Locus 2

Sequence ID sy_aureus.rRNA
Location 576,302 – 576,651
Length 349
Max. P 0.999747
window4 window5 window6 window7

overview

Window 4

Location 576,302 – 576,411
Length 109
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 62.05
Mean single sequence MFE -30.77
Consensus MFE -15.71
Energy contribution -17.02
Covariance contribution 1.31
Combinations/Pair 1.50
Mean z-score -1.69
Structure conservation index 0.51
SVM decision value 1.23
SVM RNA-class probability 0.934105
Prediction RNA

Download alignment: ClustalW | MAF

>sy_aureus.rRNA 576302 109 + 2809430
AAAAUAGGUGCCCGUACCGCAAACCGACACAGGUAGUCAAGAUGAGAAUUCUAAGGUGA------GCGAGCGAACUCUCG-----UUAAGGAACUCGGCAAAAUGACCCCGUAACUUCGG
........((((.((.((((..((((((.......))).(((.......)))..)))..------)).(((((....)))-----))..)).))..))))........(((......))) ( -24.20)
>sp_agal.rRNA 16974 105 + 2160275
----UUAUUGGGCGUA----AAGCGAGCGCAGGCGGUUC----UUUAAGUCUGAAGUUAAAGGCAGUGGCUUAACCAUUGUACGCUUUGGAAACUGGAGGACUUGAGUGCAGAA----GG
----.......((...----..))..((((....(((((----((((..((..((((.....(((((((.....)))))))..))))..))...)))))))))...))))....----.. ( -31.80)
>sp_mutans.rRNA 17448 105 + 2030929
----UUAUUGGGCGUA----AAGGGAGCGCAGGCGGUCA----GGAAAGUCUGGAGUAAAAGGCUAUGGCUCAACCAUAGUGUGCUCUGGAAACUGUCUGACUUGAGUGCAGAA----GG
----.......((...----......))(((..((((((----((....((..(((((....(((((((.....))))))).)))))..)).....)))))).))..)))....----.. ( -35.20)
>sp_pneumo.rRNA 15719 105 + 2038623
----UUAUUGGGCGUA----AAGCGAGCGCAGGCGGUUA----GAUAAGUCUGAAGUUAAAGGCUGUGGCUUAACCAUAGUAGGCUUUGGAAACUGUUUAACUUGAGUGCAAGA----GG
----.......((...----..))..((((....(((((----((((..((..(((((....(((((((.....))))))).)))))..))...)))))))))...))))....----.. ( -31.90)
>consensus
____UUAUUGGGCGUA____AAGCGAGCGCAGGCGGUCA____GAUAAGUCUGAAGUUAAAGGCUGUGGCUUAACCAUAGUA_GCUUUGGAAACUGGAUAACUUGAGUGCAGAA____GG
...........((((...........))))..(((.(((....((((..(((((((((....(((((((.....))))))).)))))))))...)))).....))).))).......... (-15.71 = -17.02 +   1.31)

alignment

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secondary structure

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dotplot

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Window 5

Location 576,411 – 576,512
Length 101
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 67.96
Mean single sequence MFE -37.77
Consensus MFE -21.69
Energy contribution -20.88
Covariance contribution -0.81
Combinations/Pair 1.39
Mean z-score -2.29
Structure conservation index 0.57
SVM decision value 2.99
SVM RNA-class probability 0.998055
Prediction RNA

Download alignment: ClustalW | MAF

>sy_aureus.rRNA 576411 101 + 2809430
GAGAAGGGGUGCUCUUUAGG--------------GUUAACGCCCAGAAGAGCCGCAGUGAAUAGGCCCAAGCGACU-----GUUUAUCAAAAACACAGGUCUCUGCUAAACCGUAAGGUG
((((..(.(.(((((((.((--------------((....)))).)))))))).).((((((((((....))..))-----))))))............))))......(((....))). ( -31.20)
>sp_agal.rRNA 17079 112 + 2160275
GGAGAGUGGAAUUCCAUGUGUAGCGGUGAAAUGCGUAGAUAUAUGGAGGAACACCGGU-----GGCGAAAGCGGCUCUCUGGUCUGUAACUGACGCUGAGGCUCG--AAAGCGU-GGGGA
((((((((...((((((((((.(((......)))....))))))))))...)))..((-----.((....)).))))))).........((.(((((........--..)))))-.)).. ( -39.60)
>sp_mutans.rRNA 17553 112 + 2030929
GGAGAGUGGAAUUCCAUGUGUAGCGGUGAAAUGCGUAGAUAUAUGGAGGAACACCAGU-----GGCGAAAGCGGCUCUCUGGUCUGUCACUGACGCUGAGGCUCG--AAAGCGU-GGGUA
((((((((...((((((((((.(((......)))....))))))))))...)))..((-----.((....)).)))))))........(((.(((((........--..)))))-.))). ( -40.70)
>sp_pneumo.rRNA 15824 112 + 2038623
GGAGAGUGGAAUUCCAUGUGUAGCGGUGAAAUGCGUAGAUAUAUGGAGGAACACCGGU-----GGCGAAAGCGGCUCUCUGGCUUGUAACUGACGCUGAGGCUCG--AAAGCGU-GGGGA
((((((((...((((((((((.(((......)))....))))))))))...)))..((-----.((....)).))))))).........((.(((((........--..)))))-.)).. ( -39.60)
>consensus
GGAGAGUGGAAUUCCAUGUGUAGCGGUGAAAUGCGUAGAUAUAUGGAGGAACACCAGU_____GGCGAAAGCGGCUCUCUGGUCUGUAACUGACGCUGAGGCUCG__AAAGCGU_GGGGA
.(((.(((...((((((((((.(((......)))....))))))))))...)))((((......((....))(((......)))..........))))...)))................ (-21.69 = -20.88 +  -0.81)

