Locus 1405

Sequence ID 2L_DroMel_CAF1
Location 3,746,787 – 3,746,882
Length 95
Max. P 0.856602
window2294 window2295

overview

Window 4

Location 3,746,787 – 3,746,882
Length 95
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 82.24
Mean single sequence MFE -24.38
Consensus MFE -17.22
Energy contribution -17.87
Covariance contribution 0.64
Combinations/Pair 1.19
Mean z-score -2.53
Structure conservation index 0.71
SVM decision value 0.81
SVM RNA-class probability 0.856602
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3746787 95 + 22407834
CCAAGAACCUGAUGGCCAACGGCGGCUGCUAUUUUGGUAAGUACACUCAUGCAGAAUUC------------------AAAAGAAAAGGCCAUAAAUUAGGUUCUAAUUGAAAA
...((((((((((.(((...)))((((....((((((...(((......))).....))------------------)))).....))))....))))))))))......... ( -25.40)
>DroSec_CAF1 208887 95 + 1
ACAAGAACCUGAUGGCCAACGGCGGCUGCUAUUUUGGUAAGUACACUCAUGCAAAAUUC------------------AAAAGAAAAGGCCAUAAAUUAGGUUCUAAUUGAAAA
...((((((((((.(((...)))((((....((((((...(((......))).....))------------------)))).....))))....))))))))))......... ( -25.40)
>DroSim_CAF1 216021 95 + 1
CCAAGAACCUGAUGGCCAACGGUGGCUGCUAUUUUGGUAAGUACACUCAUGCAAAAUUC------------------AAAAGAAAAGGCCAUAAAUUAGGUUCUAAUUGAAAA
...((((((((((((((...((((((((((.....))).))).)))).........(((------------------....)))..)))))....)))))))))......... ( -25.70)
>DroEre_CAF1 223232 95 + 1
CCAAGAACCUGAUGGCCAACGGCGGCUGCUAUUUUGGUAAGUACACUCAUGCAAUAUUC------------------AAAAGAACAGGCCAUAAAUUAGGUUCUAAUUGAAAA
...((((((((((.(((...)))((((....((((((...(((......))).....))------------------)))).....))))....))))))))))......... ( -25.40)
>DroYak_CAF1 226871 95 + 1
CCAAGAACGUGAUGGCCAACGGCGGCUGCUAUUUUGGUAAGUACACUCAUGCAAAAUGC------------------AAAGGAAAUGGCCAUAAAUUAGGUUCUAAUUGAAAA
...(((((.((((((((......))))(((((((((((......)))..(((.....))------------------)...)))))))).....)))).)))))......... ( -22.50)
>DroAna_CAF1 237758 108 + 1
GCAAGCCCCUUUUGGCCAACGGUGGCUGCUACUUUGGUAAGUACACUCUUCAAAAAUAUACAUACAAACUCUCCACGAAACAAAGAAGCCAUAAAAUAUUGGGCAAUU-----
....((((.....(((((....)))))(((.((((((((.(((...............))).)))....((.....))..))))).)))...........))))....----- ( -21.86)
>consensus
CCAAGAACCUGAUGGCCAACGGCGGCUGCUAUUUUGGUAAGUACACUCAUGCAAAAUUC__________________AAAAGAAAAGGCCAUAAAUUAGGUUCUAAUUGAAAA
...((((((((((((((...(((....)))((((((((.((....)).)).)))))).............................)))))....)))))))))......... (-17.22 = -17.87 +   0.64)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,746,787 – 3,746,882
Length 95
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 82.24
Mean single sequence MFE -22.78
Consensus MFE -15.42
Energy contribution -15.95
Covariance contribution 0.53
Combinations/Pair 1.19
Mean z-score -1.45
Structure conservation index 0.68
SVM decision value -0.05
SVM RNA-class probability 0.507677
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3746787 95 - 22407834
UUUUCAAUUAGAACCUAAUUUAUGGCCUUUUCUUUU------------------GAAUUCUGCAUGAGUGUACUUACCAAAAUAGCAGCCGCCGUUGGCCAUCAGGUUCUUGG
.........(((((((.....((((((..(((....------------------)))..((((.((.(((....))))).....))))........)))))).)))))))... ( -20.90)
>DroSec_CAF1 208887 95 - 1
UUUUCAAUUAGAACCUAAUUUAUGGCCUUUUCUUUU------------------GAAUUUUGCAUGAGUGUACUUACCAAAAUAGCAGCCGCCGUUGGCCAUCAGGUUCUUGU
.........(((((((.....((((((.........------------------..((((((..((((....)))).)))))).((....))....)))))).)))))))... ( -21.60)
>DroSim_CAF1 216021 95 - 1
UUUUCAAUUAGAACCUAAUUUAUGGCCUUUUCUUUU------------------GAAUUUUGCAUGAGUGUACUUACCAAAAUAGCAGCCACCGUUGGCCAUCAGGUUCUUGG
.........(((((((.....((((((.......((------------------(.((((((..((((....)))).))))))..)))........)))))).)))))))... ( -21.06)
>DroEre_CAF1 223232 95 - 1
UUUUCAAUUAGAACCUAAUUUAUGGCCUGUUCUUUU------------------GAAUAUUGCAUGAGUGUACUUACCAAAAUAGCAGCCGCCGUUGGCCAUCAGGUUCUUGG
.........(((((((.......(((.((((.((((------------------(.....((((....)))).....))))).)))))))(((...)))....)))))))... ( -23.20)
>DroYak_CAF1 226871 95 - 1
UUUUCAAUUAGAACCUAAUUUAUGGCCAUUUCCUUU------------------GCAUUUUGCAUGAGUGUACUUACCAAAAUAGCAGCCGCCGUUGGCCAUCACGUUCUUGG
.........(((((.......(((((((......((------------------((((((((..((((....)))).)))))).)))).......)))))))...)))))... ( -21.52)
>DroAna_CAF1 237758 108 - 1
-----AAUUGCCCAAUAUUUUAUGGCUUCUUUGUUUCGUGGAGAGUUUGUAUGUAUAUUUUUGAAGAGUGUACUUACCAAAGUAGCAGCCACCGUUGGCCAAAAGGGGCUUGC
-----....((((...........(((.(((((.(((.....)))...(((.((((((((.....)))))))).)))))))).))).((((....))))......)))).... ( -28.40)
>consensus
UUUUCAAUUAGAACCUAAUUUAUGGCCUUUUCUUUU__________________GAAUUUUGCAUGAGUGUACUUACCAAAAUAGCAGCCGCCGUUGGCCAUCAGGUUCUUGG
.........(((((((.....((((((.............................((((((..((((....)))).))))))(((.......))))))))).)))))))... (-15.42 = -15.95 +   0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:53 2006