Locus 8472

Sequence ID X_DroMel_CAF1
Location 21,035,121 – 21,035,385
Length 264
Max. P 0.760168
window13914 window13915 window13916

overview

Window 4

Location 21,035,121 – 21,035,225
Length 104
Sequences 3
Columns 104
Reading direction forward
Mean pairwise identity 90.73
Mean single sequence MFE -25.17
Consensus MFE -19.92
Energy contribution -19.70
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.25
Structure conservation index 0.79
SVM decision value 0.21
SVM RNA-class probability 0.637407
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21035121 104 + 22224390
AAGAAGAAGAAGCAGCAGCGGCAGCAAAAAACUAUUCCCGCAGCUCAUUAAAAACCCAAAGGGUUAAAAUAGUGAGGGAGGGAGGCGUCACAAUGCAGUAUGCA
..............(((((....)).....(((.(((((.(..(((((((..(((((...)))))....))))))).).)))))((((....))))))).))). ( -27.50)
>DroSim_CAF1 6295 94 + 1
AA------GAAGUAGCAGCGGCAGCGAAAAACUAUUCCCGCAGCUCAUUAAAAACCCAAAGGGUUAAAA-AGUGAGG---GGAGGCGUCACAAUGCAGUAUGCA
..------......(((((....)).....(((.(((((....((((((...(((((...)))))....-)))))))---))))((((....))))))).))). ( -23.60)
>DroYak_CAF1 6345 94 + 1
AA------GAAGCAGCAUCGGCAGCAAAAAACUAUUCCCGCAGCUCAUUAAAAACCCAAAGGGUUAAAA-AGUGAGG---GGAGGCGCCACAAUGCAGUAUGCA
..------...(((((((.(((.((.........(((((....((((((...(((((...)))))....-)))))))---)))))))))...))))....))). ( -24.40)
>consensus
AA______GAAGCAGCAGCGGCAGCAAAAAACUAUUCCCGCAGCUCAUUAAAAACCCAAAGGGUUAAAA_AGUGAGG___GGAGGCGUCACAAUGCAGUAUGCA
..............(((...((.(((........((((.....((((((...(((((...))))).....))))))....)))).........))).)).))). (-19.92 = -19.70 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,035,153 – 21,035,265
Length 112
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 91.38
Mean single sequence MFE -28.98
Consensus MFE -25.09
Energy contribution -24.87
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.13
Structure conservation index 0.87
SVM decision value 0.50
SVM RNA-class probability 0.760168
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21035153 112 + 22224390
UAUUCCCGCAGCUCAUUAAAAACCCAAAGGGUUAAAAUAGUGAGGGAGGGAGGCGUCAC--------AAUGCAGUAUGCAAAACAAGGCAAACAACAACAAUAAGCGUCGGAGCCGGAGA
...((((.(..(((((((..(((((...)))))....))))))).).))))(((.((.(--------.((((.((.(((........))).))...(....)..)))).))))))..... ( -28.40)
>DroSim_CAF1 6321 108 + 1
UAUUCCCGCAGCUCAUUAAAAACCCAAAGGGUUAAAA-AGUGAGG---GGAGGCGUCAC--------AAUGCAGUAUGCAAAACAAGGCAAACAACAACAAUAAGCGUCGGAGCCGGAGA
..((((.((..((((((...(((((...)))))....-)))))).---.((.((.....--------..((..((.(((........))).))..)).......)).))...)).)))). ( -26.04)
>DroEre_CAF1 5940 116 + 1
UAUUCCCGCAGCUCAUUAAAAACCCAAAGGGUUAAAA-AGUGAGG---GGCGGCGCCACAAUGCCACAAUGCAGUAUGCAAAACAAGGCAAACAACAACAAUAAGCGUCGGAGCUGGAGA
..((((.((..((((((...(((((...)))))....-)))))).---..((((((.....(((......)))((.(((........))).))...........))))))..)).)))). ( -32.50)
>consensus
UAUUCCCGCAGCUCAUUAAAAACCCAAAGGGUUAAAA_AGUGAGG___GGAGGCGUCAC________AAUGCAGUAUGCAAAACAAGGCAAACAACAACAAUAAGCGUCGGAGCCGGAGA
..((((.((..((((((...(((((...))))).....)))))).......(((((.............(((.....)))......(.....)...........)))))...)).)))). (-25.09 = -24.87 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 6

Location 21,035,265 – 21,035,385
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.23
Mean single sequence MFE -26.32
Consensus MFE -22.42
Energy contribution -22.50
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -1.37
Structure conservation index 0.85
SVM decision value 0.39
SVM RNA-class probability 0.718254
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21035265 120 + 22224390
AAUUGAAACUAGGCUGCCGCAAAAAAGCGACGGACAUAUUGGUGUGCGAGCGAGCAGAGAGGCUAGUGGAGAAAGUGAGCAAAGUUAAACAAUUGAAAUUGAAAUUAGUUGGUGAGCGUA
..(((..(((...((.((((......((..((.((((....)))).)).)).(((......))).))))))..)))...))).(((...(((((((........)))))))...)))... ( -27.20)
>DroSec_CAF1 5880 117 + 1
AAUUGAAACUAGGCUGCCGCAAAA-AGGGACGGACAUAGGGGUGUGCGAGCGAGCAG--GGGCUAGUGGAGAAAGUGAGCAAAGUUAAACAAUUGAAAUUGAAAUUAGUUGGUGAGCGUA
..(((..(((...((.((((....-.....((.((((....)))).))(((......--..))).))))))..)))...))).(((...(((((((........)))))))...)))... ( -24.70)
>DroSim_CAF1 6429 117 + 1
AAUUGAAACUAGGCUGCCGCAAAA-AGGGACGGACAUAGGGGUGUGCGAGCGAGCAG--GGGCUAGUGGAGAAAGUGAGCAAAGUUAAACAAUUGAAAUUGAAAUUAGUUGGUGAGCGUA
..(((..(((...((.((((....-.....((.((((....)))).))(((......--..))).))))))..)))...))).(((...(((((((........)))))))...)))... ( -24.70)
>DroEre_CAF1 6056 116 + 1
AAUUGAAACUAGGCUGCCGCAGAA-AGGGACGGACAU-GGGGUGUGCGAGCGAGCCG--GCGCUAAUGGAGAAAGUGAGCAAAGUUAAACAAUUGAAAUUGAAAUUAGUUGGCGAGCGUA
...........((((((((((.(.-..(......)..-....).)))).)).)))).--(((((..........(....)...(((((..((((........))))..))))).))))). ( -24.30)
>DroYak_CAF1 6479 117 + 1
AAUUGAAACUAGGCUGCCGCAGAA-AGGGACGGACACAGGGGUGUGCGAGCGAGGCG--GCACUAGUGGAGAAAGUGGGCAAAGUUAAAUAAUUGAAAUUGAAAUUAGUUGGCGAGCGUA
..((...(((((((((((.(....-..)..((.((((....)))).)).....))))--)).)))))...))......((...(((((.(((((........))))).)))))..))... ( -30.70)
>consensus
AAUUGAAACUAGGCUGCCGCAAAA_AGGGACGGACAUAGGGGUGUGCGAGCGAGCAG__GGGCUAGUGGAGAAAGUGAGCAAAGUUAAACAAUUGAAAUUGAAAUUAGUUGGUGAGCGUA
..(((..(((...((.((((..........((.((((....)))).))....(((......))).))))))..)))...))).(((...(((((((........)))))))...)))... (-22.42 = -22.50 +   0.08)

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 13:04:49 2006