Locus 58

Sequence ID sy_sa.0
Location 1,702,930 – 1,703,040
Length 110
Max. P 0.999771
window260 window261 window262 window263

overview

Window 0

Location 1,702,930 – 1,703,040
Length 110
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 77.62
Mean single sequence MFE -26.27
Consensus MFE -15.44
Energy contribution -15.33
Covariance contribution -0.11
Combinations/Pair 1.05
Mean z-score -2.26
Structure conservation index 0.59
SVM decision value 1.10
SVM RNA-class probability 0.914440
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1702930 110 + 2516575
UAUGCACCUCCUCUCUACGUC-AAAUUGACGCCUGAGAGAUAGGCGACUCCAUUAUUAUAUCAUUUGUAAAUACAUAAGC-AUAU----UCACUUCCGAUAAGUUGAACUAUGUUA
(((((.(((.(((((..((((-.....))))...)))))..))).).........(((((.....)))))...))))(((-((((----((((((.....))).)))).)))))). ( -23.10)
>sy_ha.0 2623585 112 + 2685015
UAUGCACCUCCUCUCUGCGUCUAAAUUGACGCCUGAGAGAUAGGCGACCUGUAUAUUAUAUCAUCUGUAC-UAGAUGAGUUACAGA---UAACUUCCGAUAAGCCGUCUUAUGUUA
....(.(((.(((((.(((((......)))))..)))))..))).)..(((((.......(((((((...-)))))))..))))).---((((....(((.....)))....)))) ( -29.40)
>sy_au.0 902487 115 - 2809422
UAUACACCUCCUCUCUGCGUCUAAAUUGACGCCUGAGAGAUAGGCGACUCUACUAUUAUAUCAUCGGCAAAUAUACAAGC-ACAGUCACUUGCUUCUGAUAAGUUAUAUGAUUCUA
....(.(((.(((((.(((((......)))))..)))))..))).)............(((((..(((((....((....-...))...)))))..)))))............... ( -26.30)
>consensus
UAUGCACCUCCUCUCUGCGUCUAAAUUGACGCCUGAGAGAUAGGCGACUCCAAUAUUAUAUCAUCUGUAAAUACAUAAGC_ACAG____UAACUUCCGAUAAGUUGUAUUAUGUUA
....(.(((.(((((.(((((......)))))..)))))..))).)............((((....((.......................))....))))............... (-15.44 = -15.33 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,702,930 – 1,703,040
Length 110
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 77.62
Mean single sequence MFE -34.03
Consensus MFE -25.74
Energy contribution -24.53
Covariance contribution -1.21
Combinations/Pair 1.29
Mean z-score -3.23
Structure conservation index 0.76
SVM decision value 4.04
SVM RNA-class probability 0.999771
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1702930 110 + 2516575
UAACAUAGUUCAACUUAUCGGAAGUGA----AUAU-GCUUAUGUAUUUACAAAUGAUAUAAUAAUGGAGUCGCCUAUCUCUCAGGCGUCAAUUU-GACGUAGAGAGGAGGUGCAUA
...(((.(((.....(((((...((((----((((-......))))))))...))))).))).)))..(.(((((.((((((..(((((.....-))))).))))))))))))... ( -32.10)
>sy_ha.0 2623585 112 + 2685015
UAACAUAAGACGGCUUAUCGGAAGUUA---UCUGUAACUCAUCUA-GUACAGAUGAUAUAAUAUACAGGUCGCCUAUCUCUCAGGCGUCAAUUUAGACGCAGAGAGGAGGUGCAUA
...((((((....))))).)...((((---((((((.((.....)-)))))))))))...........(.(((((.((((((..(((((......))))).))))))))))))... ( -35.00)
>sy_au.0 902487 115 - 2809422
UAGAAUCAUAUAACUUAUCAGAAGCAAGUGACUGU-GCUUGUAUAUUUGCCGAUGAUAUAAUAGUAGAGUCGCCUAUCUCUCAGGCGUCAAUUUAGACGCAGAGAGGAGGUGUAUA
.......(((((.(((...........((((((.(-(((..((((((.......))))))..)))).))))))....(((((..(((((......))))).)))))))).))))). ( -35.00)
>consensus
UAACAUAAUACAACUUAUCGGAAGUAA____CUGU_GCUUAUAUAUUUACAGAUGAUAUAAUAAUAGAGUCGCCUAUCUCUCAGGCGUCAAUUUAGACGCAGAGAGGAGGUGCAUA
...............(((((...((((.....((.....)).....))))...)))))..........(.(((((.((((((..(((((......))))).))))))))))))... (-25.74 = -24.53 +  -1.21) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,702,930 – 1,703,040
