Locus 1744

Sequence ID 3L_DroMel_CAF1
Location 5,041,423 – 5,041,581
Length 158
Max. P 0.926049
window2688 window2689 window2690

overview

Window 8

Location 5,041,423 – 5,041,542
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.15
Mean single sequence MFE -23.80
Consensus MFE -22.40
Energy contribution -22.24
Covariance contribution -0.16
Combinations/Pair 1.09
Mean z-score -1.36
Structure conservation index 0.94
SVM decision value 0.84
SVM RNA-class probability 0.863726
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5041423 119 + 23771897
GUCA-AAUCGAAUUUCGCAUUUGCUGGGCCAAAAACAUUAUCGCAUAAAUAAUGACAUCUACAGGCAUUUAAAAUGUCUGUCAUUGGUGGAACGUUUCAUUAAAAUAAACCAAUGAAAUG
(.((-(((((.....)).))))))...(((((...((((((.......))))))......((((((((.....))))))))..)))))....(((((((((..........))))))))) ( -24.60)
>DroSec_CAF1 247891 119 + 1
GUCA-AAUCGAAUUUCGCAUUUGCUGGGCCAAAAACAUUAUCGCAUAAAUAAUGACAUCUACAGGCAUUUAAAAUGUCUGUCAUUGGUGGAACGUUUCAUUAAAAUAAACCAAUGAAAUG
(.((-(((((.....)).))))))...(((((...((((((.......))))))......((((((((.....))))))))..)))))....(((((((((..........))))))))) ( -24.60)
>DroSim_CAF1 268753 119 + 1
GUCA-AAUCGAAUUUCGCAUUUGCUGGGCCAAAAACAUUAUCGCAUAAAUAAUGACAUCUACAGGCAUUUAAAAUGUCUGUCAUUGGUGGAACGUUUCAUUAAAAUAAACCAAUGAAAUG
(.((-(((((.....)).))))))...(((((...((((((.......))))))......((((((((.....))))))))..)))))....(((((((((..........))))))))) ( -24.60)
>DroEre_CAF1 251339 119 + 1
GUCA-AAUCGAAUUUCGCAUUUGCUGGGCCAAAAACAUUAUCGCAUAAAUGAUGACAUCUACAGGCAUUUAAAAUGUCUGUCAUUGGUGGAACGUUUCAUUAAAAUAAACCAAUGAAAUG
(.((-(((((.....)).))))))...(((((...((((((.......))))))......((((((((.....))))))))..)))))....(((((((((..........))))))))) ( -24.70)
>DroYak_CAF1 257728 120 + 1
UUAAAAAUCGAAUUUCGCAUUUGCUGGGCCAAAAACAUUAUCGCAUAAAUGAUGACAUCUACUGGCAUUUAAAAUGUCUAUCAUUGGUGGAACAUUUCAUUAAAAUAAACCAAUGGAAUG
...........(((((((....))(((((((......((((((......)))))).......)))).....((((((((((.....)))).))))))............)))..))))). ( -20.52)
>consensus
GUCA_AAUCGAAUUUCGCAUUUGCUGGGCCAAAAACAUUAUCGCAUAAAUAAUGACAUCUACAGGCAUUUAAAAUGUCUGUCAUUGGUGGAACGUUUCAUUAAAAUAAACCAAUGAAAUG
............((((((....))...(((((...((((((.......))))))......((((((((.....))))))))..)))))))))(((((((((..........))))))))) (-22.40 = -22.24 +  -0.16)

