Locus 6548

Sequence ID X_DroMel_CAF1
Location 16,395,882 – 16,396,072
Length 190
Max. P 0.999914
window10690 window10691 window10692 window10693 window10694

overview

Window 0

Location 16,395,882 – 16,395,992
Length 110
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 86.94
Mean single sequence MFE -23.07
Consensus MFE -18.36
Energy contribution -20.18
Covariance contribution 1.81
Combinations/Pair 1.04
Mean z-score -2.35
Structure conservation index 0.80
SVM decision value 1.42
SVM RNA-class probability 0.951987
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16395882 110 - 22224390
UUCAUAGCACGCGUCUAGGCAGUUUUUUAAGUGGUUUCAAAACCCAGAGAAUGAUAUUUAAAGAUAGCCAAGACGUGAUAAAAAAAUACCCAUAAA-AACUAUACUCAAAU
.........(((((((.(((...((((((((((.((((........))))....))))))))))..))).)))))))...................-.............. ( -24.50)
>DroSec_CAF1 16924 111 - 1
UUCGUAGCACACGUCUAGGCAGUUUUUGAAGUGGUUUCAAAACCCAGAGAAUGAUAUUUAAAGAUAGCCAAGACGUGAUGAAAAAAUGCCCAUAAAAAACUAUACUCAAAU
(((((....(((((((.(((.(((((((((....((((........))))......))))))))).))).))))))))))))............................. ( -26.00)
>DroSim_CAF1 15307 111 - 1
UUCGUAGCACACGUCUAGGCAGUUUUUGAAGUGGUUUCAAAACCCAGAGAAUGAUAUUUAAAGAUAGCCAAGACGUGAUGAAAAAAUGCCCAUAAAAAACUAUACUCAAAU
(((((....(((((((.(((.(((((((((....((((........))))......))))))))).))).))))))))))))............................. ( -26.00)
>DroYak_CAF1 13382 96 - 1
--CGUAGCACACAUUUUGGCAGCUUUUGAAGUGU------------GAAAACGAUAUUUAAAGAUAGCCAA-ACGUGAUGAAAAAAUGCCCAUAAGAAACUAUACUCAAAU
--.((((..(((..((((((...(((((((.(((------------....)))...)))))))...)))))-).)))(((..........)))......))))........ ( -15.80)
>consensus
UUCGUAGCACACGUCUAGGCAGUUUUUGAAGUGGUUUCAAAACCCAGAGAAUGAUAUUUAAAGAUAGCCAAGACGUGAUGAAAAAAUGCCCAUAAAAAACUAUACUCAAAU
.........(((((((.(((.(((((((((....((((........))))......))))))))).))).))))))).................................. (-18.36 = -20.18 +   1.81)

alignment

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secondary structure

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Window 1

Location 16,395,913 – 16,396,032
Length 119
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 95.51
Mean single sequence MFE -25.80
Consensus MFE -20.69
Energy contribution -21.13
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -2.49
Structure conservation index 0.80
SVM decision value 0.17
SVM RNA-class probability 0.617028
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16395913 119 + 22224390
AUCACGUCUUGGCUAUCUUUAAAUAUCAUUCUCUGGGUUUUGAAACCACUUAAAAAACUGCCUAGACGCGUGCUAUGAAAGACUUUUCAAAUCAAAAUUGUUUUGUUUUUCAUAUCAUA
....(((((.(((....(((((....((.....))((((....))))..))))).....))).))))).(((.((((((((((....(((.......)))....)))))))))).))). ( -25.70)
>DroSec_CAF1 16956 118 + 1
AUCACGUCUUGGCUAUCUUUAAAUAUCAUUCUCUGGGUUUUGAAACCACUUCAAAAACUGCCUAGACGUGUGCUACGAAAGACUUUUCGAAUGAAAAUUU-UUUGUUUUUCAUACCAUA
..(((((((.(((............(((.....))).(((((((.....)))))))...))).)))))))......(((((((.....((((....))))-...)))))))........ ( -26.30)
>DroSim_CAF1 15339 118 + 1
AUCACGUCUUGGCUAUCUUUAAAUAUCAUUCUCUGGGUUUUGAAACCACUUCAAAAACUGCCUAGACGUGUGCUACGAAAGACUUUUCGAAUGAAAAUUG-UUUGUUUUUCAUACCAUA
..(((((((.(((............(((.....))).(((((((.....)))))))...))).))))))).....(((((....))))).(((((((...-.....)))))))...... ( -25.40)
>consensus
AUCACGUCUUGGCUAUCUUUAAAUAUCAUUCUCUGGGUUUUGAAACCACUUCAAAAACUGCCUAGACGUGUGCUACGAAAGACUUUUCGAAUGAAAAUUG_UUUGUUUUUCAUACCAUA
..(((((((.(((.............((.....))((((....))))............))).)))))))......(((((((....(((.......)))....)))))))........ (-20.69 = -21.13 +   0.45)

