Locus 2194

Sequence ID X_DroMel_CAF1
Location 5,940,487 – 5,940,628
Length 141
Max. P 0.995749
window3563 window3564

overview

Window 3

Location 5,940,487 – 5,940,588
Length 101
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 78.18
Mean single sequence MFE -33.67
Consensus MFE -20.56
Energy contribution -22.10
Covariance contribution 1.54
Combinations/Pair 1.20
Mean z-score -2.79
Structure conservation index 0.61
SVM decision value 2.28
SVM RNA-class probability 0.991707
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5940487 101 - 22224390
GCUCAACCAGUCUCUUCACAUGGCAACAGAUGGUAGAGAUUGCUUUUUUAUUUGGAAGAGAUAUUCCCCUAGAA---------GCACUGAUUUGGGGUCACCUUUUCGAA
..((...(((((((((((..((....))..))).))))))))............((((((......(((((((.---------.......)))))))....)))))))). ( -27.00)
>DroSec_CAF1 27885 106 - 1
UUUCAUCCAGUGUCUUCACAUGGCAACAGAUGGAAAAGAUUGAUUUUUCAAUUGGUGAAGACAUCC----AUUUGGGGUAACCCCACUGAUUUGGGGUCACCUUUCGGUA
......((.((((((((((.((....))..(((((((......)))))))....))))))))))..----....(((((.((((((......)))))).)))))..)).. ( -37.30)
>DroSim_CAF1 34163 110 - 1
GUUCAACCAGUGUCUUCACAUGGCAACGGAUGGAAAAGAUUGAUUUUUCAAUUGGUGAAGAUAUCCACCUAUUUGGGGUCACCCCACUGAUUUGGGGUCACCUUUCGGUA
.....(((.((((((((((.((....))..(((((((......)))))))....))))))))))(((......)))(((.((((((......)))))).)))....))). ( -36.70)
>consensus
GUUCAACCAGUGUCUUCACAUGGCAACAGAUGGAAAAGAUUGAUUUUUCAAUUGGUGAAGAUAUCC_CCUAUUUGGGGU_ACCCCACUGAUUUGGGGUCACCUUUCGGUA
.........((((((((((.((....))..(((((((......)))))))....)))))))))).........((((.....))))((((...(((....))).)))).. (-20.56 = -22.10 +   1.54)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 5,940,514 – 5,940,628
Length 114
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 67.65
Mean single sequence MFE -26.50
Consensus MFE -14.52
Energy contribution -14.87
Covariance contribution 0.34
Combinations/Pair 1.26
Mean z-score -2.12
Structure conservation index 0.55
SVM decision value 2.61
SVM RNA-class probability 0.995749
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5940514 114 - 22224390
CAUUAUUUAAAGCUUUGGUUGGAUUGUAACCACAAGCCCAGCUCAACCAGUCUCUUCACAUGGCAACAGAUGGUAGAGAUUGCUUUUUUAUUUGGAAGAGAUAUUCCCCUAGAA------
........(((((.((((((((.((((....))))..))))).)))..((((((((((..((....))..))).)))))))))))).......((((......)))).......------ ( -29.20)
>DroSec_CAF1 27915 96 - 1
CCAU-----AAGCUU---------------CAUAAACAAAUUUCAUCCAGUGUCUUCACAUGGCAACAGAUGGAAAAGAUUGAUUUUUCAAUUGGUGAAGACAUCC----AUUUGGGGUA
....-----......---------------.........((..((....((((((((((.((....))..(((((((......)))))))....))))))))))..----...))..)). ( -24.70)
>DroSim_CAF1 34193 100 - 1
CCAU-----AAGCUU---------------CAUAAACCCAGUUCAACCAGUGUCUUCACAUGGCAACGGAUGGAAAAGAUUGAUUUUUCAAUUGGUGAAGAUAUCCACCUAUUUGGGGUC
....-----......---------------......(((((........((((((((((.((....))..(((((((......)))))))....))))))))))........)))))... ( -25.59)
>consensus
CCAU_____AAGCUU_______________CAUAAACCCAGUUCAACCAGUGUCUUCACAUGGCAACAGAUGGAAAAGAUUGAUUUUUCAAUUGGUGAAGAUAUCC_CCUAUUUGGGGU_
.................................................((((((((((.((....))..(((((((......)))))))....))))))))))................ (-14.52 = -14.87 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:30 2006