Locus 111

Sequence ID sy_au.0
Location 2,228,337 – 2,228,410
Length 73
Max. P 0.994826
window634 window635 window636 window637

overview

Window 4

Location 2,228,337 – 2,228,410
Length 73
Sequences 4
Columns 73
Reading direction forward
Mean pairwise identity 89.95
Mean single sequence MFE -27.12
Consensus MFE -27.73
Energy contribution -26.10
Covariance contribution -1.63
Combinations/Pair 1.24
Mean z-score -1.57
Structure conservation index 1.02
SVM decision value 1.22
SVM RNA-class probability 0.931799
Prediction RNA

Download alignment: ClustalW | MAF

>sy_au.0 2228337 73 + 2809422
AUGACUCCUACGGGACUCGAACCCGUGUUACCGCCGUGAAAGGGCGGUGUCUUAACCGCUUGACCAAGGAGCC
....((((((((((.......)))))..(((((((.......))))))).................))))).. ( -25.10)
>sy_ha.0 1800022 73 - 2685015
GUGACUCCUACGGGACUCGAACCCGUGUUACCGCCGUGAAAGGGCGGUGUCUUAACCGCUUGACCAAGGAGCC
....((((((((((.......)))))..(((((((.......))))))).................))))).. ( -25.10)
>sy_sa.0 1767743 73 - 2516575
AUGACCCCGACGGGACUCGAACCCGUGUUACCGCCGUGAAAGGGCGGUGUCUUAACCGCUUGACCACGGGGCC
....(((((.((((((.((....)).))).))).)(((...(((((((......)))))))...))))))).. ( -29.90)
>sp_pn.0 1697429 73 + 2038615
AUAGUCCGUACGGGAUUCGAACCCGUGUUACCGCCGUGAAAAGGCGGUGUCUUAACCCCUUGACCAACGGACC
...(((((((((((.......)))))..(((((((.......))))))).................)))))). ( -28.40)
>consensus
AUGACCCCUACGGGACUCGAACCCGUGUUACCGCCGUGAAAGGGCGGUGUCUUAACCGCUUGACCAAGGAGCC
....((((((((((.......)))))..(((((((.......))))))).................))))).. (-27.73 = -26.10 +  -1.63)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,228,337 – 2,228,410
Length 73
Sequences 4
Columns 73
Reading direction reverse
Mean pairwise identity 89.95
Mean single sequence MFE -29.93
Consensus MFE -31.70
Energy contribution -29.70
Covariance contribution -2.00
Combinations/Pair 1.29
Mean z-score -2.09
Structure conservation index 1.06
SVM decision value 2.51
SVM RNA-class probability 0.994826
Prediction RNA

Download alignment: ClustalW | MAF

>sy_au.0 2228337 73 + 2809422
GGCUCCUUGGUCAAGCGGUUAAGACACCGCCCUUUCACGGCGGUAACACGGGUUCGAGUCCCGUAGGAGUCAU
(((((((..(((..........)))((((((.......))))))...(((((.......)))))))))))).. ( -29.10)
>sy_ha.0 1800022 73 - 2685015
GGCUCCUUGGUCAAGCGGUUAAGACACCGCCCUUUCACGGCGGUAACACGGGUUCGAGUCCCGUAGGAGUCAC
(((((((..(((..........)))((((((.......))))))...(((((.......)))))))))))).. ( -29.10)
>sy_sa.0 1767743 73 - 2516575
GGCCCCGUGGUCAAGCGGUUAAGACACCGCCCUUUCACGGCGGUAACACGGGUUCGAGUCCCGUCGGGGUCAU
((((((((((....(((((......)))))....))))(((((..((.((....)).)).))))))))))).. ( -32.70)
>sp_pn.0 1697429 73 + 2038615
GGUCCGUUGGUCAAGGGGUUAAGACACCGCCUUUUCACGGCGGUAACACGGGUUCGAAUCCCGUACGGACUAU
(((((((..(((..........)))((((((.......))))))...(((((.......)))))))))))).. ( -28.80)
>consensus
GGCCCCUUGGUCAAGCGGUUAAGACACCGCCCUUUCACGGCGGUAACACGGGUUCGAGUCCCGUAGGAGUCAU
(((((((..(((..........)))((((((.......))))))...(((((.......)))))))))))).. (-31.70 = -29.70 +  -2.00) 
# Strand winner: reverse (0.91)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,228,337 – 2,228,410
Length 73
Sequences 4
Columns 73
Reading direction forward
Mean pairwise identity 89.95
Mean single sequence MFE -27.12
Consensus MFE -27.73
Energy contribution -26.10
Covariance contribution -1.63
Combinations/Pair 1.24
Mean z-score -1.57
Structure conservation index 1.02
SVM decision value 1.22
SVM RNA-class probability 0.931799
Prediction RNA