alignment

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secondary structure

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Window 2

Location 16,395,913 – 16,396,032
Length 119
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 95.51
Mean single sequence MFE -32.70
Consensus MFE -30.42
Energy contribution -30.64
Covariance contribution 0.23
Combinations/Pair 1.05
Mean z-score -3.83
Structure conservation index 0.93
SVM decision value 1.95
SVM RNA-class probability 0.983542
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16395913 119 - 22224390
UAUGAUAUGAAAAACAAAACAAUUUUGAUUUGAAAAGUCUUUCAUAGCACGCGUCUAGGCAGUUUUUUAAGUGGUUUCAAAACCCAGAGAAUGAUAUUUAAAGAUAGCCAAGACGUGAU
..((.(((((((.((....(((.......)))....)).))))))).))(((((((.(((...((((((((((.((((........))))....))))))))))..))).))))))).. ( -30.90)
>DroSec_CAF1 16956 118 - 1
UAUGGUAUGAAAAACAAA-AAAUUUUCAUUCGAAAAGUCUUUCGUAGCACACGUCUAGGCAGUUUUUGAAGUGGUUUCAAAACCCAGAGAAUGAUAUUUAAAGAUAGCCAAGACGUGAU
..((.(((((((.((...-...(((((....))))))).))))))).))(((((((.(((.(((((((((....((((........))))......))))))))).))).))))))).. ( -33.60)
>DroSim_CAF1 15339 118 - 1
UAUGGUAUGAAAAACAAA-CAAUUUUCAUUCGAAAAGUCUUUCGUAGCACACGUCUAGGCAGUUUUUGAAGUGGUUUCAAAACCCAGAGAAUGAUAUUUAAAGAUAGCCAAGACGUGAU
..((.(((((((.((...-...(((((....))))))).))))))).))(((((((.(((.(((((((((....((((........))))......))))))))).))).))))))).. ( -33.60)
>consensus
UAUGGUAUGAAAAACAAA_CAAUUUUCAUUCGAAAAGUCUUUCGUAGCACACGUCUAGGCAGUUUUUGAAGUGGUUUCAAAACCCAGAGAAUGAUAUUUAAAGAUAGCCAAGACGUGAU
..((.(((((((.((.......(((((....))))))).))))))).))(((((((.(((.(((((((((....((((........))))......))))))))).))).))))))).. (-30.42 = -30.64 +   0.23)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,395,952 – 16,396,072
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 77.96
Mean single sequence MFE -32.65
Consensus MFE -21.44
Energy contribution -26.00
Covariance contribution 4.56
Combinations/Pair 1.03
Mean z-score -4.24
Structure conservation index 0.66
SVM decision value 4.52
SVM RNA-class probability 0.999914
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16395952 120 + 22224390
UUGAAACCACUUAAAAAACUGCCUAGACGCGUGCUAUGAAAGACUUUUCAAAUCAAAAUUGUUUUGUUUUUCAUAUCAUACUAAGAGGCAGCUUUCGAAAUGGUUUCAAAACUCAAGGGA
(((((((((.((..(((.((((((....(..((.((((((((((....(((.......)))....)))))))))).))..)....)))))).)))..)).)))))))))........... ( -35.60)
>DroSec_CAF1 16995 118 + 1
UUGAAACCACUUCAAAAACUGCCUAGACGUGUGCUACGAAAGACUUUUCGAAUGAAAAUUU-UUUGUUUUUCAUACCAUACUGAUAGGCAGCUUUC-AAAUGGUUUCAAAACUCAAGGGA
(((((((((.((..(((.(((((((...(((((.((.(((((((.....((((....))))-...))))))).)).)))))...))))))).))).-.)))))))))))........... ( -36.20)
>DroSim_CAF1 15378 119 + 1
UUGAAACCACUUCAAAAACUGCCUAGACGUGUGCUACGAAAGACUUUUCGAAUGAAAAUUG-UUUGUUUUUCAUACCAUACUGAUAGGCAGCUUUCGAAAUGGUUUCAAAACUCAAGGGA
(((((((((.(((.(((.(((((((...(((((.((.(((((((....(.(((....))))-...))))))).)).)))))...))))))).))).))).)))))))))........... ( -39.40)
>DroYak_CAF1 13446 90 + 1
------ACACUUCAAAAGCUGCCAAAAUGUGUGCUACG------------------------UUUCUUUUUCAUACCAUAUAUAUGGACAGCUUUCGAAAUGGUUUUUAAACUCAAGCGA
------.((.(((.((((((((((..(((((((.((.(------------------------.........).)).))))))).))).))))))).))).))((((........)))).. ( -19.40)
>consensus
UUGAAACCACUUCAAAAACUGCCUAGACGUGUGCUACGAAAGACUUUUCGAAUGAAAAUUG_UUUGUUUUUCAUACCAUACUGAUAGGCAGCUUUCGAAAUGGUUUCAAAACUCAAGGGA
(((((((((.(((.(((.(((((((...(((((.((.(((((((.....................))))))).)).)))))...))))))).))).))).)))))))))........... (-21.44 = -26.00 +   4.56)

