Locus 500

Sequence ID X_DroMel_CAF1
Location 1,430,989 – 1,431,091
Length 102
Max. P 0.963259
window776 window777

overview

Window 6

Location 1,430,989 – 1,431,091
Length 102
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 88.30
Mean single sequence MFE -42.46
Consensus MFE -31.83
Energy contribution -33.70
Covariance contribution 1.87
Combinations/Pair 1.07
Mean z-score -3.03
Structure conservation index 0.75
SVM decision value 1.55
SVM RNA-class probability 0.963259
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1430989 102 + 22224390
GGCUCAUUACGA-GCUGCCUGCAUAUUAUGUGCAG-C-CAGCAAUGCAGCGGCUCAGAAGCGACUUUGCCGUUGCCGUUGGAGCAUUGACAACUGCAGGCCGCCA
(((((.....))-)))(((((((......((((..-(-((((...((((((((..((......))..)))))))).))))).)))).......)))))))..... ( -44.22)
>DroSec_CAF1 35723 99 + 1
GGCUCAUUACGA-GCUGCCUGCAUAUUAUGUGCAGGC-CAGCAGUGCAUCGGCUCAGAAGCGACUUUGCCGUUGCCGUUGGAGCAUUGACAACUGCAGA----CA
(((((.....))-)))((((((((.....))))))))-..(((((.((...((((((..(((((......)))))..)).))))..))...)))))...----.. ( -41.40)
>DroEre_CAF1 32526 103 + 1
GGCUCAUUACGA-GCUGCCUGCAUAUUAUGUGCAGGC-CAGCAGUGCAGCGGCUCAGAAGCGACUUUGCCGUUGCCGUUGGAGCAUUGACAACUGCAGGCCGCCA
(((((.....))-)))(((((((......((((...(-((((.(.((((((((..((......))..)))))))))))))).)))).......)))))))..... ( -45.52)
>DroWil_CAF1 109699 99 + 1
GGCUCAUUAUGAAGUCGCCUGCAUAUUAUGUGCAGGCUCAGCGGCGCAGCGGCUCAGAACCGACUUUGCUG------UUGGAGCAUUGACAACUGCAGGCCAUCA
((((......(..(((((((((((.....))))))))(((((((((.(((((.......))).)).)))))------))))......)))..)....)))).... ( -38.70)
>consensus
GGCUCAUUACGA_GCUGCCUGCAUAUUAUGUGCAGGC_CAGCAGUGCAGCGGCUCAGAAGCGACUUUGCCGUUGCCGUUGGAGCAUUGACAACUGCAGGCCGCCA
.((((...(((..(((((((((((.....))))))))..)))...((((((((..((......))..)))))))))))..))))..................... (-31.83 = -33.70 +   1.87)

alignment

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secondary structure

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dotplot

Postscript

Window 7

Location 1,430,989 – 1,431,091
Length 102
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 88.30
Mean single sequence MFE -37.57
Consensus MFE -26.31
Energy contribution -28.62
Covariance contribution 2.31
Combinations/Pair 1.10
Mean z-score -1.98
Structure conservation index 0.70
SVM decision value 0.39
SVM RNA-class probability 0.715451
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1430989 102 - 22224390
UGGCGGCCUGCAGUUGUCAAUGCUCCAACGGCAACGGCAAAGUCGCUUCUGAGCCGCUGCAUUGCUG-G-CUGCACAUAAUAUGCAGGCAGC-UCGUAAUGAGCC
(((((((.....)))))))..((((..((((((.((((..((......))..)))).)))...((((-.-(((((.......))))).))))-.)))...)))). ( -40.50)
>DroSec_CAF1 35723 99 - 1
UG----UCUGCAGUUGUCAAUGCUCCAACGGCAACGGCAAAGUCGCUUCUGAGCCGAUGCACUGCUG-GCCUGCACAUAAUAUGCAGGCAGC-UCGUAAUGAGCC
..----...............((((..((((((.((((..((......))..)))).)))...((((-.((((((.......))))))))))-.)))...)))). ( -35.10)
>DroEre_CAF1 32526 103 - 1
UGGCGGCCUGCAGUUGUCAAUGCUCCAACGGCAACGGCAAAGUCGCUUCUGAGCCGCUGCACUGCUG-GCCUGCACAUAAUAUGCAGGCAGC-UCGUAAUGAGCC
(((((((.....)))))))..((((..((((((.((((..((......))..)))).)))...((((-.((((((.......))))))))))-.)))...)))). ( -41.30)
>DroWil_CAF1 109699 99 - 1
UGAUGGCCUGCAGUUGUCAAUGCUCCAA------CAGCAAAGUCGGUUCUGAGCCGCUGCGCCGCUGAGCCUGCACAUAAUAUGCAGGCGACUUCAUAAUGAGCC
(((..((.....))..)))..((((...------((((..((.((((.....)))))).....)))).(((((((.......)))))))...........)))). ( -33.40)
>consensus
UGGCGGCCUGCAGUUGUCAAUGCUCCAACGGCAACGGCAAAGUCGCUUCUGAGCCGCUGCACUGCUG_GCCUGCACAUAAUAUGCAGGCAGC_UCGUAAUGAGCC
(((((((.....)))))))..((((..((((((.((((..((......))..)))).)))........(((((((.......))))))).....)))...)))). (-26.31 = -28.62 +   2.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:09 2006