Locus 5142

Sequence ID 2R_DroMel_CAF1
Location 16,735,125 – 16,735,217
Length 92
Max. P 0.804852
window8222 window8223

overview

Window 2

Location 16,735,125 – 16,735,217
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 92.28
Mean single sequence MFE -19.58
Consensus MFE -14.88
Energy contribution -15.72
Covariance contribution 0.84
Combinations/Pair 1.04
Mean z-score -1.93
Structure conservation index 0.76
SVM decision value 0.50
SVM RNA-class probability 0.759946
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16735125 92 + 20766785
CGUUCACAAAAAUAAUCAUUUCAGCCGCAGAACCAAAGCGAACCCGCAAUUUGAUUGUCAACCAAAUUGUCGGUGGCAAUUGUGACAUCUCU
.((.(((((((((....))))..(((((.........))..(((.((((((((.........)))))))).))))))..)))))))...... ( -20.30)
>DroSec_CAF1 43105 92 + 1
CGUCCACAAAAAUAAUCAUUUGAGCCGCACAACCAAAGCAAACCCGCAAUUUGAUUGUCAACCAAAUUGUCGGUGGCAAUUGUGACAUCUCU
.(((.((((......((....))(((((.........))..(((.((((((((.........)))))))).))))))..)))))))...... ( -22.00)
>DroSim_CAF1 45410 92 + 1
CGUUCACAAAAAUAAUCAUUUGAGCCGCAGAACCAAAGCAAACCCGCAAUUUGAUUGUCAACCAAAUUGUCGGUGGCAAUUGUGACAUCUUU
.((.(((((......((....))(((((.........))..(((.((((((((.........)))))))).))))))..)))))))...... ( -22.00)
>DroEre_CAF1 44506 89 + 1
---UCACAAAAAUAAUCAUUUCAACCGCCGAACCAAAGCAAACCCGCAAUUUGAUUGUCAAGCAAAUUGUCGGCGGCAAUUGUGACAUUUGU
---..(((((.....((((.....(((((((......((......))((((((.((....)))))))).))))))).....))))..))))) ( -20.20)
>DroYak_CAF1 49885 92 + 1
CGUUUACAAAAAUAAUCAUUUAAACCGCAGAACCAAAGCAAACCCGCAAUUCGAUUGUCAACCAAAUUGUCGGUGGCAAUUGUGACAUUUCU
.........................(((.........((......)).....((((((((.((........)))))))))))))........ ( -13.40)
>consensus
CGUUCACAAAAAUAAUCAUUUCAGCCGCAGAACCAAAGCAAACCCGCAAUUUGAUUGUCAACCAAAUUGUCGGUGGCAAUUGUGACAUCUCU
...((((((((((....))))..(((((.........))..(((.((((((((.........)))))))).))))))..))))))....... (-14.88 = -15.72 +   0.84)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,735,125 – 16,735,217
Length 92
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 92.28
Mean single sequence MFE -23.62
Consensus MFE -21.80
Energy contribution -21.44
Covariance contribution -0.36
Combinations/Pair 1.15
Mean z-score -1.27
Structure conservation index 0.92
SVM decision value 0.63
SVM RNA-class probability 0.804852
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16735125 92 - 20766785
AGAGAUGUCACAAUUGCCACCGACAAUUUGGUUGACAAUCAAAUUGCGGGUUCGCUUUGGUUCUGCGGCUGAAAUGAUUAUUUUUGUGAACG
((((((((((.....(((.(((.(((((((((.....))))))))))))....((.........))))).....))).)))))))....... ( -23.50)
>DroSec_CAF1 43105 92 - 1
AGAGAUGUCACAAUUGCCACCGACAAUUUGGUUGACAAUCAAAUUGCGGGUUUGCUUUGGUUGUGCGGCUCAAAUGAUUAUUUUUGUGGACG
.(((.((.(((((((((..(((.(((((((((.....))))))))))))....))...))))))))).)))..................... ( -24.20)
>DroSim_CAF1 45410 92 - 1
AAAGAUGUCACAAUUGCCACCGACAAUUUGGUUGACAAUCAAAUUGCGGGUUUGCUUUGGUUCUGCGGCUCAAAUGAUUAUUUUUGUGAACG
.......((((((..(((.(((.(((((((((.....))))))))))))....((.........)))))((....))......))))))... ( -23.40)
>DroEre_CAF1 44506 89 - 1
ACAAAUGUCACAAUUGCCGCCGACAAUUUGCUUGACAAUCAAAUUGCGGGUUUGCUUUGGUUCGGCGGUUGAAAUGAUUAUUUUUGUGA---
(((((.((((.....(((((((((((...(((((.((((...))))))))).....)))..)))))))).....))))....)))))..--- ( -25.80)
>DroYak_CAF1 49885 92 - 1
AGAAAUGUCACAAUUGCCACCGACAAUUUGGUUGACAAUCGAAUUGCGGGUUUGCUUUGGUUCUGCGGUUUAAAUGAUUAUUUUUGUAAACG
((((((((((.....(((.(((.(((((((((.....))))))))))))....((.........))))).....))).)))))))....... ( -21.20)
>consensus
AGAGAUGUCACAAUUGCCACCGACAAUUUGGUUGACAAUCAAAUUGCGGGUUUGCUUUGGUUCUGCGGCUCAAAUGAUUAUUUUUGUGAACG
((((((((((.....(((.(((.(((((((((.....))))))))))))....((.........))))).....))).)))))))....... (-21.80 = -21.44 +  -0.36)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:37 2006