Locus 1992

Sequence ID 3L_DroMel_CAF1
Location 5,467,827 – 5,467,972
Length 145
Max. P 0.599594
window3119 window3120

overview

Window 9

Location 5,467,827 – 5,467,933
Length 106
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 97.15
Mean single sequence MFE -33.44
Consensus MFE -30.48
Energy contribution -30.68
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.22
Structure conservation index 0.91
SVM decision value 0.09
SVM RNA-class probability 0.576138
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5467827 106 + 23771897
GAUCUGGGUGACGUGGAGCAUUCAUGUCAGUCGCCAGGCUUAAGCCCCCCCUUUUCCACGCCCCUGUCUACUUUUGCUUGCAAGUGGCAAGUCGCGUGGAAAAAUU
.....((((((((((((...))))))))).......(((....)))..)))((((((((((..((..((((((........))))))..))..))))))))))... ( -38.20)
>DroSec_CAF1 29403 105 + 1
GAGCUGGGUGACGUGGAGCAUUCAUGUCAGUCUCCAGGCUUAAGCCC-CCCUUUUCCACGCCCCUGUCUACUUUUGCUUGCAAGUGGCAAGUCGCUUGGAAAAAUU
.....((((((((((((...))))))))).......(((....))).-)))(((((((.((..((..((((((........))))))..))..)).)))))))... ( -32.50)
>DroSim_CAF1 31024 105 + 1
GAGCUGUGUGACGUGGAGCAUUCAUGUCAGUCGCCAGGCUUAAGCCC-CCCUUUUCCACGCCCCUGUCUACUUUUGCUUGCAAGUGGCAAGUCGCUUGGAAAAAUU
(((((((((((((((((...)))))))))..)))..)))))......-...(((((((.((..((..((((((........))))))..))..)).)))))))... ( -30.50)
>DroEre_CAF1 28899 104 + 1
GAGCUGGGUGACGUGGAGCAUUCAUGUCAGUCGCCAGGCUUAAGCCC--CCUUUUCCACGCCCCUGUCUACUUUUACUUGCAAGUGGCAAGUCGCUUGGAAAAAUU
(.((.((.(((((((((...))))))))).))))).(((....))).--..(((((((.((..((..((((((........))))))..))..)).)))))))... ( -33.00)
>DroYak_CAF1 16726 105 + 1
GAGCUGGGUGACGUGGAGCAUUCAUGUCAGUCGCCAGGCUUAAGCCC-CCCUUUUCCACGCCCCUGUCUACUUUUACUUGCAAGUGGCAAGUCGCUUGGAAAAAUU
(.((.((.(((((((((...))))))))).))))).(((....))).-...(((((((.((..((..((((((........))))))..))..)).)))))))... ( -33.00)
>consensus
GAGCUGGGUGACGUGGAGCAUUCAUGUCAGUCGCCAGGCUUAAGCCC_CCCUUUUCCACGCCCCUGUCUACUUUUGCUUGCAAGUGGCAAGUCGCUUGGAAAAAUU
.....((.(((((((((...))))))))).))....(((....))).....(((((((.((..((..((((((........))))))..))..)).)))))))... (-30.48 = -30.68 +   0.20)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,467,857 – 5,467,972
Length 115
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 98.08
Mean single sequence MFE -28.76
Consensus MFE -27.30
Energy contribution -27.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.20
Structure conservation index 0.95
SVM decision value 0.13
SVM RNA-class probability 0.599594
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5467857 115 + 23771897
UCGCCAGGCUUAAGCCCCCCCUUUUCCACGCCCCUGUCUACUUUUGCUUGCAAGUGGCAAGUCGCGUGGAAAAAUUAUGUUGCACGUGAUAUGCUUCAGCAAAUUCGCUACAUGU
..((..(((....))).....((((((((((..((..((((((........))))))..))..))))))))))........))..((((..(((....)))...))))....... ( -33.40)
>DroSec_CAF1 29433 114 + 1
UCUCCAGGCUUAAGCCC-CCCUUUUCCACGCCCCUGUCUACUUUUGCUUGCAAGUGGCAAGUCGCUUGGAAAAAUUAUGUUGCACGUGAUAUGCUUCAGCAAAUUCGCUACAUGU
......(((....))).-...(((((((.((..((..((((((........))))))..))..)).)))))))..(((((.....((((..(((....)))...)))).))))). ( -27.30)
>DroSim_CAF1 31054 114 + 1
UCGCCAGGCUUAAGCCC-CCCUUUUCCACGCCCCUGUCUACUUUUGCUUGCAAGUGGCAAGUCGCUUGGAAAAAUUAUGUUGCACGUGAUAUGCUUCAGCAAAUUCGCUACAUGU
..((..(((....))).-...(((((((.((..((..((((((........))))))..))..)).)))))))........))..((((..(((....)))...))))....... ( -27.70)
>DroEre_CAF1 28929 113 + 1
UCGCCAGGCUUAAGCCC--CCUUUUCCACGCCCCUGUCUACUUUUACUUGCAAGUGGCAAGUCGCUUGGAAAAAUUAUGUUGCACGUGAUAUGCUUCAGCAAAUUCGCUACAUGU
..((..(((....))).--..(((((((.((..((..((((((........))))))..))..)).)))))))........))..((((..(((....)))...))))....... ( -27.70)
>DroYak_CAF1 16756 114 + 1
UCGCCAGGCUUAAGCCC-CCCUUUUCCACGCCCCUGUCUACUUUUACUUGCAAGUGGCAAGUCGCUUGGAAAAAUUAUGUUGCACGUGAUAUGCUUCAGCAAAUUCGCUACAUGU
..((..(((....))).-...(((((((.((..((..((((((........))))))..))..)).)))))))........))..((((..(((....)))...))))....... ( -27.70)
>consensus
UCGCCAGGCUUAAGCCC_CCCUUUUCCACGCCCCUGUCUACUUUUGCUUGCAAGUGGCAAGUCGCUUGGAAAAAUUAUGUUGCACGUGAUAUGCUUCAGCAAAUUCGCUACAUGU
......(((....))).....(((((((.((..((..((((((........))))))..))..)).)))))))..(((((.....((((..(((....)))...)))).))))). (-27.30 = -27.30 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:59 2006