Locus 8143

Sequence ID X_DroMel_CAF1
Location 20,261,779 – 20,261,950
Length 171
Max. P 0.853588
window13381 window13382 window13383

overview

Window 1

Location 20,261,779 – 20,261,892
Length 113
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 77.99
Mean single sequence MFE -28.77
Consensus MFE -16.55
Energy contribution -16.67
Covariance contribution 0.12
Combinations/Pair 1.13
Mean z-score -1.87
Structure conservation index 0.58
SVM decision value 0.00
SVM RNA-class probability 0.535714
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20261779 113 + 22224390
AUUCAACUGCCUGCCUAGGCAGGCAGCCUACCGUUUGGUCCUGACUUUUGGCCUUUGCUCAAGCGGGCUGACUGUAAUGAAUCCAGAAUUUUUAUUGCCAGUUAUUCAGUAGU
......((((((((....))))))))....(((((((((((........)).....)).)))))))(((((((((((((((.........))))))).)))....)))))... ( -36.90)
>DroEre_CAF1 8103 92 + 1
AUUCAACUGC---------------------CAUUUGGCCCUGACUUUUGGCCUUUGCUCGAGCUGGCCGACUGUAAUGAAUCCAGCAGUUUAAUUGGCAGUUAUUCAGUAGU
....((((((---------------------((.(((............((((...((....)).))))((((((..((....))))))))))).)))))))).......... ( -27.40)
>DroYak_CAF1 8582 92 + 1
AUUCAACUGC---------------------CGUUUGGCCCUGACUUUUGGCCUUUGCUGGGGCUGGCUGACUGUAAUAAAUCCAGCAUUUUUAUUUGUAGUUAUUCAGUAGU
....((((((---------------------.....((((.........))))..(((((((....((.....))......))))))).........)))))).......... ( -22.00)
>consensus
AUUCAACUGC_____________________CGUUUGGCCCUGACUUUUGGCCUUUGCUCGAGCUGGCUGACUGUAAUGAAUCCAGCAUUUUUAUUGGCAGUUAUUCAGUAGU
.....(((((.......................................((((...((....)).))))((((((((((((.........))))))).))))).....))))) (-16.55 = -16.67 +   0.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,261,812 – 20,261,922
Length 110
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.22
Mean single sequence MFE -29.70
Consensus MFE -22.46
Energy contribution -21.90
Covariance contribution -0.56
Combinations/Pair 1.22
Mean z-score -1.40
Structure conservation index 0.76
SVM decision value -0.05
SVM RNA-class probability 0.509468
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20261812 110 + 22224390
UUUGGUCCUGACUUUUGGCCUUUGCUCAAGCGGGCUGACUGUAAUGAAUCCAGAAUUUUUAUUGCCAGUUAUUCAGUAGUUCCGAAGUAAUUGAAUUACGGCUU----------GCUGAU
...((.((........)))).....(((.(((((((((((((((((((.........))))))).))))).....(((((((..((....))))))))))))))----------))))). ( -28.60)
>DroSec_CAF1 8529 110 + 1
UUUGGCCCUGACUUUUGGCCUUUGCUCAAGCUGGCUGACUGUAAUAAAUCCACAAUUUUUAUUGCCAGUUAUUCAGCAGUUCCGCAGUAAUUGAAUUACGGCUU----------GCUGAU
...((((.........)))).........((((..(((((((((((((.........))))))).))))))..))))(((...((.(((((...))))).))..----------)))... ( -28.30)
>DroEre_CAF1 8115 120 + 1
UUUGGCCCUGACUUUUGGCCUUUGCUCGAGCUGGCCGACUGUAAUGAAUCCAGCAGUUUAAUUGGCAGUUAUUCAGUAGUUCUGAAGUAAUUGAGUUACGGUUUGCUGCUAUUUGCUGAU
.(..((....((..((((((...((....)).))))))..)).........((((((..(((((.(((((((((((.....))).)))))))).....))))).))))))....))..). ( -35.60)
>DroYak_CAF1 8594 110 + 1
UUUGGCCCUGACUUUUGGCCUUUGCUGGGGCUGGCUGACUGUAAUAAAUCCAGCAUUUUUAUUUGUAGUUAUUCAGUAGUUCUUAAGUAAGUGAAUUACGGUCU----------GCUGAU
...((((.........))))..(((((((....((.....))......))))))).................(((((((.......((((.....))))...))----------))))). ( -26.30)
>consensus
UUUGGCCCUGACUUUUGGCCUUUGCUCAAGCUGGCUGACUGUAAUAAAUCCAGAAUUUUUAUUGCCAGUUAUUCAGUAGUUCCGAAGUAAUUGAAUUACGGCUU__________GCUGAU
...((((.(((.....((((...((....)).))))((((((((((((.........))))))).)))))..)))(((((((..........)))))))))))................. (-22.46 = -21.90 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,261,852 – 20,261,950
Length 98
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 79.71
Mean single sequence MFE -23.55
Consensus MFE -14.91
Energy contribution -13.85
Covariance contribution -1.06
Combinations/Pair 1.35
Mean z-score -2.04
Structure conservation index 0.63
SVM decision value 0.80
SVM RNA-class probability 0.853588
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20261852 98 + 22224390
GUAAUGAAUCCAGAAUUUUUAUUGCCAGUUAUUCAGUAGUUCCGAAGUAAUUGAAUUACGGCUU----------GCUGAUAGCUGGU-AGUUCAUUUAACAACUUAAAC
(((((((((.............((((((((((.((((((..(((.(((......))).))).))----------)))))))))))))-))))))))..))......... ( -24.81)
>DroSec_CAF1 8569 99 + 1
GUAAUAAAUCCACAAUUUUUAUUGCCAGUUAUUCAGCAGUUCCGCAGUAAUUGAAUUACGGCUU----------GCUGAUAGCUGGCAAGUUCAUUUAACAACUUAAAC
.....................(((((((((((.((((((..(((.(((......))).))).))----------))))))))))))))).................... ( -27.60)
>DroEre_CAF1 8155 103 + 1
GUAAUGAAUCCAGCAGUUUAAUUGGCAGUUAUUCAGUAGUUCUGAAGUAAUUGAGUUACGGUUUGCUGCUAUUUGCUGAUGGCUGUU-AGUUCACUUAACAAAU-----
.........(((.((((.....(((((((..(((((.....)))))(((((...))))).....)))))))...)))).))).((((-((.....))))))...----- ( -24.30)
>DroYak_CAF1 8634 98 + 1
GUAAUAAAUCCAGCAUUUUUAUUUGUAGUUAUUCAGUAGUUCUUAAGUAAGUGAAUUACGGUCU----------GCUGAUGGCUGCU-AGUUCAUAAAACAAAUUAAAC
........................((((((((.((((((.......((((.....))))...))----------)))))))))))).-..................... ( -17.50)
>consensus
GUAAUAAAUCCAGAAUUUUUAUUGCCAGUUAUUCAGUAGUUCCGAAGUAAUUGAAUUACGGCUU__________GCUGAUAGCUGGU_AGUUCAUUUAACAAAUUAAAC
.......................((((((((((..(((((((..........)))))))(((............)))))))))))))...................... (-14.91 = -13.85 +  -1.06)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:56:53 2006