Locus 3276

Sequence ID 3L_DroMel_CAF1
Location 9,609,344 – 9,609,464
Length 120
Max. P 0.720630
window5092 window5093

overview

Window 2

Location 9,609,344 – 9,609,464
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.45
Mean single sequence MFE -22.02
Consensus MFE -18.28
Energy contribution -19.08
Covariance contribution 0.80
Combinations/Pair 1.07
Mean z-score -1.46
Structure conservation index 0.83
SVM decision value 0.40
SVM RNA-class probability 0.720630
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9609344 120 + 23771897
UUUCUUUUUUGGAAAUUAUUUAAGUGCCCACCAACAAUAAUCUUAAUUUGAAGCUCGCUCGGUUAUUUAGAUUAGAUGUUGGCCCAUAAAGGCAGAAUAAUUACAAUAAACAAAAUGCAC
(((.(((.(((..((((((((...((((..((((((.((((((....((((.(....)))))......))))))..))))))........)))))))))))).))).))).)))...... ( -20.30)
>DroSec_CAF1 5061 119 + 1
UUUCUUU-UUAAAAAUUAUUUCAGUGCCCACCAACAAUAAUCUAAAUUAGAAGCUCGCUCGGUUAUUUAGAUUAGAUGUUGGCCCAUAAAGACAAAAUAAUUACAAUAAACAAAAUGCAC
.......-...............((((...((((((.((((((((((..((.(....)))....))))))))))..))))))..(.....).........................)))) ( -18.00)
>DroSim_CAF1 5068 119 + 1
UUUCUUU-UUAAAAAUUAUUUCAGUGCCCACCAACAAUAAUCUAAUUUAGAAGCUCGCUCGGUUAUUUAGAUUAGAUGUUGGCUCAUAAAGGCAAAAUAAUUACAAUAAACAAAAUGCAC
.......-.....((((((((...((((..((((((....(((((((((((((((.....)))).)))))))))))))))))........)))))))))))).................. ( -22.40)
>DroEre_CAF1 5033 119 + 1
UUUCUUU-UUAAAAAUUAUUUAAUUGCCUACCGACAAUAAUCUAAAGUGGUAGCUCGCGGGGGUAUUUAGAUUAGAUGUUGGCCCAUAAAGGCAGAAUAAUUAUAAUAAACAAAAUACAC
.......-.....((((((((...(((((.((((((.(((((((((......((((....)))).)))))))))..)))))).......))))))))))))).................. ( -24.50)
>DroYak_CAF1 5087 119 + 1
UUUCUUU-UGAAAAUUUAUUUGAUUGCCUACCAACAAUAAUCUAAAUUGGAAGCUCGCUGGGGUAUUUAGAUUAGAUGUUGGCCCAUAAAGGCAGAAUAAUUUUAAUAAACAAAAUACAC
......(-(((((..((((((...(((((.((((((.((((((((((.....((((....))))))))))))))..)))))).......))))))))))))))))).............. ( -24.90)
>consensus
UUUCUUU_UUAAAAAUUAUUUAAGUGCCCACCAACAAUAAUCUAAAUUAGAAGCUCGCUCGGUUAUUUAGAUUAGAUGUUGGCCCAUAAAGGCAGAAUAAUUACAAUAAACAAAAUGCAC
.............((((((((...((((..((((((.((((((((((....((....)).....))))))))))..))))))........)))))))))))).................. (-18.28 = -19.08 +   0.80)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,609,344 – 9,609,464
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.45
Mean single sequence MFE -23.70
Consensus MFE -20.92
Energy contribution -21.92
Covariance contribution 1.00
Combinations/Pair 1.10
Mean z-score -1.29
Structure conservation index 0.88
SVM decision value 0.23
SVM RNA-class probability 0.645435
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9609344 120 - 23771897
GUGCAUUUUGUUUAUUGUAAUUAUUCUGCCUUUAUGGGCCAACAUCUAAUCUAAAUAACCGAGCGAGCUUCAAAUUAAGAUUAUUGUUGGUGGGCACUUAAAUAAUUUCCAAAAAAGAAA
......(((.(((.(((.(((((((.(((((......(((((((..((((((.(((....(((....)))...))).)))))).))))))))))))....)))))))..))).))).))) ( -23.60)
>DroSec_CAF1 5061 119 - 1
GUGCAUUUUGUUUAUUGUAAUUAUUUUGUCUUUAUGGGCCAACAUCUAAUCUAAAUAACCGAGCGAGCUUCUAAUUUAGAUUAUUGUUGGUGGGCACUGAAAUAAUUUUUAA-AAAGAAA
.....((((.((((....(((((((((((((......(((((((..((((((((((....(((....)))...)))))))))).))))))))))))...))))))))..)))-).)))). ( -25.50)
>DroSim_CAF1 5068 119 - 1
GUGCAUUUUGUUUAUUGUAAUUAUUUUGCCUUUAUGAGCCAACAUCUAAUCUAAAUAACCGAGCGAGCUUCUAAAUUAGAUUAUUGUUGGUGGGCACUGAAAUAAUUUUUAA-AAAGAAA
.....((((.((((....(((((((((((((......(((((((..((((((((......(((....))).....)))))))).))))))))))))...))))))))..)))-).)))). ( -25.80)
>DroEre_CAF1 5033 119 - 1
GUGUAUUUUGUUUAUUAUAAUUAUUCUGCCUUUAUGGGCCAACAUCUAAUCUAAAUACCCCCGCGAGCUACCACUUUAGAUUAUUGUCGGUAGGCAAUUAAAUAAUUUUUAA-AAAGAAA
.....((((.((((....(((((((.(((((......(((.(((..(((((((((......(....).......))))))))).))).))))))))....)))))))..)))-).)))). ( -20.62)
>DroYak_CAF1 5087 119 - 1
GUGUAUUUUGUUUAUUAAAAUUAUUCUGCCUUUAUGGGCCAACAUCUAAUCUAAAUACCCCAGCGAGCUUCCAAUUUAGAUUAUUGUUGGUAGGCAAUCAAAUAAAUUUUCA-AAAGAAA
.....(((((......(((.(((((.(((((......(((((((..((((((((((.....((....))....)))))))))).))))))))))))....))))).))).))-))).... ( -23.00)
>consensus
GUGCAUUUUGUUUAUUGUAAUUAUUCUGCCUUUAUGGGCCAACAUCUAAUCUAAAUAACCGAGCGAGCUUCCAAUUUAGAUUAUUGUUGGUGGGCACUGAAAUAAUUUUUAA_AAAGAAA
......(((.(((.(((.(((((((.(((((......(((((((..((((((((((....(((....)))...)))))))))).))))))))))))....)))))))..))).))).))) (-20.92 = -21.92 +   1.00)

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 10:53:39 2006