Locus 12

Sequence ID	sy_aureus.rRNA
Location	582,551 – 582,763
Length	212
Max. P	0.743276

overview

Window 6

Location	582,551 – 582,668
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.47
Mean single sequence MFE	-38.10
Consensus MFE	-37.51
Energy contribution	-35.70
Covariance contribution	-1.81
Combinations/Pair	1.26
Mean z-score	-1.32
Structure conservation index	0.98
SVM decision value	0.46
SVM RNA-class probability	0.743276
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_aureus.rRNA 582551 117 + 2809430
CAUACCUCUGGUGUACCAGUUGUCGUGCCAACGGCAUAGCUGGGUAGCUAUGUGUGGACGGGAUAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCCCCUCAAGAUGAGAUUUCCC---AAC
(((((...((((...(((((((((((....))))))..)))))...)))).)))))...((((...(((((...........))))).........(((.....)))...))))---... ( -35.50)
>sp_agal.rRNA 20916 120 + 2160275
CUUACCGCUGGUGUACCAGUUGUCUUGCCAAAGGCAUCGCUGGGUAGCUAUGUAGGGAAGGGAUAAGCGCUGAAAGCAUCUAAGUGCGAAGCCCACCUCAAGAUGAGAUUUCCCAUGAUU
......((((((...(((((((((((....))))))..)))))...)))).)).((((((((....(((((...........)))))....)))..(((.....)))..)))))...... ( -39.90)
>sp_mutans.rRNA 21495 120 + 2030929
CUUACCGCUGGUGUACCAGUUGUUCUGCCAAGAGCAUCGCUGGGUAGCUAAGUAGGGAGGGGAUAAACGCUGAAAGCAUCUAAGUGUGAAGCCCCCCUCAAGAUGAGAUUUCCCAUAACG
......((((((...(((((((((((....))))))..)))))...))).))).((((((((....(((((...........)))))....)))).(((.....)))...))))...... ( -40.10)
>sp_pneumo.rRNA 19626 120 + 2038623
CUUACCGCUGGUGUACCAGUUGUCUUGCCAAAGGCAUCGCUGGGUAGCUAUGUAGGGAAGGGAUAAACGCUGAAAGCAUCUAAGUGUGAAACCCACCUCAAGAUGAGAUUUCCCAUGAUU
......((((((...(((((((((((....))))))..)))))...)))).)).((((((((....(((((...........)))))....)))..(((.....)))..)))))...... ( -36.90)
>consensus
CUUACCGCUGGUGUACCAGUUGUCUUGCCAAAGGCAUCGCUGGGUAGCUAUGUAGGGAAGGGAUAAACGCUGAAAGCAUCUAAGUGUGAAGCCCACCUCAAGAUGAGAUUUCCCAUGAUU
..(((...((((...(((((((((((....))))))..)))))...)))).)))((((((((....(((((...........)))))....)))..(((.....)))..)))))...... (-37.51 = -35.70 +  -1.81)

alignment

secondary structure

dotplot

Window 7

Location	582,631 – 582,747
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	80.42
Mean single sequence MFE	-27.12
Consensus MFE	-17.48
Energy contribution	-16.67
Covariance contribution	-0.81
Combinations/Pair	1.26
Mean z-score	-1.66
Structure conservation index	0.64
SVM decision value	0.02
SVM RNA-class probability	0.541337
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_aureus.rRNA 582631 116 - 2809430
AUUCGUCAGCUCCACAUGUCACCAUGCUUCCACCUCGAACCUAUUAACCUCAUCAUCUUUGAGGGAUCUUA-UAACCGAAGUU---GGGAAAUCUCAUCUUGAGGGGGGCUUCAUGCUUA
.......((((((.((((....))))......((((...........(((((.......))))).......-......(((.(---(((....)))).)))))))))))))......... ( -29.40)
>sp_agal.rRNA 20996 120 - 2160275
AUUAGUCCGCUAAAUGUGUCACCACAAUUACACUCCUAACCUAUCUACCUGAUCAUCUCUCAGGGCUCUUACUGAUAUAAAAUCAUGGGAAAUCUCAUCUUGAGGUGGGCUUCGCACUUA
...(((((((....((((....)))).......(((((.........(((((.......)))))........((((.....)))))))))...(((.....))))))))))......... ( -25.80)
>sp_mutans.rRNA 21575 120 - 2030929
AUUGGUCCGCUUCACGUCUCACAACGCUUCCACUCCCAACCUAUCUACCUGUUCUUCUCUCAGGGCUCUUACUAACUGAACGUUAUGGGAAAUCUCAUCUUGAGGGGGGCUUCACACUUA
...(((((.((((((((......))).......(((((.........((((.........))))........((((.....)))))))))..........))))).)))))......... ( -26.30)
>sp_pneumo.rRNA 19706 120 - 2038623
AUUAGUCCGCUACAUGUGUCGCCACACUUCCACUUCUAACCUAUCUACCUGAUCAUCUCUCAGGGCUCUUACUGAUAUAUAAUCAUGGGAAAUCUCAUCUUGAGGUGGGUUUCACACUUA
..(((....)))..((((..(((.((((((.................(((((.......)))))..(((((.((((.....)))))))))...........)))))))))..)))).... ( -27.00)
>consensus
AUUAGUCCGCUACACGUGUCACCACACUUCCACUCCUAACCUAUCUACCUGAUCAUCUCUCAGGGCUCUUACUAACAGAAAAUCAUGGGAAAUCUCAUCUUGAGGGGGGCUUCACACUUA
.((((.........((((....)))).........))))(((((((.(((((.......)))))......................(((....)))......)))))))........... (-17.48 = -16.67 +  -0.81) 
# Strand winner: forward (0.99)