Download alignment: ClustalW | MAF

>sy_au.0 2228337 73 + 2809422/0-73
AUGACUCCUACGGGACUCGAACCCGUGUUACCGCCGUGAAAGGGCGGUGUCUUAACCGCUUGACCAAGGAGCC
....((((((((((.......)))))..(((((((.......))))))).................))))).. ( -25.10)
>sy_ha.0 1800022 73 - 2685015/0-73
GUGACUCCUACGGGACUCGAACCCGUGUUACCGCCGUGAAAGGGCGGUGUCUUAACCGCUUGACCAAGGAGCC
....((((((((((.......)))))..(((((((.......))))))).................))))).. ( -25.10)
>sy_sa.0 1767743 73 - 2516575/0-73
AUGACCCCGACGGGACUCGAACCCGUGUUACCGCCGUGAAAGGGCGGUGUCUUAACCGCUUGACCACGGGGCC
....(((((.((((((.((....)).))).))).)(((...(((((((......)))))))...))))))).. ( -29.90)
>sp_pn.0 1697429 73 + 2038615/0-73
AUAGUCCGUACGGGAUUCGAACCCGUGUUACCGCCGUGAAAAGGCGGUGUCUUAACCCCUUGACCAACGGACC
...(((((((((((.......)))))..(((((((.......))))))).................)))))). ( -28.40)
>consensus
AUGACCCCUACGGGACUCGAACCCGUGUUACCGCCGUGAAAGGGCGGUGUCUUAACCGCUUGACCAAGGAGCC
....((((((((((.......)))))..(((((((.......))))))).................))))).. (-27.73 = -26.10 +  -1.63)

alignment

Postscript

secondary structure

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dotplot

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Window 7

Location 2,228,337 – 2,228,410
Length 73
Sequences 4
Columns 73
Reading direction reverse
Mean pairwise identity 89.95
Mean single sequence MFE -29.93
Consensus MFE -31.70
Energy contribution -29.70
Covariance contribution -2.00
Combinations/Pair 1.29
Mean z-score -2.09
Structure conservation index 1.06
SVM decision value 2.51
SVM RNA-class probability 0.994826
Prediction RNA

Download alignment: ClustalW | MAF

>sy_au.0 2228337 73 + 2809422/0-73
GGCUCCUUGGUCAAGCGGUUAAGACACCGCCCUUUCACGGCGGUAACACGGGUUCGAGUCCCGUAGGAGUCAU
(((((((..(((..........)))((((((.......))))))...(((((.......)))))))))))).. ( -29.10)
>sy_ha.0 1800022 73 - 2685015/0-73
GGCUCCUUGGUCAAGCGGUUAAGACACCGCCCUUUCACGGCGGUAACACGGGUUCGAGUCCCGUAGGAGUCAC
(((((((..(((..........)))((((((.......))))))...(((((.......)))))))))))).. ( -29.10)
>sy_sa.0 1767743 73 - 2516575/0-73
GGCCCCGUGGUCAAGCGGUUAAGACACCGCCCUUUCACGGCGGUAACACGGGUUCGAGUCCCGUCGGGGUCAU
((((((((((....(((((......)))))....))))(((((..((.((....)).)).))))))))))).. ( -32.70)
>sp_pn.0 1697429 73 + 2038615/0-73
GGUCCGUUGGUCAAGGGGUUAAGACACCGCCUUUUCACGGCGGUAACACGGGUUCGAAUCCCGUACGGACUAU
(((((((..(((..........)))((((((.......))))))...(((((.......)))))))))))).. ( -28.80)
>consensus
GGCCCCUUGGUCAAGCGGUUAAGACACCGCCCUUUCACGGCGGUAACACGGGUUCGAGUCCCGUAGGAGUCAU
(((((((..(((..........)))((((((.......))))))...(((((.......)))))))))))).. (-31.70 = -29.70 +  -2.00) 
# Strand winner: reverse (0.91)

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 18:59:23 2006