Locus 533

Sequence ID 3L_DroMel_CAF1
Location 1,562,895 – 1,563,033
Length 138
Max. P 0.707999
window805 window806

overview

Window 5

Location 1,562,895 – 1,562,993
Length 98
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 77.08
Mean single sequence MFE -23.75
Consensus MFE -13.32
Energy contribution -15.45
Covariance contribution 2.13
Combinations/Pair 1.21
Mean z-score -1.98
Structure conservation index 0.56
SVM decision value 0.37
SVM RNA-class probability 0.707999
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1562895 98 - 23771897
AUUUUGGG--UUUUGUGCGUGGGU--UUUCUUUUCACAGUGCUAGCGUAUAAGUAAUAAGUAAACAGAGUAGUCUGGCUGUUUAUUGAUAUAUUCGAGGAGU
.(((((((--((((((((((.(((--...((......)).))).)))))))))(((((((((..((((....))))..)))))))))....))))))))... ( -20.50)
>DroSec_CAF1 7323 95 - 1
AUUUUGGG--CUUUGUGAGUGGAUGGUUUCCAUUCACAGUGCUAGCGU--AAGUAAUAAGUAAACAGCGAAGUCUGCCUGUUUAUUGAUAUAUUCGA---GU
......((--(.(((((((((((.....))))))))))).))).((..--..))....(((((((((((.....)).)))))))))...........---.. ( -29.20)
>DroSim_CAF1 7419 95 - 1
AUUUUGGG--UUUUGUGAGUGGAUGGUUUCCAUUCACAGUGCUAGCGU--AAGUAAUAAGUAAACAGAGAAGUCUGCCUGUUUAUUGAUAUAUUCGA---GU
......((--(.(((((((((((.....))))))))))).))).((..--..))....(((((((((((....))..)))))))))...........---.. ( -27.10)
>DroYak_CAF1 7514 80 - 1
AUAUUAUGUAUUUUGUGGGUG-----------------CUGCCAGCAU--AGGCAAUAAAUAAACAAAGAAGUCUGACUGUUUAUUGAUGCAUUCGA---GU
...............((((((-----------------(((((.....--.))))...((((((((.((....))...))))))))...))))))).---.. ( -18.20)
>consensus
AUUUUGGG__UUUUGUGAGUGGAU__UUUCCAUUCACAGUGCUAGCGU__AAGUAAUAAGUAAACAGAGAAGUCUGCCUGUUUAUUGAUAUAUUCGA___GU
............(((((((((((.....)))))))))))((((........))))...(((((((((..........)))))))))................ (-13.32 = -15.45 +   2.13) 

alignment

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secondary structure

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dotplot

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Window 6

Location 1,562,917 – 1,563,033
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.30
Mean single sequence MFE -26.41
Consensus MFE -16.14
Energy contribution -19.45
Covariance contribution 3.31
Combinations/Pair 1.10
Mean z-score -1.97
Structure conservation index 0.61
SVM decision value 0.37
SVM RNA-class probability 0.707716
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1562917 116 + 23771897
CAGCCAGACUACUCUGUUUACUUAUUACUUAUACGCUAGCACUGUGAAAAGAAA--ACCCACGCACAAAA--CCCAAAAUAAGCGGAGAUAAGCUGUUGGGCAACCAAAAUAUCGUUUGC
....(((((..(((((((((..............(....)..((((....(...--..)....))))...--.......)))))))))........((((....))))......))))). ( -20.80)
>DroSec_CAF1 7342 116 + 1
CAGGCAGACUUCGCUGUUUACUUAUUACUU--ACGCUAGCACUGUGAAUGGAAACCAUCCACUCACAAAG--CCCAAAAUAAGCGGAGAUAAGCUCUUGGGCAACCAAAAUAUCGUUUGC
...((((((((((((((.............--))....((..(((((.((((.....)))).)))))..)--)........))))))((((.....((((....))))..)))))))))) ( -30.72)
>DroSim_CAF1 7438 116 + 1
CAGGCAGACUUCUCUGUUUACUUAUUACUU--ACGCUAGCACUGUGAAUGGAAACCAUCCACUCACAAAA--CCCAAAAUAAGCAGAGAUAAGCUCUUGGGCAACCAAAAUAUCGUUUGC
...((((((.((((((((((..........--..(....)..(((((.((((.....)))).)))))...--.......)))))))))).......((((....))))......)))))) ( -33.70)
>DroYak_CAF1 7533 101 + 1
CAGUCAGACUUCUUUGUUUAUUUAUUGCCU--AUGCUGGCAG-----------------CACCCACAAAAUACAUAAUAUAAGAGGAGAUAAGCUCUUGGGCAACCAAAAUAUCGGUUGC
.....((((......))))......((((.--.....))))(-----------------((.((................(((((........)))))((....))........)).))) ( -20.40)
>consensus
CAGGCAGACUUCUCUGUUUACUUAUUACUU__ACGCUAGCACUGUGAAUGGAAA__AUCCACUCACAAAA__CCCAAAAUAAGCGGAGAUAAGCUCUUGGGCAACCAAAAUAUCGUUUGC
...((((((.((((((((((.......((........))...(((((.(((.......))).)))))............)))))))))).......((((....))))......)))))) (-16.14 = -19.45 +   3.31) 

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 09:44:33 2006