Locus 53

Sequence ID sy_sa.0
Location 1,569,641 – 1,569,757
Length 116
Max. P 0.999972
window235 window236 window237 window238

overview

Window 5

Location 1,569,641 – 1,569,757
Length 116
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 74.37
Mean single sequence MFE -28.38
Consensus MFE -16.96
Energy contribution -17.86
Covariance contribution 0.90
Combinations/Pair 1.17
Mean z-score -3.96
Structure conservation index 0.60
SVM decision value 4.88
SVM RNA-class probability 0.999959
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1569641 116 + 2516575
UCUUAUCCUCUCUAUUGUAAAAAUAUGUAAAUUAUACAAGUAAAGAAGACACAAUAG-GUCUUCCAAUACAAAAGUGAAUCUUUCAU--ACGGAGCACAAAAGGUGUCUUCUUCCUUGU
...................................(((((..((((((((((.....-((.((((......((((.....))))...--..)))).)).....)))))))))).))))) ( -23.50)
>sy_au.0 1522863 118 - 2809422
UCUUAUCCUCUCUAUCGUGAAUAUAUGUAACAUAUACAAGUAAAGAAGACACAGUUG-UCGUUUUAUUAGAAUGAUUUACAUUUUAAUAAAGCAACAUUAAAGGUGUCUUCUUCCUUGU
.....................((((((...))))))((((..((((((((((...((-(.((((((((((((((.....)))))))))))))).)))......)))))))))).)))). ( -33.10)
>sy_ha.0 1710338 118 + 2685015
UUUUUUCCUCUCUAUUGUAAAAAUAUGUAAUAUAUACAAGUAAAGAAGACACUGACGCGCCUUCUAACAUAAAGUAUCACUUUAUAAU-AGAAAACCUCAAAGGUGUCUUCUUUCUUGU
...................................(((((.((((((((((((........(((((..((((((.....))))))..)-)))).........))))))))))))))))) ( -28.53)
>consensus
UCUUAUCCUCUCUAUUGUAAAAAUAUGUAAAAUAUACAAGUAAAGAAGACACAGUAG_GCCUUCUAAUACAAAGAUUAACAUUUUAAU_AAGAAACAUAAAAGGUGUCUUCUUCCUUGU
...................................(((((...(((((((((.............(((((((((.....)))))))))...............)))))))))..))))) (-16.96 = -17.86 +   0.90)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,569,641 – 1,569,757
Length 116
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 74.37
Mean single sequence MFE -32.80
Consensus MFE -20.19
Energy contribution -19.42
Covariance contribution -0.76
Combinations/Pair 1.25
Mean z-score -4.19
Structure conservation index 0.62
SVM decision value 5.07
SVM RNA-class probability 0.999972
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1569641 116 + 2516575
ACAAGGAAGAAGACACCUUUUGUGCUCCGU--AUGAAAGAUUCACUUUUGUAUUGGAAGAC-CUAUUGUGUCUUCUUUACUUGUAUAAUUUACAUAUUUUUACAAUAGAGAGGAUAAGA
((((((((((((((((..(..((..(((((--(..((((.....))))..)).))))..))-..)..))))))))))).)))))..........(((((((........)))))))... ( -31.30)
>sy_au.0 1522863 118 - 2809422
ACAAGGAAGAAGACACCUUUAAUGUUGCUUUAUUAAAAUGUAAAUCAUUCUAAUAAAACGA-CAACUGUGUCUUCUUUACUUGUAUAUGUUACAUAUAUUCACGAUAGAGAGGAUAAGA
((((((((((((((((......(((((.(((((((.((((.....)))).))))))).)))-))...))))))))))).)))))............(((((.(......).)))))... ( -32.00)
>sy_ha.0 1710338 118 + 2685015
ACAAGAAAGAAGACACCUUUGAGGUUUUCU-AUUAUAAAGUGAUACUUUAUGUUAGAAGGCGCGUCAGUGUCUUCUUUACUUGUAUAUAUUACAUAUUUUUACAAUAGAGAGGAAAAAA
((((((((((((((((...(((((((((((-(.(((((((.....))))))).)))))))).).)))))))))))))).)))))................................... ( -35.10)
>consensus
ACAAGGAAGAAGACACCUUUAAUGUUCCCU_AUUAAAAAGUAAAACUUUAUAUUAGAAGGC_CAACUGUGUCUUCUUUACUUGUAUAUAUUACAUAUUUUUACAAUAGAGAGGAUAAGA
((((((((((((((((...............((((.((((.....)))).)))).............))))))))))).)))))..........(((((((.(....).)))))))... (-20.19 = -19.42 +  -0.76) 
