Locus 2285

Sequence ID 2R_DroMel_CAF1
Location 8,409,932 – 8,410,076
Length 144
Max. P 0.999450
window3754 window3755

overview

Window 4

Location 8,409,932 – 8,410,046
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 95.17
Mean single sequence MFE -27.97
Consensus MFE -26.93
Energy contribution -26.68
Covariance contribution -0.25
Combinations/Pair 1.15
Mean z-score -2.04
Structure conservation index 0.96
SVM decision value 3.61
SVM RNA-class probability 0.999450
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8409932 114 - 20766785
GACAGGCAUGAACAAA------CGAAACGUUUAUCUUCAUUAAAGGAGGUAAUUAAUUUUGAAAUCGAAAGAACAAGCGAGUGGCAAGUGGCAACUUGAUUUAUUUGUUUUAUUGUGCGC
.....(((..(.....------(((((...((((((((......))))))))....)))))...((....))..(((((((((.(((((....)))))...)))))))))..)..))).. ( -27.10)
>DroVir_CAF1 26795 120 - 1
GACAGGCAUGAACAAACAUGAACAAAACGUUUAUCUUCAUUAAAGGAGGUAAUUAAUUUUGAAAUCGAAAGAACAACCGAGUGGCAAGUGGCAACUUGAUUUAUUUGGUUUAUUGUGCGA
.....(((..(...........(((((...((((((((......))))))))....)))))...((....))..(((((((((.(((((....)))))...)))))))))..)..))).. ( -29.80)
>DroGri_CAF1 28828 114 - 1
GACAGGCAUGAACAAA------CGAAACGUUUAUCUUCAUUAAAGGAGGUAAUUAAUUUUGAAAUCGAAAGAACAACCGAGUGGCAAGUGGCAACUUGAUUUAUUCGGUUUAUUGUGCGA
.....(((..(.....------(((((...((((((((......))))))))....)))))...((....))..(((((((((.(((((....)))))...)))))))))..)..))).. ( -31.60)
>DroWil_CAF1 26871 114 - 1
GACAGGCAUGAACAAA------CGAAACGUUUAUCUUCAUUAAAGGAGGUAAUUAAUUUUGAAAUCGAAAGAACAAGCGAGUGGCAAGUGGCAACUUGAUUUAUUUGGUUUAUUGUGUGC
..((.((((((((...------(((((...((((((((......))))))))....)))))...((....)).....((((((.(((((....)))))...))))))))))).))).)). ( -26.80)
>DroMoj_CAF1 30505 114 - 1
GACAAGCAUGAACAAA------CAAAACGUUUAUCUUCAUUAAAGGAGGUAAUUAAUUUUGAAAUCGAAAGAACAAGCGAGUGGCAAGUGGCAACUUGAUUUAUUUGGUUUAUUGUGCGA
.....(((..(.....------(((((...((((((((......))))))))....)))))((((((((.(((....(((((.((.....)).))))).))).)))))))).)..))).. ( -26.60)
>DroPer_CAF1 20695 114 - 1
GACAGGCAUGAACAAA------CGAAACGUUUAUCUUCAUUAAAGGAGGUAAUUAAUUUUGAAAUCGAAAGAACAAGCGAGUGGCAAGUGGCAACUUGAUUUAUAUGCUUUAUUGUGCGC
.....(((..(.....------(((((...((((((((......))))))))....)))))...((....))..(((((.(((.(((((....)))))...))).)))))..)..))).. ( -25.90)
>consensus
GACAGGCAUGAACAAA______CGAAACGUUUAUCUUCAUUAAAGGAGGUAAUUAAUUUUGAAAUCGAAAGAACAAGCGAGUGGCAAGUGGCAACUUGAUUUAUUUGGUUUAUUGUGCGA
.....(((..(...........(((((...((((((((......))))))))....)))))...((....))..(((((((((.(((((....)))))...)))))))))..)..))).. (-26.93 = -26.68 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,409,972 – 8,410,076
Length 104
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.21
Mean single sequence MFE -17.78
Consensus MFE -12.77
Energy contribution -12.88
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -0.90
Structure conservation index 0.72
SVM decision value -0.04
SVM RNA-class probability 0.511774
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8409972 104 - 20766785
GCAGCAGAUAGA----------CGACGGACAGGCAAAACAGACAGGCAUGAACAAA------CGAAACGUUUAUCUUCAUUAAAGGAGGUAAUUAAUUUUGAAAUCGAAAGAACAAGCGA
...((.......----------....(..((.((...........)).))..)...------(((((...((((((((......))))))))....)))))...((....))....)).. ( -15.30)
>DroVir_CAF1 26835 94 - 1
GGGGCGAG-------------------------CA-GAGCGACAGGCAUGAACAAACAUGAACAAAACGUUUAUCUUCAUUAAAGGAGGUAAUUAAUUUUGAAAUCGAAAGAACAACCGA
(..((...-------------------------..-..))..).((((((......))))..(((((...((((((((......))))))))....)))))...((....))....)).. ( -17.40)
>DroGri_CAF1 28868 94 - 1
AAGG--GGUUGG-------------GGG-----AGAGUGCGACAGGCAUGAACAAA------CGAAACGUUUAUCUUCAUUAAAGGAGGUAAUUAAUUUUGAAAUCGAAAGAACAACCGA
....--(((((.-------------...-----...((((.....)))).......------(((((...((((((((......))))))))....)))))...((....)).))))).. ( -21.80)
>DroWil_CAF1 26911 114 - 1
GACACAGAGAGACUAAAAUGAAUGCAGGAGAAGAUAGACAGACAGGCAUGAACAAA------CGAAACGUUUAUCUUCAUUAAAGGAGGUAAUUAAUUUUGAAAUCGAAAGAACAAGCGA
......................(((....((((((((((.....(...........------).....))))))))))..........................((....))....))). ( -15.90)
>DroMoj_CAF1 30545 95 - 1
GCGGCUGGUUGA-------------GGG-----AA-CGGGGACAAGCAUGAACAAA------CAAAACGUUUAUCUUCAUUAAAGGAGGUAAUUAAUUUUGAAAUCGAAAGAACAAGCGA
((.(((.(((..-------------(..-----..-)...))).))).((......------(((((...((((((((......))))))))....)))))...((....)).)).)).. ( -19.80)
>DroAna_CAF1 21267 101 - 1
GGAGCUGAUAGA-------------CGGACAGGCAAAGCAGACAGGCAUGAACAAA------CGAAACGUUUAUCUUCAUUAAAGGAGGUAAUUAAUUUUGAAAUCGAAAGAACAAGCGA
...(((......-------------(.....)....)))......((.((......------(((((...((((((((......))))))))....)))))...((....)).)).)).. ( -16.50)
>consensus
GAGGCAGAUAGA_____________CGG_____AAAGACAGACAGGCAUGAACAAA______CGAAACGUUUAUCUUCAUUAAAGGAGGUAAUUAAUUUUGAAAUCGAAAGAACAAGCGA
.............................................((.((............(((((...((((((((......))))))))....)))))...((....)).)).)).. (-12.77 = -12.88 +   0.11)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:43 2006