Locus 5920

Sequence ID 3L_DroMel_CAF1
Location 15,906,377 – 15,906,524
Length 147
Max. P 0.784249
window9449 window9450

overview

Window 9

Location 15,906,377 – 15,906,484
Length 107
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.98
Mean single sequence MFE -37.53
Consensus MFE -27.40
Energy contribution -27.24
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -2.07
Structure conservation index 0.73
SVM decision value 0.57
SVM RNA-class probability 0.784249
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15906377 107 + 23771897
GACCAAGUCGAUAGGCGGCCACAAUUAAAGUCUGGCCGAGAUGUGG----CC--AAACCUGUUGGCGUUCGAGAGGCAGACGGA------GCACACG-AGUUGCAGAGAUGCAACUGCAA
..((..(((((((((.(((((((.......(((.....))))))))----))--...)))))))))((.(....)))....)).------(((....-.((((((....))))))))).. ( -36.31)
>DroSec_CAF1 5774 108 + 1
GACCAAGUCGAUAGGCGGCCACAAUUAAAGUCUGGCCGAGAUGUGG----CC--AAACCUGUUGGCAAUGGAGAAGCAGGCGGA------GCACACAAAGUUGCACAUAUGCAACUGCAA
..(((.(((((((((.(((((((.......(((.....))))))))----))--...)))))))))..)))....((..((...------))......(((((((....))))))))).. ( -35.61)
>DroSim_CAF1 8245 108 + 1
GACCAAGUCGAUAGGCGGCCACAAUUAAAGUCUGGCCGAGAUGUGG----CC--AAACCUGUUGGCGUUGGAGAGGCAGACGGA------GCACACAAAGUUGCACAUAUGCAACUGCAA
..(((((((((((((.(((((((.......(((.....))))))))----))--...))))))))).))))....((....(..------...)....(((((((....))))))))).. ( -37.21)
>DroEre_CAF1 5963 107 + 1
GACCAAGUCGGCAGUCGGCCACAAUUAAAGUCUGGCCGAGAUGUGG----GC--AAACCUGUUGGCGAUGGAGAGGCAGACGGA------GCACACG-AGUUGCAGAGAUGCAACUGGAA
..((..(((.(((.(((((((...........)))))))..))).)----))--....(((((..(......).)))))..)).------.....(.-(((((((....))))))).).. ( -37.10)
>DroYak_CAF1 5874 119 + 1
GACCAAGUCGAUAGUCGGCCACAAUUAAAGUCUGGCCGAGAUGUGGCUGUGCAAAAACCUGUUGGCGUUGGAGAGGCAGACGGAGACGGCGCACAUG-AGUUGCAGAGAUGCAACUGGAA
..((.(((((....(((((((...........)))))))....)))))((((......(((((..(......).))))).((....))..))))...-(((((((....))))))))).. ( -41.40)
>consensus
GACCAAGUCGAUAGGCGGCCACAAUUAAAGUCUGGCCGAGAUGUGG____CC__AAACCUGUUGGCGUUGGAGAGGCAGACGGA______GCACACG_AGUUGCAGAGAUGCAACUGCAA
..(((.(((......((((((...........)))))).))).)))............(((((.((.........)).)))))...............(((((((....))))))).... (-27.40 = -27.24 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,906,417 – 15,906,524
Length 107
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.69
Mean single sequence MFE -28.16
Consensus MFE -21.86
Energy contribution -21.70
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.48
Structure conservation index 0.78
SVM decision value 0.05
SVM RNA-class probability 0.560218
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15906417 107 + 23771897
AUGUGG----CC--AAACCUGUUGGCGUUCGAGAGGCAGACGGA------GCACACG-AGUUGCAGAGAUGCAACUGCAAAAAGUGCGUGGAAAAAGGCGAUACAUAUUUUACAUAAUAC
.(((.(----((--....(((((.((.((...)).)).))))).------...(((.-(((((((....)))))))(((.....))))))......))).)))................. ( -28.80)
>DroSec_CAF1 5814 108 + 1
AUGUGG----CC--AAACCUGUUGGCAAUGGAGAAGCAGGCGGA------GCACACAAAGUUGCACAUAUGCAACUGCAAAAAGUGCGUGGAAAAAGGCGAUACAUAUUUUACAUAAUAC
.(((.(----((--...((((((..(....)...))))))....------((((....(((((((....))))))).......)))).........))).)))................. ( -27.40)
>DroSim_CAF1 8285 108 + 1
AUGUGG----CC--AAACCUGUUGGCGUUGGAGAGGCAGACGGA------GCACACAAAGUUGCACAUAUGCAACUGCAAAAAGUGCGUGGAAAAAGGCGAUACAUAUUUUACAUAAUAC
.(((.(----((--....(((((.((.((...)).)).))))).------((((....(((((((....))))))).......)))).........))).)))................. ( -27.70)
>DroEre_CAF1 6003 107 + 1
AUGUGG----GC--AAACCUGUUGGCGAUGGAGAGGCAGACGGA------GCACACG-AGUUGCAGAGAUGCAACUGGAAAAAGUGCGUGGAAAAAGGCGAAACAUAUUUUACAUAAUAC
((((..----((--....(((((.((.........)).))))).------((((.(.-(((((((....))))))).).....))))..........))...)))).............. ( -25.00)
>DroYak_CAF1 5914 119 + 1
AUGUGGCUGUGCAAAAACCUGUUGGCGUUGGAGAGGCAGACGGAGACGGCGCACAUG-AGUUGCAGAGAUGCAACUGGAAAAAGUGCGUGGAAAAAGGCGAAACAUAUUUUACAUAAUAC
(((((....(((......(((((.((.((...)).)).)))))...(.((((((.(.-(((((((....))))))).).....)))))).)......)))...)))))............ ( -31.90)
>consensus
AUGUGG____CC__AAACCUGUUGGCGUUGGAGAGGCAGACGGA______GCACACG_AGUUGCAGAGAUGCAACUGCAAAAAGUGCGUGGAAAAAGGCGAUACAUAUUUUACAUAAUAC
(((((.............(((((.((.........)).))))).......((((....(((((((....))))))).......)))).......................)))))..... (-21.86 = -21.70 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:02 2006