
Mean single sequence MFE	-36.30
Consensus MFE	-18.16
Energy contribution	-20.85
Covariance contribution	2.69
Combinations/Pair	1.40
Mean z-score	-1.84
Structure conservation index	0.50
SVM decision value	1.33
SVM RNA-class probability	0.942494
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_aureus.rRNA 576942 108 + 2809430
UGACUGGGGCGGUCGCCUCCUAAAA----GGUAACGGAGGCGCUCAAAGGUUCCCUCAGAAUGGUUGGAAAUCAUUCAUAGAGUGUAAAGGCAUAAGGG--------AGCUUGACUGCGA
........((((((((((((.....----......))))))......(((((((((..(((((((.....))))))).....((((....)))).))))--------))))))))))).. ( -41.80)
>sp_agal.rRNA 17617 108 + 2160275
-------------UGCCCCUUAUGACCUGGGCUACACACGUGCUACAAUGGUUGGUACAACGAGUCGCAAGCCGGUGACGGCAAGCUAAUCUCUUAAAGCCAAUCUCAGUUCGGAUUGUA
-------------.((((..........))))((((..((.(((.....(((((((.....(((..((..((((....))))..))....))).....)))))))..))).))...)))) ( -32.70)
>sp_mutans.rRNA 18091 108 + 2030929
-------------UGCCCCUUAUGACCUGGGCUACACACGUGCUACAAUGGUCGGUACAACGAGUUGCGAGCCGGUGACGGCAAGCUAAUCUCUGAAAGCCGAUCUCAGUUCGGAUUGGA
-------------....((...(((.((((((.((....))))).....(((((((.....(((..((..((((....))))..))....))).....))))))).))).)))....)). ( -35.70)
>sp_pneumo.rRNA 16362 108 + 2038623
-------------UGCCCCUUAUGACCUGGGCUACACACGUGCUACAAUGGCUGGUACAACGAGUCGCAAGCCGGUGACGGCAAGCUAAUCUCUUAAAGCCAGUCUCAGUUCGGAUUGUA
-------------.((((..........))))((((..((.(((.....(((((((.....(((..((..((((....))))..))....))).....)))))))..))).))...)))) ( -35.00)
>consensus
_____________UGCCCCUUAUGACCUGGGCUACACACGUGCUACAAUGGUCGGUACAACGAGUCGCAAGCCGGUGACGGCAAGCUAAUCUCUUAAAGCCAAUCUCAGUUCGGAUUGGA
..............((((..........))))......((.(((.....(((((((.....(((..((..((((....))))..))....))).....)))))))..))).))....... (-18.16 = -20.85 +   2.69)

alignment

secondary structure

dotplot

Window 9

Location	576,978 – 577,085
Length	107
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	68.09
Mean single sequence MFE	-40.98
Consensus MFE	-15.27
Energy contribution	-18.15
Covariance contribution	2.88
Combinations/Pair	1.39
Mean z-score	-2.69
Structure conservation index	0.37
SVM decision value	0.81
SVM RNA-class probability	0.856572
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_aureus.rRNA 576978 107 + 2809430
CGCUCAAAGGUUCCCUCAGAAUGGUUGGAAAUCAUUCAUAGAGUGUAAAGGCAUAAGGG--------AGCUUGACUGCGAGACCUACAAGUCGA--GCAGGGUCGAAAGACGGACU---U
.((((..(((((((((..(((((((.....))))))).....((((....)))).))))--------)))))((((............))))))--))...(((....))).....---. ( -36.50)
>sp_agal.rRNA 17645 114 + 2160275
UGCUACAAUGGUUGGUACAACGAGUCGCAAGCCGGUGACGGCAAGCUAAUCUCUUAAAGCCAAUCUCAGUUCGGAUUGUAGG-CUGCAACUCGCCUACAUG-----AAGUCGGAAUCGCU
.((......(((((((.....(((..((..((((....))))..))....))).....)))))))...((((.(((((((((-(........)))))))..-----..))).)))).)). ( -39.80)
>sp_mutans.rRNA 18119 114 + 2030929
UGCUACAAUGGUCGGUACAACGAGUUGCGAGCCGGUGACGGCAAGCUAAUCUCUGAAAGCCGAUCUCAGUUCGGAUUGGAGG-CUGCAACUCGCCUCCAUG-----AAGUCGGAAUCGCU
.((......(((((((.....(((..((..((((....))))..))....))).....)))))))...((((.(((((((((-(........)))))))..-----..))).)))).)). ( -45.50)
>sp_pneumo.rRNA 16390 114 + 2038623
UGCUACAAUGGCUGGUACAACGAGUCGCAAGCCGGUGACGGCAAGCUAAUCUCUUAAAGCCAGUCUCAGUUCGGAUUGUAGG-CUGCAACUCGCCUACAUG-----AAGUCGGAAUCGCU
.((......(((((((.....(((..((..((((....))))..))....))).....)))))))...((((.(((((((((-(........)))))))..-----..))).)))).)). ( -42.10)
>consensus
UGCUACAAUGGUCGGUACAACGAGUCGCAAGCCGGUGACGGCAAGCUAAUCUCUUAAAGCCAAUCUCAGUUCGGAUUGGAGG_CUGCAACUCGCCUACAUG_____AAGUCGGAAUCGCU
..((((((((((((((.....(((..((..((((....))))..))....))).....))))))).........)))))))....................................... (-15.27 = -18.15 +   2.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Fri Apr 7 15:50:31 2006