Locus 1452

Sequence ID 3R_DroMel_CAF1
Location 4,180,059 – 4,180,174
Length 115
Max. P 0.816725
window2416 window2417

overview

Window 6

Location 4,180,059 – 4,180,174
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 89.30
Mean single sequence MFE -34.91
Consensus MFE -26.60
Energy contribution -27.16
Covariance contribution 0.56
Combinations/Pair 1.08
Mean z-score -2.78
Structure conservation index 0.76
SVM decision value 0.67
SVM RNA-class probability 0.816725
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4180059 115 + 27905053
UGCAAAUGAAAUGCAAACUUUGGCAGGCGGGAAAAUUGCUUUCGAAUGUUUCGUUUUUUACUCGCUUUUUAUUGGGCAUUUCCCUUUCUCGCCGGCCGG-----UGCCAACGCUCCAAAU
((((.......))))......(((.(((((((((........(((.....)))..........((((......)))).......))))))))).)))((-----.((....)).)).... ( -30.90)
>DroSim_CAF1 30483 115 + 1
UGCAUAUGAAAUGCAAACUUUGGCAGGCGGGAAAAUUGCUUUCGAAUGUCUCGUUUUUUACUCGCUUUUUAUUCGCUCUCUCCCUUUCUCGCCUGCCGG-----UGCCAACGCUCCAAAU
(((((.....)))))......(((((((((((((........((((((...((.........)).....)))))).........)))))))))))))((-----.((....)).)).... ( -35.43)
>DroYak_CAF1 30551 120 + 1
UGCAUAUGAAAUGCAAACACUGGCAGGCGGGAAAAUUGCUUUCGAAUGCUUCGUUUUUUACUCGCUUUUUACUCGUUUUUUCCCUUUCUUGCCUGCCGGUGCGGUGCCAACGCUCCAAAU
(((((.....)))))..(((((((((((((((((...((........))...((.....)).......................))))))))))))))))).((.((....)).)).... ( -38.40)
>consensus
UGCAUAUGAAAUGCAAACUUUGGCAGGCGGGAAAAUUGCUUUCGAAUGUUUCGUUUUUUACUCGCUUUUUAUUCGCUAUUUCCCUUUCUCGCCUGCCGG_____UGCCAACGCUCCAAAU
............(((....(((((((((((((((........((((((...((.........)).....)))))).........))))))))))))))).....)))............. (-26.60 = -27.16 +   0.56)

alignment

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secondary structure

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dotplot

Postscript

Window 7

Location 4,180,059 – 4,180,174
Length 115
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 89.30
Mean single sequence MFE -33.41
Consensus MFE -24.48
Energy contribution -25.59
Covariance contribution 1.11
Combinations/Pair 1.03
Mean z-score -2.16
Structure conservation index 0.73
SVM decision value -0.04
SVM RNA-class probability 0.512697
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4180059 115 - 27905053
AUUUGGAGCGUUGGCA-----CCGGCCGGCGAGAAAGGGAAAUGCCCAAUAAAAAGCGAGUAAAAAACGAAACAUUCGAAAGCAAUUUUCCCGCCUGCCAAAGUUUGCAUUUCAUUUGCA
.....((((.((((((-----..(((.((.(((((.(((.....))).........(((((............))))).......)))))))))))))))).))))(((.......))). ( -30.00)
>DroSim_CAF1 30483 115 - 1
AUUUGGAGCGUUGGCA-----CCGGCAGGCGAGAAAGGGAGAGAGCGAAUAAAAAGCGAGUAAAAAACGAGACAUUCGAAAGCAAUUUUCCCGCCUGCCAAAGUUUGCAUUUCAUAUGCA
....((.((....)).-----))((((((((.....((((((..((..........(((((............)))))...))..))))))))))))))......(((((.....))))) ( -33.02)
>DroYak_CAF1 30551 120 - 1
AUUUGGAGCGUUGGCACCGCACCGGCAGGCAAGAAAGGGAAAAAACGAGUAAAAAGCGAGUAAAAAACGAAGCAUUCGAAAGCAAUUUUCCCGCCUGCCAGUGUUUGCAUUUCAUAUGCA
....((.((....)).))((((.(((((((......(((((((............((..((.....))...))...(....)...)))))))))))))).)))).(((((.....))))) ( -37.20)
>consensus
AUUUGGAGCGUUGGCA_____CCGGCAGGCGAGAAAGGGAAAAAACGAAUAAAAAGCGAGUAAAAAACGAAACAUUCGAAAGCAAUUUUCCCGCCUGCCAAAGUUUGCAUUUCAUAUGCA
.....((((...((.......))((((((((.(((((........(((((......((.........))....))))).......))))).))))))))...))))((((.....)))). (-24.48 = -25.59 +   1.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:56 2006