Locus 5748

Sequence ID 2R_DroMel_CAF1
Location 18,201,904 – 18,202,036
Length 132
Max. P 0.995182
window9205 window9206 window9207 window9208

overview

Window 5

Location 18,201,904 – 18,202,007
Length 103
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 85.01
Mean single sequence MFE -34.33
Consensus MFE -25.29
Energy contribution -26.47
Covariance contribution 1.19
Combinations/Pair 1.08
Mean z-score -4.03
Structure conservation index 0.74
SVM decision value 2.55
SVM RNA-class probability 0.995182
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18201904 103 + 20766785
ACCGAAGAUUCCACUGCAACAUGUUUCCUCUUUAUCUGCUAGCAUCAGUUUUC----------------GAAGACGCAUGUUGUAGUGGACUCCAGACAUCAAUUAUUCUAUUCGAUAA
..((((((.(((((((((((((((.((.((.....(((.......))).....----------------)).)).))))))))))))))).)).(((..........))).)))).... ( -31.10)
>DroSec_CAF1 26970 119 + 1
ACCGAAGAUUCCACUGCAACAUGGUUUCUCUUUAUCUGGUAGCAUCCGUUUUCAACUUCUGAAUCUGGAGAACACGCAUGUUGUAGUGGACUCCAGGCAUCAAUUAUUCUAUAUGAUAA
.((...((.((((((((((((((((((((((......((......))...((((.....))))...)))))).)).)))))))))))))).))..)).....(((((.....))))).. ( -35.60)
>DroSim_CAF1 28575 119 + 1
ACCGAAGAUUCCACUGCAACAUGUUUUCUCUUUAUCUGGUAGCAUCAGUUUUCAACUUCUGAAUCUGGAGAAGACGCAUGUUGUAGUGGACUCCAGGCAUCAAUUAUUCUAUUCGAUAA
.((...((.((((((((((((((((((((((....(((((...)))))..((((.....))))...)))))))..))))))))))))))).))..))...................... ( -36.40)
>DroEre_CAF1 27644 116 + 1
ACCGAAGAUUCCACUGCAACAUGUUUUCUCUUUAUCUGCUAGCAUCGCUUUUUCAAUUCUCAGUCCAGAGAA---GCAUGUUGUAGUGGGCUCAAGGCAUCAAUUAUUCUAUUCGAUAA
..((((....((((((((((((((((.((((....(((..(((...)))...........)))...))))))---))))))))))))))((.....)).............)))).... ( -34.22)
>consensus
ACCGAAGAUUCCACUGCAACAUGUUUUCUCUUUAUCUGCUAGCAUCAGUUUUCAACUUCUGAAUCUGGAGAAGACGCAUGUUGUAGUGGACUCCAGGCAUCAAUUAUUCUAUUCGAUAA
.((...((.(((((((((((((((.((((((...................................))))))...))))))))))))))).))..))...................... (-25.29 = -26.47 +   1.19)