alignment

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secondary structure

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Window 9

Location 5,041,462 – 5,041,581
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.83
Mean single sequence MFE -24.10
Consensus MFE -20.56
Energy contribution -20.20
Covariance contribution -0.36
Combinations/Pair 1.11
Mean z-score -1.40
Structure conservation index 0.85
SVM decision value 0.47
SVM RNA-class probability 0.750069
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5041462 119 + 23771897
UCGCAUAAAUAAUGACAUCUACAGGCAUUUAAAAUGUCUGUCAUUGGUGGAACGUUUCAUUAAAAUAAACCAAUGAAAUGGCUUACUUUGGUUCCCUUUUCGCUUACACGGAA-AAAAUA
..((...........((((.((((((((.....))))))))....))))...(((((((((..........)))))))))))..............((((((......)))))-)..... ( -23.60)
>DroSec_CAF1 247930 120 + 1
UCGCAUAAAUAAUGACAUCUACAGGCAUUUAAAAUGUCUGUCAUUGGUGGAACGUUUCAUUAAAAUAAACCAAUGAAAUGGCUUACUUUGGUUCCCUUUUCGCUUACACGGAACAAAAUA
..((...........((((.((((((((.....))))))))....))))...(((((((((..........)))))))))))........(((((..............)))))...... ( -25.04)
>DroSim_CAF1 268792 120 + 1
UCGCAUAAAUAAUGACAUCUACAGGCAUUUAAAAUGUCUGUCAUUGGUGGAACGUUUCAUUAAAAUAAACCAAUGAAAUGGCUUACUUUAGUUCCCUUUUCGCUUACACGGAAGAAAAUA
..((...........((((.((((((((.....))))))))....))))...(((((((((..........)))))))))))..............((((((......))))))...... ( -23.30)
>DroEre_CAF1 251378 120 + 1
UCGCAUAAAUGAUGACAUCUACAGGCAUUUAAAAUGUCUGUCAUUGGUGGAACGUUUCAUUAAAAUAAACCAAUGAAAUGGCUUACUUUGGUUGCCUUUCGGCUUACACAAGAAAAAAUA
..((...........((((.((((((((.....))))))))....))))...(((((((((..........)))))))))))....((((((.(((....)))..)).))))........ ( -26.70)
>DroYak_CAF1 257768 120 + 1
UCGCAUAAAUGAUGACAUCUACUGGCAUUUAAAAUGUCUAUCAUUGGUGGAACAUUUCAUUAAAAUAAACCAAUGGAAUGGAUUACUUUGGUUCUCUUUUCGCUUACACACGAAAAAAUA
((((...(((((((((((...............))))).)))))).))))..(((((((((..........)))))))))((..((....))..))((((((........)))))).... ( -21.86)
>consensus
UCGCAUAAAUAAUGACAUCUACAGGCAUUUAAAAUGUCUGUCAUUGGUGGAACGUUUCAUUAAAAUAAACCAAUGAAAUGGCUUACUUUGGUUCCCUUUUCGCUUACACGGAAAAAAAUA
..((......(((((((......(((((.....))))))))))))(((((..(((((((((..........)))))))))..)))))..............))................. (-20.56 = -20.20 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,041,462 – 5,041,581
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.83
Mean single sequence MFE -28.24
Consensus MFE -22.38
Energy contribution -22.66
Covariance contribution 0.28
Combinations/Pair 1.09
Mean z-score -2.12
Structure conservation index 0.79
SVM decision value 1.17
SVM RNA-class probability 0.926049
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5041462 119 - 23771897
UAUUUU-UUCCGUGUAAGCGAAAAGGGAACCAAAGUAAGCCAUUUCAUUGGUUUAUUUUAAUGAAACGUUCCACCAAUGACAGACAUUUUAAAUGCCUGUAGAUGUCAUUAUUUAUGCGA
......-...((((((((.......(((((.(((((((((((......)))))))))))........)))))...(((((((.(((...........)))...))))))).)))))))). ( -27.90)
>DroSec_CAF1 247930 120 - 1
UAUUUUGUUCCGUGUAAGCGAAAAGGGAACCAAAGUAAGCCAUUUCAUUGGUUUAUUUUAAUGAAACGUUCCACCAAUGACAGACAUUUUAAAUGCCUGUAGAUGUCAUUAUUUAUGCGA
..........((((((((.......(((((.(((((((((((......)))))))))))........)))))...(((((((.(((...........)))...))))))).)))))))). ( -27.90)
>DroSim_CAF1 268792 120 - 1
UAUUUUCUUCCGUGUAAGCGAAAAGGGAACUAAAGUAAGCCAUUUCAUUGGUUUAUUUUAAUGAAACGUUCCACCAAUGACAGACAUUUUAAAUGCCUGUAGAUGUCAUUAUUUAUGCGA
..........((((((((.......(((((((((((((((((......)))))))))))).......)))))...(((((((.(((...........)))...))))))).)))))))). ( -30.21)
>DroEre_CAF1 251378 120 - 1
UAUUUUUUCUUGUGUAAGCCGAAAGGCAACCAAAGUAAGCCAUUUCAUUGGUUUAUUUUAAUGAAACGUUCCACCAAUGACAGACAUUUUAAAUGCCUGUAGAUGUCAUCAUUUAUGCGA
.........(((((((((((....)))....(((((((((((......))))))))))).((((...(((........))).(((((((...........))))))).)))))))))))) ( -29.70)
>DroYak_CAF1 257768 120 - 1
UAUUUUUUCGUGUGUAAGCGAAAAGAGAACCAAAGUAAUCCAUUCCAUUGGUUUAUUUUAAUGAAAUGUUCCACCAAUGAUAGACAUUUUAAAUGCCAGUAGAUGUCAUCAUUUAUGCGA
..(((((((((......))))))))).....(((((((.(((......))).)))))))..........((((..((((((.(((((((...........)))))))))))))..)).)) ( -25.50)
>consensus
UAUUUUUUUCCGUGUAAGCGAAAAGGGAACCAAAGUAAGCCAUUUCAUUGGUUUAUUUUAAUGAAACGUUCCACCAAUGACAGACAUUUUAAAUGCCUGUAGAUGUCAUUAUUUAUGCGA
..........((((((((.((....(((((.(((((((((((......)))))))))))........)))))..........(((((((...........))))))).)).)))))))). (-22.38 = -22.66 +   0.28)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:05 2006