Locus 47

Sequence ID	sy_sapro.rRNA
Location	2,352,176 – 2,352,536
Length	360
Max. P	0.997133

overview

Window 0

Location	2,352,176 – 2,352,296
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-35.64
Consensus MFE	-35.94
Energy contribution	-35.83
Covariance contribution	-0.11
Combinations/Pair	1.06
Mean z-score	-2.52
Structure conservation index	1.01
SVM decision value	1.88
SVM RNA-class probability	0.981278
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2352176 120 - 2516583
CCGAAUGCCAAUCAAUUUAACUUGGGAGUCAGAACGCGGGUGAUAAGGUCCGUGUUCGAAAGGGAAACAGCCCAGACCACCAGCUAAGGUCCCAAAAUAUAUGUUAAGUGGAAAAGGAUG
.......((..((.((((((((((((((((.(((((((((........)))))))))....(((......))).)))..((......)))))))).......))))))).))...))... ( -34.11)
>sy_haemo.rRNA 2541064 120 + 2685023
CCGAAUGCCAAUUAAUUUAACUUGGGAGUCAGAACACGGGUGAUAAGGUCCGUGUUCGAAAGGGAAACAGCCCAGACCACCAGCUAAGGUCCCAAAAUAUAUGUUAAGUGGAAAAGGAUG
((.....(((.(((((.((..(((((((((.(((((((((........)))))))))....(((......))).)))..((......))))))))..))...))))).)))....))... ( -37.30)
>sy_aureus.rRNA 2277283 120 + 2809430
CCGAAUGCCAAUUAAUUUAACUUGGGAGUCAGAACAUGGGUGAUAAGGUCCGUGUUCGAAAGGGAAACAGCCCAGACCACCAGCUAAGGUCCCAAAAUAUAUGUUAAGUGGAAAAGGAUG
((.....(((.(((((.((..(((((((((.(((((((((........)))))))))....(((......))).)))..((......))))))))..))...))))).)))....))... ( -35.50)
>consensus
CCGAAUGCCAAUUAAUUUAACUUGGGAGUCAGAACACGGGUGAUAAGGUCCGUGUUCGAAAGGGAAACAGCCCAGACCACCAGCUAAGGUCCCAAAAUAUAUGUUAAGUGGAAAAGGAUG
((.....(((.(((((.((..(((((((((.(((((((((........)))))))))....(((......))).)))..((......))))))))..))...))))).)))....))... (-35.94 = -35.83 +  -0.11) 
# Strand winner: reverse (0.95)

alignment

secondary structure

dotplot

Window 1

Location	2,352,296 – 2,352,416
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-39.57
Consensus MFE	-37.91
Energy contribution	-37.80
Covariance contribution	-0.11
Combinations/Pair	1.05
Mean z-score	-1.48
Structure conservation index	0.96
SVM decision value	-0.03
SVM RNA-class probability	0.517695
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2352296 120 - 2516583
ACCUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGGGCUAGCCUCAAGUGAUGAUUAUUGGAGGUAGAGCACUGUUUGGACGAGGGGCCCUUAUCGGGUUACCGAAUUCAGACAAACU
.(((((((.((..(((......)))...)).)))))))(((.(((((.(((((...))))).)))))..)))..((((((((...(((((((.....))))).))...)))))))).... ( -38.20)
>sy_haemo.rRNA 2541184 120 + 2685023
ACUUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGGGCUAGCCUCAAGUGAUGAUUAUUGGAGGUAGAGCACUGUUUGGACGAGGGGCCCCUCUCGGGUUACCGAAUUCAGACAAACU
..(((((((.((....)).)))))))..(((((....)))))(((((.(((((...))))).))))).......((((((((.((((....))))((((....)))).)))))))).... ( -39.50)
>sy_aureus.rRNA 2277403 120 + 2809430
ACCUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGGGCUAGCCUCAAGUGAUGAUUAUUGGAGGUAGAGCACUGUUUGGACGAGGGGCCCCUCUCGGGUUACCGAAUUCAGACAAACU
.(((((((.((..(((......)))...)).)))))))(((.(((((.(((((...))))).)))))..)))..((((((((.((((....))))((((....)))).)))))))).... ( -41.00)
>consensus
ACCUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGGGCUAGCCUCAAGUGAUGAUUAUUGGAGGUAGAGCACUGUUUGGACGAGGGGCCCCUCUCGGGUUACCGAAUUCAGACAAACU
.(((((((.((..(((......)))...)).)))))))(((.(((((.(((((...))))).)))))..)))..((((((((.((((....))))((((....)))).)))))))).... (-37.91 = -37.80 +  -0.11) 
# Strand winner: reverse (1.00)

alignment

secondary structure

dotplot

Window 2

Location	2,352,416 – 2,352,536
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	96.67
Mean single sequence MFE	-41.57
Consensus MFE	-42.86
Energy contribution	-41.53
Covariance contribution	-1.33
Combinations/Pair	1.08
Mean z-score	-3.44
Structure conservation index	1.03
SVM decision value	2.80
SVM RNA-class probability	0.997133
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_sapro.rRNA 2352416 120 - 2516583
GAAACCAGGUGAUCUACCCAUGACCAGGUUGAAGUUCAGGUAACACUGAAUGGAGGACCGAACCGACUUACGUUGAAAAGUGAGCGGAUGAGUUGUGGGUAGCGGAGAAAUUCCAAUCGA
.......(((...(((((((..((((((((...((((((......))))))....))))...(((.(((((........)))))))).)).))..))))))).((((...)))).))).. ( -41.60)
>sy_haemo.rRNA 2541304 120 + 2685023
GAAACCAGGUGAUCUACCCAUGGUCAGGUUGAAGUUCAGGUAACACUGAAUGGAGGACCGAACCGACUUACGUUGAAAAGUGAGCGGAUGAACUGUGGGUAGCGGAGAAAUUCCAAUCGA
.......(((...(((((((((((((((((...((((((......))))))....))))...(((.(((((........)))))))).)).))))))))))).((((...)))).))).. ( -41.40)
>sy_aureus.rRNA 2277523 120 + 2809430
GAAACCAGGUGAUCUACCCUUGGUCAGGUUGAAGUUCAGGUAACACUGAAUGGAGGACCGAACCGACUUACGUUGAAAAGUGAGCGGAUGAACUGAGGGUAGCGGAGAAAUUCCAAUCGA
.......(((...(((((((..((((((((...((((((......))))))....))))...(((.(((((........)))))))).)).))..))))))).((((...)))).))).. ( -41.70)
>consensus
GAAACCAGGUGAUCUACCCAUGGUCAGGUUGAAGUUCAGGUAACACUGAAUGGAGGACCGAACCGACUUACGUUGAAAAGUGAGCGGAUGAACUGUGGGUAGCGGAGAAAUUCCAAUCGA
.......(((...(((((((..((((((((...((((((......))))))....))))...(((.(((((........)))))))).)).))..))))))).((((...)))).))).. (-42.86 = -41.53 +  -1.33) 
# Strand winner: reverse (0.99)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Fri Apr 7 15:52:27 2006