Locus 83

Sequence ID sy_sa.0
Location 2,278,358 – 2,278,428
Length 70
Max. P 0.999365
window419 window420 window421 window422

overview

Window 9

Location 2,278,358 – 2,278,428
Length 70
Sequences 3
Columns 71
Reading direction forward
Mean pairwise identity 76.89
Mean single sequence MFE -23.07
Consensus MFE -15.07
Energy contribution -15.30
Covariance contribution 0.23
Combinations/Pair 1.12
Mean z-score -5.93
Structure conservation index 0.65
SVM decision value 2.41
SVM RNA-class probability 0.993652
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 2278358 70 + 2516575
AAAUAAGAUAAAA-CCCCGUUAUAUGGAUAACGGGGUUUUCACUUCUCAAAGAUAUCAGCCUAUCUAUAGC
....(((..((((-(((((((((....)))))))))))))..))).....(((((......)))))..... ( -20.40)
>sy_au.0 2203320 67 - 2809422
AAAUGA-AUAAAA-CCCCGUUAUCAAAAUAACGGGGUUUUAACUUCUCAAAGA-AUCAUUAUAU-UAUAGC
.(((((-.(((((-(((((((((....))))))))))))))..(((.....))-))))))....-...... ( -21.80)
>sy_ha.0 2470186 71 + 2685015
AAAUGAAGUAAAAACCCCGUUAUCGUGAUAACGGGGUUUUAAUUUCUCAAAGAAUUCAGGUUAGUUCUGAU
....(((((.(((((((((((((....))))))))))))).))))).........(((((.....))))). ( -27.00)
>consensus
AAAUGA_AUAAAA_CCCCGUUAUCAAGAUAACGGGGUUUUAACUUCUCAAAGA_AUCAGCAUAU_UAUAGC
....(((.(((((.(((((((((....)))))))))))))).))).......................... (-15.07 = -15.30 +   0.23)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,278,358 – 2,278,428
Length 70
Sequences 3
Columns 71
Reading direction reverse
Mean pairwise identity 76.89
Mean single sequence MFE -22.60
Consensus MFE -15.63
Energy contribution -16.30
Covariance contribution 0.67
Combinations/Pair 1.11
Mean z-score -5.22
Structure conservation index 0.69
SVM decision value 3.54
SVM RNA-class probability 0.999365
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 2278358 70 + 2516575
GCUAUAGAUAGGCUGAUAUCUUUGAGAAGUGAAAACCCCGUUAUCCAUAUAACGGGG-UUUUAUCUUAUUU
.....(((((......))))).(((((....(((((((((((((....)))))))))-)))).)))))... ( -23.00)
>sy_au.0 2203320 67 - 2809422
GCUAUA-AUAUAAUGAU-UCUUUGAGAAGUUAAAACCCCGUUAUUUUGAUAACGGGG-UUUUAU-UCAUUU
......-....((((((-((.....)))..((((((((((((((....)))))))))-))))).-))))). ( -21.20)
>sy_ha.0 2470186 71 + 2685015
AUCAGAACUAACCUGAAUUCUUUGAGAAAUUAAAACCCCGUUAUCACGAUAACGGGGUUUUUACUUCAUUU
.((((.......)))).........(((...(((((((((((((....)))))))))))))...))).... ( -23.60)
>consensus
GCUAUA_AUAAACUGAU_UCUUUGAGAAGUUAAAACCCCGUUAUCAAGAUAACGGGG_UUUUAU_UCAUUU
......................(((((...((((((((((((((....))))))))).))))))))))... (-15.63 = -16.30 +   0.67) 
# Strand winner: forward (0.53)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,278,358 – 2,278,428
Length 70
Sequences 3
Columns 71
Reading direction forward
Mean pairwise identity 76.89
Mean single sequence MFE -23.07
Consensus MFE -15.07
Energy contribution -15.30
Covariance contribution 0.23
Combinations/Pair 1.12
Mean z-score -5.93
Structure conservation index 0.65
SVM decision value 2.41
SVM RNA-class probability 0.993652
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 2278358 70 + 2516575/0-71
AAAUAAGAUAAAA-CCCCGUUAUAUGGAUAACGGGGUUUUCACUUCUCAAAGAUAUCAGCCUAUCUAUAGC
....(((..((((-(((((((((....)))))))))))))..))).....(((((......)))))..... ( -20.40)
>sy_au.0 2203320 67 - 2809422/0-71
AAAUGA-AUAAAA-CCCCGUUAUCAAAAUAACGGGGUUUUAACUUCUCAAAGA-AUCAUUAUAU-UAUAGC
.(((((-.(((((-(((((((((....))))))))))))))..(((.....))-))))))....-...... ( -21.80)
>sy_ha.0 2470186 71 + 2685015/0-71
AAAUGAAGUAAAAACCCCGUUAUCGUGAUAACGGGGUUUUAAUUUCUCAAAGAAUUCAGGUUAGUUCUGAU
....(((((.(((((((((((((....))))))))))))).))))).........(((((.....))))). ( -27.00)
>consensus
AAAUGA_AUAAAA_CCCCGUUAUCAAGAUAACGGGGUUUUAACUUCUCAAAGA_AUCAGCAUAU_UAUAGC
....(((.(((((.(((((((((....)))))))))))))).))).......................... (-15.07 = -15.30 +   0.23)

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 2,278,358 – 2,278,428
Length 70
Sequences 3
Columns 71
Reading direction reverse
Mean pairwise identity 76.89
Mean single sequence MFE -22.60
Consensus MFE -15.63
Energy contribution -16.30
Covariance contribution 0.67
Combinations/Pair 1.11
Mean z-score -5.22
Structure conservation index 0.69
SVM decision value 3.54
SVM RNA-class probability 0.999365
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 2278358 70 + 2516575/0-71
GCUAUAGAUAGGCUGAUAUCUUUGAGAAGUGAAAACCCCGUUAUCCAUAUAACGGGG-UUUUAUCUUAUUU
.....(((((......))))).(((((....(((((((((((((....)))))))))-)))).)))))... ( -23.00)
>sy_au.0 2203320 67 - 2809422/0-71
GCUAUA-AUAUAAUGAU-UCUUUGAGAAGUUAAAACCCCGUUAUUUUGAUAACGGGG-UUUUAU-UCAUUU
......-....((((((-((.....)))..((((((((((((((....)))))))))-))))).-))))). ( -21.20)
>sy_ha.0 2470186 71 + 2685015/0-71
AUCAGAACUAACCUGAAUUCUUUGAGAAAUUAAAACCCCGUUAUCACGAUAACGGGGUUUUUACUUCAUUU
.((((.......)))).........(((...(((((((((((((....)))))))))))))...))).... ( -23.60)
>consensus
GCUAUA_AUAAACUGAU_UCUUUGAGAAGUUAAAACCCCGUUAUCAAGAUAACGGGG_UUUUAU_UCAUUU
......................(((((...((((((((((((((....))))))))).))))))))))... (-15.63 = -16.30 +   0.67) 
# Strand winner: forward (0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:56:26 2006