alignment

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secondary structure

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Window 6

Location 18,201,904 – 18,202,007
Length 103
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 85.01
Mean single sequence MFE -32.50
Consensus MFE -22.67
Energy contribution -23.54
Covariance contribution 0.87
Combinations/Pair 1.07
Mean z-score -2.74
Structure conservation index 0.70
SVM decision value 1.56
SVM RNA-class probability 0.963674
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18201904 103 - 20766785
UUAUCGAAUAGAAUAAUUGAUGUCUGGAGUCCACUACAACAUGCGUCUUC----------------GAAAACUGAUGCUAGCAGAUAAAGAGGAAACAUGUUGCAGUGGAAUCUUCGGU
.((((((.........)))))).((((((((((((.(((((((..(((((----------------.....(((.......))).....)))))..))))))).))))))..)))))). ( -33.80)
>DroSec_CAF1 26970 119 - 1
UUAUCAUAUAGAAUAAUUGAUGCCUGGAGUCCACUACAACAUGCGUGUUCUCCAGAUUCAGAAGUUGAAAACGGAUGCUACCAGAUAAAGAGAAACCAUGUUGCAGUGGAAUCUUCGGU
.(((((...........))))).((((((((((((.(((((((.((.(((((....(((((...)))))...((......)).......)))))))))))))).))))))..)))))). ( -33.20)
>DroSim_CAF1 28575 119 - 1
UUAUCGAAUAGAAUAAUUGAUGCCUGGAGUCCACUACAACAUGCGUCUUCUCCAGAUUCAGAAGUUGAAAACUGAUGCUACCAGAUAAAGAGAAAACAUGUUGCAGUGGAAUCUUCGGU
.((((((.........)))))).((((((((((((.(((((((....(((((....(((((...)))))..(((.......))).....)))))..))))))).))))))..)))))). ( -31.10)
>DroEre_CAF1 27644 116 - 1
UUAUCGAAUAGAAUAAUUGAUGCCUUGAGCCCACUACAACAUGC---UUCUCUGGACUGAGAAUUGAAAAAGCGAUGCUAGCAGAUAAAGAGAAAACAUGUUGCAGUGGAAUCUUCGGU
..(((((.........)))))(((..((..(((((.(((((((.---((((((..((((...((((......)))).....))).)..))))))..))))))).)))))..))...))) ( -31.90)
>consensus
UUAUCGAAUAGAAUAAUUGAUGCCUGGAGUCCACUACAACAUGCGUCUUCUCCAGAUUCAGAAGUUGAAAACUGAUGCUACCAGAUAAAGAGAAAACAUGUUGCAGUGGAAUCUUCGGU
.((((((.........)))))).((((((((((((.(((((((....(((((.....................................)))))..))))))).))))))..)))))). (-22.67 = -23.54 +   0.87)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,201,944 – 18,202,036
Length 92
Sequences 3
Columns 108
Reading direction forward
Mean pairwise identity 87.04
Mean single sequence MFE -29.21
Consensus MFE -23.26
Energy contribution -23.92
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.80
Structure conservation index 0.80
SVM decision value 1.12
SVM RNA-class probability 0.918793
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18201944 92 + 20766785
AGCAUCAGUUUUC----------------GAAGACGCAUGUUGUAGUGGACUCCAGACAUCAAUUAUUCUAUUCGAUAACUGAUGCAGAAACUUUGAGUUCACUCAGU
.(((((((((.((----------------(((.......((((...(((...))).....)))).......))))).))))))))).......(((((....))))). ( -26.94)
>DroSec_CAF1 27010 108 + 1
AGCAUCCGUUUUCAACUUCUGAAUCUGGAGAACACGCAUGUUGUAGUGGACUCCAGGCAUCAAUUAUUCUAUAUGAUAACUGAUGCAGAAACUUUGAGUUCACUCAGU
.......(((((............((((((..(((((.....)).)))..))))))((((((.(((((......))))).)))))).))))).(((((....))))). ( -30.70)
>DroSim_CAF1 28615 108 + 1
AGCAUCAGUUUUCAACUUCUGAAUCUGGAGAAGACGCAUGUUGUAGUGGACUCCAGGCAUCAAUUAUUCUAUUCGAUAACUGAUGCAGAAACUUUGAGUUCACUCAGU
.(((((((((.((..(....)..(((((((....(((........)))..))))))).................)).))))))))).......(((((....))))). ( -30.00)
>consensus
AGCAUCAGUUUUCAACUUCUGAAUCUGGAGAAGACGCAUGUUGUAGUGGACUCCAGGCAUCAAUUAUUCUAUUCGAUAACUGAUGCAGAAACUUUGAGUUCACUCAGU
(((((..((((((................))))))..)))))(.(((((((((.((((((((.(((((......))))).)))))).....))..))))))))))... (-23.26 = -23.92 +   0.67)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,201,944 – 18,202,036
Length 92
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 87.04
Mean single sequence MFE -30.47
Consensus MFE -22.31
Energy contribution -22.67
Covariance contribution 0.36
Combinations/Pair 1.03
Mean z-score -3.33
Structure conservation index 0.73
SVM decision value 1.22
SVM RNA-class probability 0.931731
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18201944 92 - 20766785
ACUGAGUGAACUCAAAGUUUCUGCAUCAGUUAUCGAAUAGAAUAAUUGAUGUCUGGAGUCCACUACAACAUGCGUCUUC----------------GAAAACUGAUGCU
..((((....))))........(((((((((.(((((..........(((((.((..((.....))..)).))))))))----------------)).))))))))). ( -28.30)
>DroSec_CAF1 27010 108 - 1
ACUGAGUGAACUCAAAGUUUCUGCAUCAGUUAUCAUAUAGAAUAAUUGAUGCCUGGAGUCCACUACAACAUGCGUGUUCUCCAGAUUCAGAAGUUGAAAACGGAUGCU
..((((....)))).(((.((((((((((((((........)))))))))))((((((..(((..........)))..)))))).................))).))) ( -33.00)
>DroSim_CAF1 28615 108 - 1
ACUGAGUGAACUCAAAGUUUCUGCAUCAGUUAUCGAAUAGAAUAAUUGAUGCCUGGAGUCCACUACAACAUGCGUCUUCUCCAGAUUCAGAAGUUGAAAACUGAUGCU
..((((....))))........(((((((((.((((...((((....(((((.((..((.....))..)).)))))........)))).....)))).))))))))). ( -30.10)
>consensus
ACUGAGUGAACUCAAAGUUUCUGCAUCAGUUAUCGAAUAGAAUAAUUGAUGCCUGGAGUCCACUACAACAUGCGUCUUCUCCAGAUUCAGAAGUUGAAAACUGAUGCU
..((((((.((((..((.....((((((((((((.....).))))))))))))).)))).)))).))....(((((.......(((......))).......))))). (-22.31 = -22.67 +   0.36)

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 11:53:24 2006