alignment

secondary structure

dotplot

Window 8

Location	582,647 – 582,763
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.25
Mean single sequence MFE	-31.72
Consensus MFE	-26.79
Energy contribution	-26.23
Covariance contribution	-0.56
Combinations/Pair	1.29
Mean z-score	-1.46
Structure conservation index	0.84
SVM decision value	0.20
SVM RNA-class probability	0.629534
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_aureus.rRNA 582647 116 + 2809430
CUCAAGAUGAGAUUUCCC---AACUUCGGUUA-UAAGAUCCCUCAAAGAUGAUGAGGUUAAUAGGUUCGAGGUGGAAGCAUGGUGACAUGUGGAGCUGACGAAUACUAAUCGAUCGAAGA
(((.....))).......---..((((((((.-.......(((((.......)))))....((((((((.(((....(((((....)))))...)))..))))).)))...)))))))). ( -33.80)
>sp_agal.rRNA 21012 120 + 2160275
CUCAAGAUGAGAUUUCCCAUGAUUUUAUAUCAGUAAGAGCCCUGAGAGAUGAUCAGGUAGAUAGGUUAGGAGUGUAAUUGUGGUGACACAUUUAGCGGACUAAUACUAAUAGCUCGAGGA
(((...((((((((......))))))))........(((((((((.......)))))....((((((((..((.(((.((((....)))).)))))...))))).)))...))))))).. ( -32.90)
>sp_mutans.rRNA 21591 120 + 2030929
CUCAAGAUGAGAUUUCCCAUAACGUUCAGUUAGUAAGAGCCCUGAGAGAAGAACAGGUAGAUAGGUUGGGAGUGGAAGCGUUGUGAGACGUGAAGCGGACCAAUACUAAUCGCUCGAGGA
(((.....)))...((((.((((.....))))....((((((((.........))))..((((((((((..((....(((((....)))))...))...))))).)).)))))))).))) ( -29.60)
>sp_pneumo.rRNA 19722 120 + 2038623
CUCAAGAUGAGAUUUCCCAUGAUUAUAUAUCAGUAAGAGCCCUGAGAGAUGAUCAGGUAGAUAGGUUAGAAGUGGAAGUGUGGCGACACAUGUAGCGGACUAAUACUAAUAGCUCGAGGA
(((.....)))...((((.((((.....))))....(((((((((.......)))))....((((((((..((....(((((....)))))...))...))))).)))...))))).))) ( -30.60)
>consensus
CUCAAGAUGAGAUUUCCCAUGAUUUUAUAUCAGUAAGAGCCCUGAGAGAUGAUCAGGUAGAUAGGUUAGAAGUGGAAGCGUGGUGACACAUGUAGCGGACUAAUACUAAUAGCUCGAGGA
(((.....))).((((...((((.....))))....(((((((((.......)))))....((((((((..((....(((((....)))))...))...))))).)))...)))))))). (-26.79 = -26.23 +  -0.56)

alignment

secondary structure

dotplot

Window 9

Location	582,647 – 582,763
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	81.25
Mean single sequence MFE	-24.24
Consensus MFE	-20.62
Energy contribution	-19.74
Covariance contribution	-0.88
Combinations/Pair	1.29
Mean z-score	-1.53
Structure conservation index	0.85
SVM decision value	0.36
SVM RNA-class probability	0.704954
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_aureus.rRNA 582647 116 - 2809430
UCUUCGAUCGAUUAGUAUUCGUCAGCUCCACAUGUCACCAUGCUUCCACCUCGAACCUAUUAACCUCAUCAUCUUUGAGGGAUCUUA-UAACCGAAGUU---GGGAAAUCUCAUCUUGAG
.....((((..((((((((((.........((((....)))).........))))..))))))(((((.......)))))))))...-......(((.(---(((....)))).)))... ( -22.17)
>sp_agal.rRNA 21012 120 - 2160275
UCCUCGAGCUAUUAGUAUUAGUCCGCUAAAUGUGUCACCACAAUUACACUCCUAACCUAUCUACCUGAUCAUCUCUCAGGGCUCUUACUGAUAUAAAAUCAUGGGAAAUCUCAUCUUGAG
..((((((.((((((((..((((((.(((.((((....)))).))))...........(((.....))).........)))))..)))))))).......(((((....))))))))))) ( -26.90)
>sp_mutans.rRNA 21591 120 - 2030929
UCCUCGAGCGAUUAGUAUUGGUCCGCUUCACGUCUCACAACGCUUCCACUCCCAACCUAUCUACCUGUUCUUCUCUCAGGGCUCUUACUAACUGAACGUUAUGGGAAAUCUCAUCUUGAG
..((((((.((((((..(((....((.....))....)))..)).....(((((.........((((.........))))........((((.....)))))))))))))....)))))) ( -21.50)
>sp_pneumo.rRNA 19722 120 - 2038623
UCCUCGAGCUAUUAGUAUUAGUCCGCUACAUGUGUCGCCACACUUCCACUUCUAACCUAUCUACCUGAUCAUCUCUCAGGGCUCUUACUGAUAUAUAAUCAUGGGAAAUCUCAUCUUGAG
..((((((.((((((((..(((((.......((((....))))...............(((.....))).........)))))..)))))))).......(((((....))))))))))) ( -26.40)
>consensus
UCCUCGAGCGAUUAGUAUUAGUCCGCUACACGUGUCACCACACUUCCACUCCUAACCUAUCUACCUGAUCAUCUCUCAGGGCUCUUACUAACAGAAAAUCAUGGGAAAUCUCAUCUUGAG
..(((((((((((((((((((.........((((....)))).........))))........(((((.......))))).....)))))))))........(((....)))..)))))) (-20.62 = -19.74 +  -0.88) 
# Strand winner: forward (1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Fri Apr 7 15:51:09 2006