Locus 8216

Sequence ID X_DroMel_CAF1
Location 20,418,095 – 20,418,236
Length 141
Max. P 0.999855
window13501 window13502

overview

Window 1

Location 20,418,095 – 20,418,197
Length 102
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 88.29
Mean single sequence MFE -28.23
Consensus MFE -24.32
Energy contribution -24.85
Covariance contribution 0.53
Combinations/Pair 1.03
Mean z-score -1.69
Structure conservation index 0.86
SVM decision value 0.37
SVM RNA-class probability 0.708144
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20418095 102 + 22224390
-CGCGUUCACGUUGCACCC-------C----------CCCGCCAACACAUGUACGACAUGUAAAUUGUUUCAAUUUGCGGCAUUUGCCGUAAAGCUGCGCAAUUUUCGACAUGCCAUGGA
-.(((.......)))....-------.----------....(((...(((((.(((.....(((((((.....((((((((....)))))))).....)))))))))))))))...))). ( -28.10)
>DroSec_CAF1 7464 106 + 1
-CGCGCUCACGUUGCACCC-------CCCC------CCCCGCCAACACAUGUACGACAUGUAAAUUGUUUCAAUUUGCGGCAUUUGCCGUAAAGCUGCGCAAUUUUCGACAUGCCAUGGA
-...((.......))....-------....------.....(((...(((((.(((.....(((((((.....((((((((....)))))))).....)))))))))))))))...))). ( -27.60)
>DroAna_CAF1 8083 103 + 1
CCCCAUCCUCGCUUCAAUU-------C----------GCGGCCAACACAUGUACAACAUGUAAAUUGUUUCAAUUUGCGGCAUUUGCCGUAAAGCUGCGCAAUUUUCGACAUGCCAUGGA
..((((....((.......-------.----------))(((....(((((.....)))))(((((((.....((((((((....)))))))).....))))))).......))))))). ( -29.60)
>DroSim_CAF1 3887 102 + 1
-CGCGCUCACGUUGCACCC-------C----------CCCGCCAACACAUGUACGACAUGUAAAUUGUUUCAAUUUGCGGCAUUUGCCGUAAAGCUGCGCAAUUUUCGACAUGCCAUGGA
-...((.......))....-------.----------....(((...(((((.(((.....(((((((.....((((((((....)))))))).....)))))))))))))))...))). ( -27.60)
>DroEre_CAF1 6737 119 + 1
-CGCGUUCACGUUGCACACCACCCACACCCCCCGUCCCCCGCCAACACAUGUAGGACAUGUAAAUUGUUUCAAUUUGCGGCAUUUGCCGUAAAGCUGCGCAAUUUUCGACAUGCCAUGGA
-.(((.......)))...(((............((((..((........))..))))(((((((((((.....((((((((....)))))))).....)))))))...))))....))). ( -28.40)
>DroYak_CAF1 3509 106 + 1
-CGCGUUCACGUUGCACAC-------ACCC------CCCCGCCAACACAUGUACGACAUGUAAAUUGUUUCAAUUUGCGGCAUUUGCCGUAAAGCUGCGCAAUUUUCGACAUGCCAUGGA
-.(((.......)))....-------....------.....(((...(((((.(((.....(((((((.....((((((((....)))))))).....)))))))))))))))...))). ( -28.10)
>consensus
_CGCGUUCACGUUGCACCC_______C__________CCCGCCAACACAUGUACGACAUGUAAAUUGUUUCAAUUUGCGGCAUUUGCCGUAAAGCUGCGCAAUUUUCGACAUGCCAUGGA
..(((.......)))..........................(((...(((((.(((.....(((((((.....((((((((....)))))))).....)))))))))))))))...))). (-24.32 = -24.85 +   0.53)

alignment

Postscript

secondary structure

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dotplot

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Window 2

Location 20,418,117 – 20,418,236
Length 119
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.26
Mean single sequence MFE -33.15
Consensus MFE -31.24
Energy contribution -31.60
Covariance contribution 0.36
Combinations/Pair 1.03
Mean z-score -2.91
Structure conservation index 0.94
SVM decision value 4.27
SVM RNA-class probability 0.999855
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20418117 119 + 22224390
GCCAACACAUGUACGACAUGUAAAUUGUUUCAAUUUGCGGCAUUUGCCGUAAAGCUGCGCAAUUUUCGACAUGCCAUGGAUACCCAUGGACCUGUCCGUUCGUCCACCAACAACCC-CAU
((.((((((((.....)))))(((((((.....((((((((....)))))))).....)))))))..((((.(((((((....)))))).).)))).))).)).............-... ( -35.50)
>DroSec_CAF1 7490 119 + 1
GCCAACACAUGUACGACAUGUAAAUUGUUUCAAUUUGCGGCAUUUGCCGUAAAGCUGCGCAAUUUUCGACAUGCCAUGGAUACCCAUGGACCUGUCCGUCCGUCCGCCAACAACCC-CAU
((..(((((((.....)))))(((((((.....((((((((....)))))))).....)))))))..((((.(((((((....)))))).).)))).....))..)).........-... ( -36.00)
>DroAna_CAF1 8106 115 + 1
GCCAACACAUGUACAACAUGUAAAUUGUUUCAAUUUGCGGCAUUUGCCGUAAAGCUGCGCAAUUUUCGACAUGCCAUGGAUACUCAUAGA---GUCCUUU-UUCGA-GUCCAACCCUUAU
......(((((.....)))))(((((((.....((((((((....)))))))).....)))))))..(((.((....((((.(.....).---))))...-..)).-))).......... ( -26.20)
>DroSim_CAF1 3909 119 + 1
GCCAACACAUGUACGACAUGUAAAUUGUUUCAAUUUGCGGCAUUUGCCGUAAAGCUGCGCAAUUUUCGACAUGCCAUGGAUACCCAUGGACCUGUCCGUCCGUCCGCCAACAACCC-CAU
((..(((((((.....)))))(((((((.....((((((((....)))))))).....)))))))..((((.(((((((....)))))).).)))).....))..)).........-... ( -36.00)
>DroEre_CAF1 6776 115 + 1
GCCAACACAUGUAGGACAUGUAAAUUGUUUCAAUUUGCGGCAUUUGCCGUAAAGCUGCGCAAUUUUCGACAUGCCAUGGAUACCCAUGGACUUGUCC----AUCCACCAACAACCC-CAU
.........(((.((....(.(((((((.....((((((((....)))))))).....))))))).)((((..((((((....))))))...)))).----.....)).)))....-... ( -35.30)
>DroYak_CAF1 3535 115 + 1
GCCAACACAUGUACGACAUGUAAAUUGUUUCAAUUUGCGGCAUUUGCCGUAAAGCUGCGCAAUUUUCGACAUGCCAUGGAUACCCAUGAACUUGUCC----GUCCACCAACAACCC-CAU
......(((((.....)))))(((((((.....((((((((....)))))))).....)))))))..((((...(((((....)))))....)))).----...............-... ( -29.90)
>consensus
GCCAACACAUGUACGACAUGUAAAUUGUUUCAAUUUGCGGCAUUUGCCGUAAAGCUGCGCAAUUUUCGACAUGCCAUGGAUACCCAUGGACCUGUCCGU__GUCCACCAACAACCC_CAU
......(((((.....)))))(((((((.....((((((((....)))))))).....)))))))..((((..((((((....))))))...))))........................ (-31.24 = -31.60 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:58:39 2006