alignment

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secondary structure

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dotplot

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Window 6

Location 576,512 – 576,617
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 69.92
Mean single sequence MFE -42.33
Consensus MFE -23.00
Energy contribution -23.00
Covariance contribution 0.00
Combinations/Pair 1.33
Mean z-score -1.97
Structure conservation index 0.54
SVM decision value 1.41
SVM RNA-class probability 0.951668
Prediction RNA

Download alignment: ClustalW | MAF

>sy_aureus.rRNA 576512 105 + 2809430
AUGUAUAGGGGCUGACGCC----UGCCCGGUGCUGGAAGGUUAAGAGGAGUG------GUUAG--CUUCUGCGAAGCUACGAAUCGAAGC---CCCAGUAAACGGCGGCCGUAACUAUAA
...(((((..((....(((----.(((...((((((..((((..((...(((------(((.(--(....))..))))))...))..)))---)))))))...)))))).))..))))). ( -38.70)
>sp_agal.rRNA 17191 116 + 2160275
GCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAA----ACGAUGAGUGCUAGGUGUUAGGCCCUUUCCGGGGCUUAGUGCCGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUA
.....((((.........))))....((((.((((...----.))..(((((((.((..(((((((((....)))))))))..))...((....))....))))))).)).))))..... ( -44.70)
>sp_mutans.rRNA 17665 116 + 2030929
GCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAA----ACGAUGAGUGCUAGGUGUUAGGCCCUUUCCGGGGCUUAGUGCCGGAGCUAACGCAAUAAGCACUCCGCCUGGGGAGUA
.....((((.........))))....((((.((((...----.))..(((((((.((..(((((((((....)))))))))..))...((....))....))))))).)).))))..... ( -44.70)
>sp_pneumo.rRNA 15936 116 + 2038623
GCAAACAGGAUUAGAUACCCUGGUAGUCCACGCUGUAA----ACGAUGAGUGCUAGGUGUUAGACCCUUUCCGGGGUUUAGUGCCGUAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUA
.................(((.((((((....)))....----.....(((((((.((..(((((((((....)))))))))..))...((....))....))))))).))).)))..... ( -41.20)
>consensus
GCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAA____ACGAUGAGUGCUAGGUGUUAGGCCCUUUCCGGGGCUUAGUGCCGAAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUA
((.....((((((..........))))))...................(((....((..(((((((((....)))))))))..))...)))..........))(((((......))))). (-23.00 = -23.00 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 576,548 – 576,651
Length 103
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 72.39
Mean single sequence MFE -45.95
Consensus MFE -23.51
Energy contribution -25.95
Covariance contribution 2.44
Combinations/Pair 1.28
Mean z-score -3.46
Structure conservation index 0.51
SVM decision value 3.99
SVM RNA-class probability 0.999747
Prediction RNA

Download alignment: ClustalW | MAF

>sy_aureus.rRNA 576548 103 + 2809430
UUAAGAGGAGUG------GUUAG--CUUCUGCGAAGCUACGAAUCGAAGC---CCCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUC------CUUGUCGGGUAA
....(((((((.------..(((--((((...)))))))....(((..((---(((.......)).((((((.......))))))....)))..))).))))------)))......... ( -28.30)
>sp_agal.rRNA 17228 114 + 2160275
--ACGAUGAGUGCUAGGUGUUAGGCCCUUUCCGGGGCUUAGUGCCGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGACCGCAAGGU--UGAAACUCAAAGGAAUUGACGGG---
--.(((((((((((.((..(((((((((....)))))))))..))...((....))....)))))))..(((...((((.(((((....)))--))..))))..))).)))).....--- ( -52.50)
>sp_mutans.rRNA 17702 114 + 2030929
--ACGAUGAGUGCUAGGUGUUAGGCCCUUUCCGGGGCUUAGUGCCGGAGCUAACGCAAUAAGCACUCCGCCUGGGGAGUACGACCGCAAGGU--UGAAACUCAAAGGAAUUGACGGG---
--.(((((((((((.((..(((((((((....)))))))))..))...((....))....)))))))..(((...((((.(((((....)))--))..))))..))).)))).....--- ( -52.50)
>sp_pneumo.rRNA 15973 114 + 2038623
--ACGAUGAGUGCUAGGUGUUAGACCCUUUCCGGGGUUUAGUGCCGUAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGACCGCAAGGU--UGAAACUCAAAGGAAUUGACGGG---
--.(((((((((((.((..(((((((((....)))))))))..))...((....))....)))))))..(((...((((.(((((....)))--))..))))..))).)))).....--- ( -50.50)
>consensus
__ACGAUGAGUGCUAGGUGUUAGGCCCUUUCCGGGGCUUAGUGCCGAAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGACCGCAAGGU__UGAAACUCAAAGGAAUUGACGGG___
......((((((((.((..(((((((((....)))))))))..))...((....))....)))(((((......)))))...(((....)))......)))))................. (-23.51 = -25.95 +   2.44)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Fri Apr 7 15:50:29 2006