Locus 4942

Sequence ID 3R_DroMel_CAF1
Location 13,008,327 – 13,008,421
Length 94
Max. P 0.884355
window8087 window8088

overview

Window 7

Location 13,008,327 – 13,008,421
Length 94
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 80.45
Mean single sequence MFE -25.56
Consensus MFE -19.33
Energy contribution -19.50
Covariance contribution 0.17
Combinations/Pair 1.20
Mean z-score -1.73
Structure conservation index 0.76
SVM decision value 0.75
SVM RNA-class probability 0.840643
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13008327 94 + 27905053
--------------AAUCCAUCCAAGCCCCCUGGCUGAAUGGAC---CAUACAUAUUGCCAUUUUCAGCGACCUAUGCAAUUCGCCGGCCUUGUUGACAUUGUCCGGCAAC
--------------..(((((...((((....))))..))))).---....((((((((........))))..))))......((((((..((....))..).)))))... ( -25.10)
>DroPse_CAF1 36319 81 + 1
----------------UCCC-----CCCUU---------UGGGCCCACACGCAUAUUGCCGUUUUCAGCGACCUAUGCAAUUCGUUGGCCAUGUGGACAUUGGCCAGCAAC
----------------...(-----((...---------.))).......(((((((((.(....).))))..))))).....((((((((((....)).))))))))... ( -25.20)
>DroSec_CAF1 28452 94 + 1
--------------AAUCCAUCCAGGCCCUACGGCUGAAUGGAC---CAUACAUAUUGCCAUUUUCAGCGACCUAUGCAAUUCGCCGGCGUUGUUGACAUUGUCCGGCAAC
--------------..(((((...((((....))))..))))).---....((((((((........))))..))))......(((((((.((....)).)).)))))... ( -25.90)
>DroSim_CAF1 20817 94 + 1
--------------AAUCCAUCCAGGCCCUACGGCUGAAUGGAC---CAUACAUAUUGCCAUUUUCAGCGACCUAUGCAAUUCGCCGGCGUUGUUGACAUUGUCCGGCAAC
--------------..(((((...((((....))))..))))).---....((((((((........))))..))))......(((((((.((....)).)).)))))... ( -25.90)
>DroEre_CAF1 29060 100 + 1
--------CCAUCCAAUCCAUCCAAGCCCUCCGGCUGAAUGGGC---CAUACAUAUUGCCAUUUUCAGCGACCUAUGCAAUUCGCCGGCCUUGUUGACAUUGUCCGGCAAC
--------.................((......((((((..(((---.((....)).)))...)))))).......)).....((((((..((....))..).)))))... ( -24.72)
>DroYak_CAF1 29631 108 + 1
CAUCCAGUCCAUCCAGUCCACCCAAGCCCUCCGGCUGAAUGGGC---CAUACAUAUUGCCAUUUUCAGCGACCUAUGCAAUUCGCUGUCCUUGUUGACAUUGUCCGGCAAC
......((((((.(((((..............))))).))))))---........(((((.....((((((..........))))))........(((...))).))))). ( -26.54)
>consensus
______________AAUCCAUCCAAGCCCUCCGGCUGAAUGGAC___CAUACAUAUUGCCAUUUUCAGCGACCUAUGCAAUUCGCCGGCCUUGUUGACAUUGUCCGGCAAC
................(((((...((((....))))..)))))........((((((((........))))..))))......((((((..((....))..).)))))... (-19.33 = -19.50 +   0.17)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,008,327 – 13,008,421
Length 94
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 80.45
Mean single sequence MFE -32.68
Consensus MFE -25.31
Energy contribution -26.03
Covariance contribution 0.73
Combinations/Pair 1.14
Mean z-score -1.90
Structure conservation index 0.77
SVM decision value 0.93
SVM RNA-class probability 0.884355
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13008327 94 - 27905053
GUUGCCGGACAAUGUCAACAAGGCCGGCGAAUUGCAUAGGUCGCUGAAAAUGGCAAUAUGUAUG---GUCCAUUCAGCCAGGGGGCUUGGAUGGAUU--------------
.(((((((.(..((....))..))))))))..((((((....(((......)))..)))))).(---((((((((((((....))).))))))))))-------------- ( -35.30)
>DroPse_CAF1 36319 81 - 1
GUUGCUGGCCAAUGUCCACAUGGCCAACGAAUUGCAUAGGUCGCUGAAAACGGCAAUAUGCGUGUGGGCCCA---------AAGGG-----GGGA----------------
.(((.((((((.((....)))))))).)))...(((((....((((....))))..))))).......(((.---------...))-----)...---------------- ( -25.30)
>DroSec_CAF1 28452 94 - 1
GUUGCCGGACAAUGUCAACAACGCCGGCGAAUUGCAUAGGUCGCUGAAAAUGGCAAUAUGUAUG---GUCCAUUCAGCCGUAGGGCCUGGAUGGAUU--------------
.(((((((....((....))...)))))))..((((((....(((......)))..)))))).(---((((((((((((....)).)))))))))))-------------- ( -34.60)
>DroSim_CAF1 20817 94 - 1
GUUGCCGGACAAUGUCAACAACGCCGGCGAAUUGCAUAGGUCGCUGAAAAUGGCAAUAUGUAUG---GUCCAUUCAGCCGUAGGGCCUGGAUGGAUU--------------
.(((((((....((....))...)))))))..((((((....(((......)))..)))))).(---((((((((((((....)).)))))))))))-------------- ( -34.60)
>DroEre_CAF1 29060 100 - 1
GUUGCCGGACAAUGUCAACAAGGCCGGCGAAUUGCAUAGGUCGCUGAAAAUGGCAAUAUGUAUG---GCCCAUUCAGCCGGAGGGCUUGGAUGGAUUGGAUGG--------
....(((..(((((((((((.((((.((.....))...))))(((......)))....))).))---))((((((((((....))).)))))))))))..)))-------- ( -34.60)
>DroYak_CAF1 29631 108 - 1
GUUGCCGGACAAUGUCAACAAGGACAGCGAAUUGCAUAGGUCGCUGAAAAUGGCAAUAUGUAUG---GCCCAUUCAGCCGGAGGGCUUGGGUGGACUGGAUGGACUGGAUG
((((((((((...)))........((((((..........))))))....))))))).......---..((((((((((....))).))))))).(..(.....)..)... ( -31.70)
>consensus
GUUGCCGGACAAUGUCAACAAGGCCGGCGAAUUGCAUAGGUCGCUGAAAAUGGCAAUAUGUAUG___GCCCAUUCAGCCGGAGGGCUUGGAUGGAUU______________
.(((((((.(..((....))..))))))))..((((((....(((......)))..)))))).......((((((((((....))).)))))))................. (-25.31 = -26.03 +   0.73)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:37 2006