Locus 6166

Sequence ID X_DroMel_CAF1
Location 15,731,930 – 15,732,083
Length 153
Max. P 0.733123
window10043 window10044

overview

Window 3

Location 15,731,930 – 15,732,043
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.79
Mean single sequence MFE -25.67
Consensus MFE -18.58
Energy contribution -18.86
Covariance contribution 0.28
Combinations/Pair 1.32
Mean z-score -1.66
Structure conservation index 0.72
SVM decision value 0.26
SVM RNA-class probability 0.655947
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15731930 113 - 22224390
AUGAGGGAUGCUGGAUGAAACCACCAGGCGACUGACUGGCACACAAUGAUUUGGAAGGAAACAGCGUCCUAAAAGUUCCGAAAAGGAAGGAAAUAGGUAGAGUUAU-------AAGCCCA
....(((((((((.......(((.(((....)))..)))....(((....)))........))))))))).....((((.....)))).......(((........-------..))).. ( -26.50)
>DroSec_CAF1 4748 111 - 1
AUGAGGGAUGCUGGAUGAAA---------GGUCGACUGGUGUACAAUGAGUUGGAAGGAAACAGCAUCCUAAAAGUCCCGAAAAGGAAGGAAAUAGAUAGUCAUGUAUAGCUGAAGCCUA
....(((((...(((((...---------..((((((.((.....)).))))))..(....)..))))).....)))))....(((..((..(((.((....)).)))..))....))). ( -28.40)
>DroSim_CAF1 5064 111 - 1
AUGAGGGAUGCUGGAUGAAA---------GGUCGGCUGGUUUACAAUGAGUUGGAAGGAAACAGCAUCCUAAAAGUCCCGAAAAGGAAGGAAAUAGAUAGUUAUGUAUAGCUGAAGCCCA
....(((((((((.......---------..((((((.((.....)).)))))).......))))))))).....(((......)))..........((((((....))))))....... ( -25.69)
>DroEre_CAF1 4772 107 - 1
AUGAGGGAAUCUGGAUGAAA---------GGUCGACUGGCUUACAAUGAGUUGGAAGGAAACAACCUCUUAAAAGUCCCGAAAAGGAAGGAAAUAGGUAGUU----ACAGCUUACACCCA
....(((............(---------((((....)))))....(((((((...(....).((((........(((......))).......))))....----.)))))))..))). ( -22.66)
>DroYak_CAF1 4902 107 - 1
AUGAGGGAAACUGGAUGAAA---------GAUCGACUGGUUUACAAUGAGUUGGAAGGAAACAACAUCCUAAAAGUCCCGAAAAGGAAGGAAAUAGAUAGCU----AUAGCUUACACCCA
....((((....(((((...---------..((((((.((.....)).))))))..(....)..)))))......)))).....((.(((..((((....))----))..)))....)). ( -25.10)
>consensus
AUGAGGGAUGCUGGAUGAAA_________GGUCGACUGGUUUACAAUGAGUUGGAAGGAAACAGCAUCCUAAAAGUCCCGAAAAGGAAGGAAAUAGAUAGUU_U_UAUAGCUGAAGCCCA
....(((((...(((((..............((((((.((.....)).))))))..(....)..))))).....)))))......................................... (-18.58 = -18.86 +   0.28)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,731,963 – 15,732,083
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.65
Mean single sequence MFE -28.66
Consensus MFE -24.40
Energy contribution -24.60
Covariance contribution 0.20
Combinations/Pair 1.27
Mean z-score -1.65
Structure conservation index 0.85
SVM decision value 0.43
SVM RNA-class probability 0.733123
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15731963 120 - 22224390
GCUGUUCAAUUCAGAGGCAGGAAGGAAGUUUCUGGCAUAAAUGAGGGAUGCUGGAUGAAACCACCAGGCGACUGACUGGCACACAAUGAUUUGGAAGGAAACAGCGUCCUAAAAGUUCCG
((((((...(((...(.(((...((.....((..((((.........))))..)).....))..(((....))).))).)...(((....))))))...))))))............... ( -30.20)
>DroSec_CAF1 4788 110 - 1
GCA-UAGUAUUCAGAGGCAGGAAGGAAGUUUCUGGCAUAAAUGAGGGAUGCUGGAUGAAA---------GGUCGACUGGUGUACAAUGAGUUGGAAGGAAACAGCAUCCUAAAAGUCCCG
.((-(..(((((((((((.........)))))))).))).))).(((((...(((((...---------..((((((.((.....)).))))))..(....)..))))).....))))). ( -32.10)
>DroSim_CAF1 5104 110 - 1
GCA-UAGUAUUCAGAGGCAGGAAGGAAGUUUCUGGCAUAAAUGAGGGAUGCUGGAUGAAA---------GGUCGGCUGGUUUACAAUGAGUUGGAAGGAAACAGCAUCCUAAAAGUCCCG
.((-(..(((((((((((.........)))))))).))).))).(((((...(((((...---------..((((((.((.....)).))))))..(....)..))))).....))))). ( -30.50)
>DroEre_CAF1 4808 110 - 1
GCA-AAGUAUUUAAAGGCAACAAGGAAAUUGCUGGCAUAUAUGAGGGAAUCUGGAUGAAA---------GGUCGACUGGCUUACAAUGAGUUGGAAGGAAACAACCUCUUAAAAGUCCCG
...-..((((.....(((((........))))).....))))..((((..((...(((.(---------(((...(..((((.....))))..)..(....).)))).)))..)))))). ( -23.40)
>DroYak_CAF1 4938 110 - 1
GCA-AAGUAUUUAAAGGCAACAAGGAAAUUGCUGGCAUAAAUGAGGGAAACUGGAUGAAA---------GAUCGACUGGUUUACAAUGAGUUGGAAGGAAACAACAUCCUAAAAGUCCCG
...-...((((((..(((((........)))))....)))))).((((....(((((...---------..((((((.((.....)).))))))..(....)..)))))......)))). ( -27.10)
>consensus
GCA_UAGUAUUCAGAGGCAGGAAGGAAGUUUCUGGCAUAAAUGAGGGAUGCUGGAUGAAA_________GGUCGACUGGUUUACAAUGAGUUGGAAGGAAACAGCAUCCUAAAAGUCCCG
...............(.((((((.....)))))).)........(((((...(((((..............((((((.((.....)).))))))..(....)..))))).....))))). (-24.40 = -24.60 +   0.20)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:10 2006