alignment

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secondary structure

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Window 4

Location 16,395,952 – 16,396,072
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.96
Mean single sequence MFE -39.11
Consensus MFE -34.03
Energy contribution -37.28
Covariance contribution 3.25
Combinations/Pair 1.11
Mean z-score -5.71
Structure conservation index 0.87
SVM decision value 2.94
SVM RNA-class probability 0.997840
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16395952 120 - 22224390
UCCCUUGAGUUUUGAAACCAUUUCGAAAGCUGCCUCUUAGUAUGAUAUGAAAAACAAAACAAUUUUGAUUUGAAAAGUCUUUCAUAGCACGCGUCUAGGCAGUUUUUUAAGUGGUUUCAA
...........((((((((((((.(((((((((((....(..((.(((((((.((....(((.......)))....)).))))))).))..)....))))))))))).)))))))))))) ( -40.40)
>DroSec_CAF1 16995 118 - 1
UCCCUUGAGUUUUGAAACCAUUU-GAAAGCUGCCUAUCAGUAUGGUAUGAAAAACAAA-AAAUUUUCAUUCGAAAAGUCUUUCGUAGCACACGUCUAGGCAGUUUUUGAAGUGGUUUCAA
...........((((((((((((-((((((((((((...((.((.(((((((.((...-...(((((....))))))).))))))).)).))...)))))))))))).)))))))))))) ( -42.00)
>DroSim_CAF1 15378 119 - 1
UCCCUUGAGUUUUGAAACCAUUUCGAAAGCUGCCUAUCAGUAUGGUAUGAAAAACAAA-CAAUUUUCAUUCGAAAAGUCUUUCGUAGCACACGUCUAGGCAGUUUUUGAAGUGGUUUCAA
...........(((((((((((((((((((((((((...((.((.(((((((.((...-...(((((....))))))).))))))).)).))...))))))))))))))))))))))))) ( -48.60)
>DroYak_CAF1 13446 90 - 1
UCGCUUGAGUUUAAAAACCAUUUCGAAAGCUGUCCAUAUAUAUGGUAUGAAAAAGAAA------------------------CGUAGCACACAUUUUGGCAGCUUUUGAAGUGU------
..................((((((((((((((.(((......((.((((.........------------------------)))).)).......))))))))))))))))).------ ( -25.42)
>consensus
UCCCUUGAGUUUUGAAACCAUUUCGAAAGCUGCCUAUCAGUAUGGUAUGAAAAACAAA_CAAUUUUCAUUCGAAAAGUCUUUCGUAGCACACGUCUAGGCAGUUUUUGAAGUGGUUUCAA
............((((((((((((((((((((((((...((.((.(((((((.((.....................)).))))))).)).))...)))))))))))))))))))))))). (-34.03 = -37.28 +   3.25)

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 12:16:35 2006