# Strand winner: reverse (0.98)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,569,641 – 1,569,757
Length 116
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 74.37
Mean single sequence MFE -28.38
Consensus MFE -16.96
Energy contribution -17.86
Covariance contribution 0.90
Combinations/Pair 1.17
Mean z-score -3.96
Structure conservation index 0.60
SVM decision value 4.88
SVM RNA-class probability 0.999959
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1569641 116 + 2516575/0-119
UCUUAUCCUCUCUAUUGUAAAAAUAUGUAAAUUAUACAAGUAAAGAAGACACAAUAG-GUCUUCCAAUACAAAAGUGAAUCUUUCAU--ACGGAGCACAAAAGGUGUCUUCUUCCUUGU
...................................(((((..((((((((((.....-((.((((......((((.....))))...--..)))).)).....)))))))))).))))) ( -23.50)
>sy_au.0 1522863 118 - 2809422/0-119
UCUUAUCCUCUCUAUCGUGAAUAUAUGUAACAUAUACAAGUAAAGAAGACACAGUUG-UCGUUUUAUUAGAAUGAUUUACAUUUUAAUAAAGCAACAUUAAAGGUGUCUUCUUCCUUGU
.....................((((((...))))))((((..((((((((((...((-(.((((((((((((((.....)))))))))))))).)))......)))))))))).)))). ( -33.10)
>sy_ha.0 1710338 118 + 2685015/0-119
UUUUUUCCUCUCUAUUGUAAAAAUAUGUAAUAUAUACAAGUAAAGAAGACACUGACGCGCCUUCUAACAUAAAGUAUCACUUUAUAAU-AGAAAACCUCAAAGGUGUCUUCUUUCUUGU
...................................(((((.((((((((((((........(((((..((((((.....))))))..)-)))).........))))))))))))))))) ( -28.53)
>consensus
UCUUAUCCUCUCUAUUGUAAAAAUAUGUAAAAUAUACAAGUAAAGAAGACACAGUAG_GCCUUCUAAUACAAAGAUUAACAUUUUAAU_AAGAAACAUAAAAGGUGUCUUCUUCCUUGU
...................................(((((...(((((((((.............(((((((((.....)))))))))...............)))))))))..))))) (-16.96 = -17.86 +   0.90)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,569,641 – 1,569,757
Length 116
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 74.37
Mean single sequence MFE -32.80
Consensus MFE -20.19
Energy contribution -19.42
Covariance contribution -0.76
Combinations/Pair 1.25
Mean z-score -4.19
Structure conservation index 0.62
SVM decision value 5.07
SVM RNA-class probability 0.999972
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1569641 116 + 2516575/0-119
ACAAGGAAGAAGACACCUUUUGUGCUCCGU--AUGAAAGAUUCACUUUUGUAUUGGAAGAC-CUAUUGUGUCUUCUUUACUUGUAUAAUUUACAUAUUUUUACAAUAGAGAGGAUAAGA
((((((((((((((((..(..((..(((((--(..((((.....))))..)).))))..))-..)..))))))))))).)))))..........(((((((........)))))))... ( -31.30)
>sy_au.0 1522863 118 - 2809422/0-119
ACAAGGAAGAAGACACCUUUAAUGUUGCUUUAUUAAAAUGUAAAUCAUUCUAAUAAAACGA-CAACUGUGUCUUCUUUACUUGUAUAUGUUACAUAUAUUCACGAUAGAGAGGAUAAGA
((((((((((((((((......(((((.(((((((.((((.....)))).))))))).)))-))...))))))))))).)))))............(((((.(......).)))))... ( -32.00)
>sy_ha.0 1710338 118 + 2685015/0-119
ACAAGAAAGAAGACACCUUUGAGGUUUUCU-AUUAUAAAGUGAUACUUUAUGUUAGAAGGCGCGUCAGUGUCUUCUUUACUUGUAUAUAUUACAUAUUUUUACAAUAGAGAGGAAAAAA
((((((((((((((((...(((((((((((-(.(((((((.....))))))).)))))))).).)))))))))))))).)))))................................... ( -35.10)
>consensus
ACAAGGAAGAAGACACCUUUAAUGUUCCCU_AUUAAAAAGUAAAACUUUAUAUUAGAAGGC_CAACUGUGUCUUCUUUACUUGUAUAUAUUACAUAUUUUUACAAUAGAGAGGAUAAGA
((((((((((((((((...............((((.((((.....)))).)))).............))))))))))).)))))..........(((((((.(....).)))))))... (-20.19 = -19.42 +  -0.76) 
# Strand winner: reverse (0.98)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:53:53 2006