Locus 4265

Sequence ID 3R_DroMel_CAF1
Location 11,396,932 – 11,397,130
Length 198
Max. P 0.599222
window6921 window6922

overview

Window 1

Location 11,396,932 – 11,397,052
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.07
Mean single sequence MFE -27.32
Consensus MFE -23.50
Energy contribution -24.18
Covariance contribution 0.68
Combinations/Pair 1.06
Mean z-score -1.26
Structure conservation index 0.86
SVM decision value 0.13
SVM RNA-class probability 0.599222
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11396932 120 - 27905053
AUUAAAAAGCAAUUUUGCGGCUCAGUUUCAUCGAAAGCUUCACCCAGUUUGACUGCCAGUUAUUUUGGGUCUCGGCUUUUCGCAAUAUUCCCUUAGUUUUGGUUUUUAUUUUGUUGUUGA
..((((((.(((..(((.((...(((.....((((((((..((((((..((((.....))))..))))))...))).)))))....))).)).)))..))).))))))............ ( -26.30)
>DroSec_CAF1 144639 120 - 1
AUUAAAAAGCUAUUUUGCGGCUCAGUUUCAUCGAAAGGUUCACCCAGUUUGACUGCCAGUUAUUUUGGGUCUCGGCUUUUCGCAAUAUUCCCUUAGUUUUGGUUUUUAUUUUGUUUGGUA
....((((((((..(((.((...(((.....(((((((((.((((((..((((.....))))..))))))...)))))))))....))).)).)))...))))))))............. ( -26.30)
>DroSim_CAF1 135717 120 - 1
AUUAAAAAGCAAUUUUGCGGCUCAGUUUCAUCGAAAGGUUCACCCAGUUUGACUGCCAGUUAUUUUGGGUCUCGGCUUUUCGCAAUAUUCCCUUAGUUUUGGUUUUUAUUUUGUUUGGGA
..((((((.(((..(((.((...(((.....(((((((((.((((((..((((.....))))..))))))...)))))))))....))).)).)))..))).))))))............ ( -27.80)
>DroEre_CAF1 132819 117 - 1
AUUAAAAAGCAAUUUUGCAGCUCAGUUUCAUCGAAAGGUUCGCCCAGUUUGACUGGCAGUUAUUUUGGGUCUCGGCUUUUCGCUGUACUCCCUUAGUU-UGGUUUUUAUUUUGUU--GCA
........(((((..((((((...(......)((((((((.((((((..((((.....))))..))))))...))))))))))))))...((......-.))..........)))--)). ( -31.00)
>DroYak_CAF1 135557 118 - 1
AUUAAAAAGCAAUUUUGCGGCUCAGUUUCAUCGAAAGGUUCAGCCAGUUUGACUGCCAGUUAUUUUGGGUCUCGGCUUUUCGCAAUAUUCCCUUAGUUUUGGUUUUUAUUUUGCU--GGA
........(((....)))...........(((....)))....(((((.(((..(((((..(((..(((.....((.....))......)))..))).)))))..)))....)))--)). ( -25.20)
>consensus
AUUAAAAAGCAAUUUUGCGGCUCAGUUUCAUCGAAAGGUUCACCCAGUUUGACUGCCAGUUAUUUUGGGUCUCGGCUUUUCGCAAUAUUCCCUUAGUUUUGGUUUUUAUUUUGUU__GGA
..((((((.(((..(((.((...(((.....(((((((((.((((((..((((.....))))..))))))...)))))))))....))).)).)))..))).))))))............ (-23.50 = -24.18 +   0.68)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,397,012 – 11,397,130
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.69
Mean single sequence MFE -30.28
Consensus MFE -21.70
Energy contribution -22.46
Covariance contribution 0.76
Combinations/Pair 1.04
Mean z-score -1.57
Structure conservation index 0.72
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11397012 118 + 27905053
AAGCUUUCGAUGAAACUGAGCCGCAAAAUUGCUUUUUAAUGCCACAUCGACUAUCGCCAAUUGGAGUGAGUGAAAAGCACACA--UCAGUGCAUCUCCCUUGCUCCCGUUCUAUGGCACC
......((((((....((((..(((....)))..))))......)))))).....((((((.((((..((.((...((((...--...))))...)).))..)))).))....))))... ( -31.00)
>DroSec_CAF1 144719 118 + 1
AACCUUUCGAUGAAACUGAGCCGCAAAAUAGCUUUUUAAUGCCACAUCGACACUCGCCAAUUGGAGUGAGUGAAAAGCACACA--UCGGUGCAUCUCCCUCGCUCCCGCUCUAUGGCGCC
......((((((....((.((...((((.....))))...))))))))))....(((((...((((((((.((...((((...--...))))...)).)))))))).......))))).. ( -32.60)
>DroSim_CAF1 135797 118 + 1
AACCUUUCGAUGAAACUGAGCCGCAAAAUUGCUUUUUAAUGCCACAUCGACACUCGCCAAUUGGAGUGAGUGAAAAGCACACA--UCGGUGCAUCUCCCUCGCUCACGCUCUAUGGCCCC
......((((((....((((..(((....)))..))))......)))))).....((((...((.((((((((...((((...--...)))).......)))))))).))...))))... ( -30.00)
>DroEre_CAF1 132896 107 + 1
AACCUUUCGAUGAAACUGAGCUGCAAAAUUGCUUUUUAAUGCCACAUCGCCGUGCGGCAAUUGGAGUGAGUGAGAAGCACACACGUCAGUGCAUCUCCCUUGCUCCC-------------
........((((....((((..(((....)))..))))......))))(((....)))....((((..((.((((.((((........)))).)))).))..)))).------------- ( -34.20)
>DroYak_CAF1 135635 117 + 1
AACCUUUCGAUGAAACUGAGCCGCAAAAUUGCUUUUUAAUGCCACACCGCCGUUCGCCAAUUGGAGUGAGUGAAAAGCACACA--UCGCUGCAUCUCCCUCGCUCCCCCUCCCCCU-CCC
.................((((.((......((........))......)).)))).......((((((((.((...(((....--....)))...)).))))))))..........-... ( -23.60)
>consensus
AACCUUUCGAUGAAACUGAGCCGCAAAAUUGCUUUUUAAUGCCACAUCGACACUCGCCAAUUGGAGUGAGUGAAAAGCACACA__UCGGUGCAUCUCCCUCGCUCCCGCUCUAUGGCCCC
......((((((....((((..((......))..))))......))))))............((((((((.((...((((........))))...)).)))))))).............. (-21.70 = -22.46 +   0.76)

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 11:23:55 2006