Locus 3258

Sequence ID 2R_DroMel_CAF1
Location 11,140,957 – 11,141,049
Length 92
Max. P 0.996608
window5343 window5344

overview

Window 3

Location 11,140,957 – 11,141,049
Length 92
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 73.34
Mean single sequence MFE -34.51
Consensus MFE -22.21
Energy contribution -24.78
Covariance contribution 2.58
Combinations/Pair 1.34
Mean z-score -3.81
Structure conservation index 0.64
SVM decision value 2.72
SVM RNA-class probability 0.996608
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11140957 92 + 20766785
GCUGGGAAAAGUUGGUA-----AAAGUGGGGGGGCAAA-AUGGUGAAUGGCUGGCUAGCUGU-------AUAGCUGGCCAGUCAAGUGGCCAACUUUGUUGUGGC
((((.(((((((((((.-----...((......))...-........(((((((((((((..-------..)))))))))))))....))))))))).)).)))) ( -37.10)
>DroSec_CAF1 55531 85 + 1
GCUGGGAAAAUUUGG-A-----AAAGUGG--GGGCAAA-AGGC--CAUGGGCCGCCACCUUU-------AAGG--GGGCACAACAGGGGGCAACUUUUGUGUGGC
(((......((((..-.-----.))))..--.)))...-.(((--(...))))(((.(((..-------..))--))))(((.((((((....)))))))))... ( -26.30)
>DroSim_CAF1 51814 90 + 1
GCUGGGAAAAGUUGGUA-----AAAGUGG--GGGCAAA-AUGGUGAAUGGCUGGCUAGCUGU-------AUAGCUGGCCAGUCAAGUGGCCAACUUUGUUGUGGC
((((.(((((((((((.-----...((..--..))...-........(((((((((((((..-------..)))))))))))))....))))))))).)).)))) ( -36.90)
>DroEre_CAF1 58496 90 + 1
GCUGGGAAAAGUUGGUA-----AACGUGG--GGGCAAA-GUGGUGGAUGGCUGGCUAGCUGU-------AUAGCUGGCCAGUCAAGUGGGCAACUUUGUUGUGGC
((..(......)..)).-----...((.(--.((((((-((.((...(((((((((((((..-------..))))))))))))).....)).)))))))).).)) ( -34.90)
>DroYak_CAF1 55010 103 + 1
GCUGGGAAAAGUUGGGAAAGCAAAGUUGG--GGGCAAACGUGGUGGAUGACUGGCUAGCUGUAUGCUAUAUAGCUGGCCAGUUAAGUGGCCAACUUUGUUGUGGC
((((.((((((((((....((...(((..--.....)))...))...(((((((((((((((((...))))))))))))))))).....)))))))).)).)))) ( -40.40)
>DroAna_CAF1 54418 84 + 1
GGGCAGAAGAGGCGGCAGG------GCGA--GUGGAGA-AUGGAGGAGGGC----UA-CUGG-------CCAGUUGGCCAGUCAAGUGGCCAACUUUGUUGUGGC
...........((((((((------((.(--((((...-...........)----))-)).)-------))(((((((((......))))))))))))))))... ( -31.44)
>consensus
GCUGGGAAAAGUUGGUA_____AAAGUGG__GGGCAAA_AUGGUGGAUGGCUGGCUAGCUGU_______AUAGCUGGCCAGUCAAGUGGCCAACUUUGUUGUGGC
((((.(((((((((((.........((......)).............(((((((((((((((.....))))))))))))))).....))))))))).)).)))) (-22.21 = -24.78 +   2.58)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,140,957 – 11,141,049
Length 92
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 73.34
Mean single sequence MFE -19.80
Consensus MFE -9.18
Energy contribution -10.10
Covariance contribution 0.92
Combinations/Pair 1.33
Mean z-score -2.61
Structure conservation index 0.46
SVM decision value 2.30
SVM RNA-class probability 0.992055
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11140957 92 - 20766785
GCCACAACAAAGUUGGCCACUUGACUGGCCAGCUAU-------ACAGCUAGCCAGCCAUUCACCAU-UUUGCCCCCCCACUUU-----UACCAACUUUUCCCAGC
........((((((((.....((.(((((.((((..-------..)))).))))).))........-..((......))....-----..))))))))....... ( -20.30)
>DroSec_CAF1 55531 85 - 1
GCCACACAAAAGUUGCCCCCUGUUGUGCCC--CCUU-------AAAGGUGGCGGCCCAUG--GCCU-UUUGCCC--CCACUUU-----U-CCAAAUUUUCCCAGC
(((..((((.((.......)).))))(((.--((..-------...)).))))))....(--((..-...))).--.......-----.-............... ( -16.10)
>DroSim_CAF1 51814 90 - 1
GCCACAACAAAGUUGGCCACUUGACUGGCCAGCUAU-------ACAGCUAGCCAGCCAUUCACCAU-UUUGCCC--CCACUUU-----UACCAACUUUUCCCAGC
........((((((((.....((.(((((.((((..-------..)))).))))).))..((....-..))...--.......-----..))))))))....... ( -20.10)
>DroEre_CAF1 58496 90 - 1
GCCACAACAAAGUUGCCCACUUGACUGGCCAGCUAU-------ACAGCUAGCCAGCCAUCCACCAC-UUUGCCC--CCACGUU-----UACCAACUUUUCCCAGC
.......((((((........((.(((((.((((..-------..)))).))))).))......))-))))...--.......-----................. ( -18.34)
>DroYak_CAF1 55010 103 - 1
GCCACAACAAAGUUGGCCACUUAACUGGCCAGCUAUAUAGCAUACAGCUAGCCAGUCAUCCACCACGUUUGCCC--CCAACUUUGCUUUCCCAACUUUUCCCAGC
.......(((((((((.......((((((.((((.(((...))).)))).))))))((..(.....)..))...--))))))))).................... ( -24.20)
>DroAna_CAF1 54418 84 - 1
GCCACAACAAAGUUGGCCACUUGACUGGCCAACUGG-------CCAG-UA----GCCCUCCUCCAU-UCUCCAC--UCGC------CCUGCCGCCUCUUCUGCCC
((........(((((((((......)))))))))((-------(..(-((----(..(........-.......--..).------.)))).)))......)).. ( -19.73)
>consensus
GCCACAACAAAGUUGGCCACUUGACUGGCCAGCUAU_______ACAGCUAGCCAGCCAUCCACCAU_UUUGCCC__CCACUUU_____UACCAACUUUUCCCAGC
..........(((((((((......)))))))))............(((....)))................................................. ( -9.18 = -10.10 +   0.92)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:12 2006