Length 110
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 77.62
Mean single sequence MFE -26.27
Consensus MFE -15.44
Energy contribution -15.33
Covariance contribution -0.11
Combinations/Pair 1.05
Mean z-score -2.26
Structure conservation index 0.59
SVM decision value 1.10
SVM RNA-class probability 0.914440
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1702930 110 + 2516575/0-116
UAUGCACCUCCUCUCUACGUC-AAAUUGACGCCUGAGAGAUAGGCGACUCCAUUAUUAUAUCAUUUGUAAAUACAUAAGC-AUAU----UCACUUCCGAUAAGUUGAACUAUGUUA
(((((.(((.(((((..((((-.....))))...)))))..))).).........(((((.....)))))...))))(((-((((----((((((.....))).)))).)))))). ( -23.10)
>sy_ha.0 2623585 112 + 2685015/0-116
UAUGCACCUCCUCUCUGCGUCUAAAUUGACGCCUGAGAGAUAGGCGACCUGUAUAUUAUAUCAUCUGUAC-UAGAUGAGUUACAGA---UAACUUCCGAUAAGCCGUCUUAUGUUA
....(.(((.(((((.(((((......)))))..)))))..))).)..(((((.......(((((((...-)))))))..))))).---((((....(((.....)))....)))) ( -29.40)
>sy_au.0 902487 115 - 2809422/0-116
UAUACACCUCCUCUCUGCGUCUAAAUUGACGCCUGAGAGAUAGGCGACUCUACUAUUAUAUCAUCGGCAAAUAUACAAGC-ACAGUCACUUGCUUCUGAUAAGUUAUAUGAUUCUA
....(.(((.(((((.(((((......)))))..)))))..))).)............(((((..(((((....((....-...))...)))))..)))))............... ( -26.30)
>consensus
UAUGCACCUCCUCUCUGCGUCUAAAUUGACGCCUGAGAGAUAGGCGACUCCAAUAUUAUAUCAUCUGUAAAUACAUAAGC_ACAG____UAACUUCCGAUAAGUUGUAUUAUGUUA
....(.(((.(((((.(((((......)))))..)))))..))).)............((((....((.......................))....))))............... (-15.44 = -15.33 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 1,702,930 – 1,703,040
Length 110
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 77.62
Mean single sequence MFE -34.03
Consensus MFE -25.74
Energy contribution -24.53
Covariance contribution -1.21
Combinations/Pair 1.29
Mean z-score -3.23
Structure conservation index 0.76
SVM decision value 4.04
SVM RNA-class probability 0.999771
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1702930 110 + 2516575/0-116
UAACAUAGUUCAACUUAUCGGAAGUGA----AUAU-GCUUAUGUAUUUACAAAUGAUAUAAUAAUGGAGUCGCCUAUCUCUCAGGCGUCAAUUU-GACGUAGAGAGGAGGUGCAUA
...(((.(((.....(((((...((((----((((-......))))))))...))))).))).)))..(.(((((.((((((..(((((.....-))))).))))))))))))... ( -32.10)
>sy_ha.0 2623585 112 + 2685015/0-116
UAACAUAAGACGGCUUAUCGGAAGUUA---UCUGUAACUCAUCUA-GUACAGAUGAUAUAAUAUACAGGUCGCCUAUCUCUCAGGCGUCAAUUUAGACGCAGAGAGGAGGUGCAUA
...((((((....))))).)...((((---((((((.((.....)-)))))))))))...........(.(((((.((((((..(((((......))))).))))))))))))... ( -35.00)
>sy_au.0 902487 115 - 2809422/0-116
UAGAAUCAUAUAACUUAUCAGAAGCAAGUGACUGU-GCUUGUAUAUUUGCCGAUGAUAUAAUAGUAGAGUCGCCUAUCUCUCAGGCGUCAAUUUAGACGCAGAGAGGAGGUGUAUA
.......(((((.(((...........((((((.(-(((..((((((.......))))))..)))).))))))....(((((..(((((......))))).)))))))).))))). ( -35.00)
>consensus
UAACAUAAUACAACUUAUCGGAAGUAA____CUGU_GCUUAUAUAUUUACAGAUGAUAUAAUAAUAGAGUCGCCUAUCUCUCAGGCGUCAAUUUAGACGCAGAGAGGAGGUGCAUA
...............(((((...((((.....((.....)).....))))...)))))..........(.(((((.((((((..(((((......))))).))))))))))))... (-25.74 = -24.53 +  -1.21) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:54:14 2006