Locus 4142

Sequence ID 3L_DroMel_CAF1
Location 12,103,387 – 12,103,547
Length 160
Max. P 0.979943
window6433 window6434

overview

Window 3

Location 12,103,387 – 12,103,507
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.83
Mean single sequence MFE -43.62
Consensus MFE -40.88
Energy contribution -41.28
Covariance contribution 0.40
Combinations/Pair 1.05
Mean z-score -1.09
Structure conservation index 0.94
SVM decision value 0.14
SVM RNA-class probability 0.601116
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12103387 120 + 23771897
CAGUGGCAUUGCUGGCUACUCUCGGCCAGGCCAAGCACCUGGACUCCAAGGUGGCGGACAAGGACUUUCUGAUGAAACAGAAGUUCAUGUACCAGAUCCUGCAGCACAUCUACCAGGACG
..((((...((((((((((.((.(((((((.......)))))...)).)))))))(((((.((((((.(((......))))))))).))).))........)))))...))))....... ( -40.80)
>DroSec_CAF1 4510 120 + 1
CGGUGGCAUUGCUGGCUACUCUCGGCCAGGCCAAGCACCUGGACUCCAAGGUGGCGGACAAGGACUUUCUGAUGAAGCAGAAGUUCGUGUUCCACAUCCUGCAGCACAUCUACCAGGCCG
.(((((...((((((((((.((.(((((((.......)))))...)).)))))))(((((.((((((.(((......))))))))).))))).........)))))...)))))...... ( -45.30)
>DroSim_CAF1 3890 120 + 1
CGGUGGCAUUGCUGGCUACUCUCGGCCAGGCCAAGCACCUGGACUCCAAGGUGGCGGACAAGGACUUUCUGGUGAAGCAGCAGUUCAUGUUCCACAUCCUGCAGCACAUCUACCAGGAUG
.(((((...((((((((((.((.(((((((.......)))))...)).)))))))(((((.(((((..(((......))).))))).))))).........)))))...)))))...... ( -42.90)
>DroEre_CAF1 4027 120 + 1
CGGUGGCAUUGCUGGCUGCUCUGGGCCAGGCCAAGCACCUGGACUCCAAGGUGGCGGACAAGGACUUCCUGACCAAGCAGAGCUUCAUGUUCCAGAUCCUGCAGCACAUCUACCAGGACG
.(((((...(((((((..(..(((((((((.......))))).).)))..)..))((((.(((....))).........((((.....))))..).)))..)))))...)))))...... ( -43.50)
>DroYak_CAF1 4028 120 + 1
CGGUGGCAUUGCUGGCUGCUCUGGGCCAGGCCAAGCACCUGGACUCCAAGGUGGCGGACAAGGACUUUCUGAUGAAGCAGAACUUCGUGUUCCAGAUCCUGCAGCACAUCUACCAGGACG
.(((((...(((((((..(..(((((((((.......))))).).)))..)..)).....((((...((((((((((.....))))))....)))))))).)))))...)))))...... ( -45.60)
>consensus
CGGUGGCAUUGCUGGCUACUCUCGGCCAGGCCAAGCACCUGGACUCCAAGGUGGCGGACAAGGACUUUCUGAUGAAGCAGAAGUUCAUGUUCCAGAUCCUGCAGCACAUCUACCAGGACG
.(((((...((((((((((.((.(((((((.......)))))...)).)))))))(((((.((((((.(((......))))))))).))).))........)))))...)))))...... (-40.88 = -41.28 +   0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,103,427 – 12,103,547
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.67
Mean single sequence MFE -44.32
Consensus MFE -35.40
Energy contribution -36.04
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -2.36
Structure conservation index 0.80
SVM decision value 1.85
SVM RNA-class probability 0.979943
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12103427 120 + 23771897
GGACUCCAAGGUGGCGGACAAGGACUUUCUGAUGAAACAGAAGUUCAUGUACCAGAUCCUGCAGCACAUCUACCAGGACGAUGUGUUCACCACGCCCUUCGGGGGCAGCUACGUGGAGUA
..((((((..((((((((((.((((((.(((......))))))))).))).))......(((((((((((.........)))))))).......(((....))))))))))).)))))). ( -48.90)
>DroSec_CAF1 4550 120 + 1
GGACUCCAAGGUGGCGGACAAGGACUUUCUGAUGAAGCAGAAGUUCGUGUUCCACAUCCUGCAGCACAUCUACCAGGCCGAUGUGUUCACCACCCCAUUCGGAGGCAGCUACGUGGAGUA
..((((((..((((((((((.((((((.(((......))))))))).))))).......(((((((((((.........)))))))).....(.((....)).))))))))).)))))). ( -42.50)
>DroSim_CAF1 3930 120 + 1
GGACUCCAAGGUGGCGGACAAGGACUUUCUGGUGAAGCAGCAGUUCAUGUUCCACAUCCUGCAGCACAUCUACCAGGAUGAUGUGUUCACCACCCCAUUCGGGGGCAGCUACGUGGAGUA
..((((((..((((((((((.(((((..(((......))).))))).))))).......(((((((((((.........)))))))).....((((....)))))))))))).)))))). ( -47.60)
>DroEre_CAF1 4067 120 + 1
GGACUCCAAGGUGGCGGACAAGGACUUCCUGACCAAGCAGAGCUUCAUGUUCCAGAUCCUGCAGCACAUCUACCAGGACGAUGUGUUCACAACCCACUUCCCGGCCACCUACAUGGAGUA
..(((((((((((((((...(((....)))..))..((((.(..((........)).)))))((((((((.........))))))))................)))))))...)))))). ( -40.00)
>DroYak_CAF1 4068 120 + 1
GGACUCCAAGGUGGCGGACAAGGACUUUCUGAUGAAGCAGAACUUCGUGUUCCAGAUCCUGCAGCACAUCUACCAGGACGAUGUGUUCACAACCCCAUUCUCCGCCAGCUACGUGGAGUA
..((((((((.(((((((..((((...((((((((((.....))))))....))))))))(.((((((((.........)))))))))............))))))).))...)))))). ( -42.60)
>consensus
GGACUCCAAGGUGGCGGACAAGGACUUUCUGAUGAAGCAGAAGUUCAUGUUCCAGAUCCUGCAGCACAUCUACCAGGACGAUGUGUUCACCACCCCAUUCGGGGGCAGCUACGUGGAGUA
..((((((..((((((((((.((((((.(((......))))))))).))).))......((.((((((((.........))))))))))..................))))).)))))). (-35.40 = -36.04 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:23 2006