Locus 5

Sequence ID	sy_aureus.rRNA
Location	580,446 – 580,685
Length	239
Max. P	0.999573

overview

Window 0

Location	580,446 – 580,565
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.28
Mean single sequence MFE	-35.19
Consensus MFE	-38.59
Energy contribution	-35.09
Covariance contribution	-3.50
Combinations/Pair	1.38
Mean z-score	-1.60
Structure conservation index	1.10
SVM decision value	2.21
SVM RNA-class probability	0.990283
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_aureus.rRNA 580446 119 + 2809430
GAUGGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUUUGAUGCAAGGUUAAGCAGUAAAUGUGGAGCCGUAGCGAAAGCGAGUCUGAAUAGGGCG-UUUAGUAUUUGGUCGUAGAC
....((.((((................)))).))((((((..(((((..((((..(((.....)))..))))...((....))..((((.....)))).-....)))))..))))))... ( -31.79)
>sp_agal.rRNA 18822 120 + 2160275
GAGAGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUAUGAUGCGAGGUUAAGUUGAAGAGACGGAGCCGUAGGGAAACCGAGUCUUAAUAGGGCGUCAUAGUAUCAUGUUGUAGAC
....((.((((................)))).))(((((((((((((..((((..(((.....)))..))))...((....))((((((.....)))).))...)))))))))))))... ( -35.79)
>sp_mutans.rRNA 19402 120 + 2030929
GAGAGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGUUUACGUGCGAGGUUAAGUUGAAGAGACGAAGCCGUAGGGAAACCGAGUCUGAAAAGGGCGGUUAAGUACGUAGAUGUAGAC
....((.((((................)))).))(((((((((((((........(((.....)))..((((((.((....))...(((....)))))))))..)))))))))))))... ( -36.19)
>sp_pneumo.rRNA 17532 120 + 2038623
GAGAGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGUUAUGAUGCGAGGUUAAGUUGAAGAGACGGAGCCGUAGGGAAACCGAGUCUGAAUAGGGCACCUUAGUAUCAUGACGUAGAC
....((.((((................)))).))((((((((((((((((((............(((....))).((....))..((((.....))))))))).)))))))))))))... ( -36.99)
>consensus
GAGAGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUAUGAUGCGAGGUUAAGUUGAAGAGACGGAGCCGUAGGGAAACCGAGUCUGAAUAGGGCG_CUUAGUAUCAUGACGUAGAC
....((.((((................)))).))(((((((((((((..((((..(((.....)))..))))...((....))..((((.....))))......)))))))))))))... (-38.59 = -35.09 +  -3.50)

alignment

secondary structure

dotplot

Window 1

Location	580,565 – 580,685
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.61
Mean single sequence MFE	-42.85
Consensus MFE	-46.74
Energy contribution	-42.80
Covariance contribution	-3.94
Combinations/Pair	1.33
Mean z-score	-3.03
Structure conservation index	1.09
SVM decision value	3.74
SVM RNA-class probability	0.999573
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_aureus.rRNA 580565 120 + 2809430
CCGAAACCAGGUGAUCUACCCUUGGUCAGGUUGAAGUUCAGGUAACACUGAAUGGAGGACCGAACCGACUUACGUUGAAAAGUGAGCGGAUGAACUGAGGGUAGCGGAGAAAUUCCAAUC
((.......))....(((((((..((((((((...((((((......))))))....))))...(((.(((((........)))))))).)).))..))))))).((((...)))).... ( -41.20)
>sp_agal.rRNA 18942 120 + 2160275
CCGAAACCAUGUGACCUACCCAUGAGCAGGUUGAAGGUGAGGUAAAACUCACUGGAGGACCGAACCAGGGCACGUUGAAAAGUGCUUGGAUGACUUGUGGGUAGCGGAGAAAUUCCAAAC
...............(((((((..((((((((...((((((......))))))....))))...(((((.(((........)))))))).)).))..))))))).((((...)))).... ( -43.20)
>sp_mutans.rRNA 19522 120 + 2030929
CCGAAACCAAGUGACCUACCCAUGAGCAGGUUGAAGGUGCGGUAAAACGCACUGGAGGACCGAACCAGGACACGUUGAAAAGUGUUUGGAUGACUUGUGGGUAGCGGAGAAAUUCCAAAC
...............(((((((..((((((((...((((((......))))))....))))...((((.((((........)))))))).)).))..))))))).((((...)))).... ( -42.50)
>sp_pneumo.rRNA 17652 120 + 2038623
CCGAAACCAUGUGACCUACCCAUGAGCAGGUUGAAGGUGCGGUAAGACGCACUGGAGGACCGAACCAGGGCACGUUGAAAAGUGCUUGGAUGACUUGUGGGUAGCGGAGAAAUUCCAAAC
...............(((((((..((((((((...((((((......))))))....))))...(((((.(((........)))))))).)).))..))))))).((((...)))).... ( -44.50)
>consensus
CCGAAACCAUGUGACCUACCCAUGAGCAGGUUGAAGGUGAGGUAAAACGCACUGGAGGACCGAACCAGGGCACGUUGAAAAGUGCUUGGAUGACUUGUGGGUAGCGGAGAAAUUCCAAAC
...............(((((((..((((((((...((((((......))))))....))))...(((.(((((........)))))))).)).))..))))))).((((...)))).... (-46.74 = -42.80 +  -3.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Fri Apr 7 15:50:42 2006