Locus 1945

Sequence ID 3R_DroMel_CAF1
Location 5,492,943 – 5,493,063
Length 120
Max. P 0.824300
window3198 window3199

overview

Window 8

Location 5,492,943 – 5,493,063
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.39
Mean single sequence MFE -35.15
Consensus MFE -31.21
Energy contribution -31.10
Covariance contribution -0.11
Combinations/Pair 1.03
Mean z-score -1.46
Structure conservation index 0.89
SVM decision value 0.64
SVM RNA-class probability 0.809065
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5492943 120 + 27905053
UCCAAUAUGUUCUUGAGCGAGAAACCCUCCGAGUCGAACUCGAAGAUGUAGCGAGUAACAUCCAUGAUCCGUUGCCAGUGGCGUGGCUUCAUGGCUUUAUUCGCCAUCAACUCCAGUAGC
........(((((.(((.(((.....)))((((.....))))..((((..((((((((...((((((.((((.(((...)))))))..))))))..))))))))))))..))).)).))) ( -34.20)
>DroVir_CAF1 33989 120 + 1
UCCAGUAUGUUCUUGAGCGAGAAACCCUCCGAGUCGAACUCGAAGAUGUAGCGAGUAACGUCCAUGAUCCGCUGCCAAUGGCGUGGCUUCAUGGCUUUAUUCGCCAUCAACUCCAAUAAC
........(((....)))(((........((((.....))))..((((..((((((((.(.((((((.((((.(((...)))))))..))))))).))))))))))))..)))....... ( -38.90)
>DroGri_CAF1 27853 120 + 1
UCCAGUAUGUUCUUGAGCGAGAAACCCUCCGAGUCGAACUCGAAGAUGUAGCGAGUAACAUCCAUGAUCCGUUGCCAAUGGCGUGGCUUCAUGGCUUUAUUCGCCAUCAACUCCAGUAAU
...........((.(((.(((.....)))((((.....))))..((((..((((((((...((((((.((((.(((...)))))))..))))))..))))))))))))..))).)).... ( -33.20)
>DroWil_CAF1 26000 120 + 1
UCCAAAAUGUUCUUGAGCGAGAAACCCUCGGAAUCAAAUUCAAAGAUGUAGCGAGUAACGUCCAUGAUCCGUUGCCAAUGGCGUGGCUUCAUGGCUUUAUUCGCCAUCAACUCCAGGAGC
........(((((((((((((.....))))..............((((..((((((((.(.((((((.((((.(((...)))))))..))))))).))))))))))))..)).))))))) ( -38.10)
>DroMoj_CAF1 33637 120 + 1
UCCAGUAUGUUCUUAAGCGAGAAACCCUCCGAGUCGAACUCGAAGAUGUAGCGAGUAACAUCCAUGAUCCGUUGCCAAUGGCGUGGCUUCAUGGCUUUAUUCGCCAUCAACUCCAAUAGU
................(.(((........((((.....))))..((((..((((((((...((((((.((((.(((...)))))))..))))))..))))))))))))..))))...... ( -32.50)
>DroAna_CAF1 26165 120 + 1
UCCAAUAUGUUCUUGAGCGAGAAACCCUCCGAGUCGAACUCGAAGAUGUAGCGAGUAACAUCCAUGAUUCGUUGCCAAUGACGUGGCUUCAUGGCUUUAUUCGCCAUCAACUCCAGUAGC
........(((((.(((.(((.....)))((((.....))))..((((..((((((((...((((((......((((......)))).))))))..))))))))))))..))).)).))) ( -34.00)
>consensus
UCCAAUAUGUUCUUGAGCGAGAAACCCUCCGAGUCGAACUCGAAGAUGUAGCGAGUAACAUCCAUGAUCCGUUGCCAAUGGCGUGGCUUCAUGGCUUUAUUCGCCAUCAACUCCAGUAGC
................(.(((........((((.....))))..((((..((((((((...((((((......((((......)))).))))))..))))))))))))..))))...... (-31.21 = -31.10 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 5,492,943 – 5,493,063
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 94.39
Mean single sequence MFE -36.92
Consensus MFE -34.30
Energy contribution -33.83
Covariance contribution -0.47
Combinations/Pair 1.09
Mean z-score -1.17
Structure conservation index 0.93
SVM decision value 0.69
SVM RNA-class probability 0.824300
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5492943 120 - 27905053
GCUACUGGAGUUGAUGGCGAAUAAAGCCAUGAAGCCACGCCACUGGCAACGGAUCAUGGAUGUUACUCGCUACAUCUUCGAGUUCGACUCGGAGGGUUUCUCGCUCAAGAACAUAUUGGA
....((.((((((.((((((.(((..((((((..((..(((...)))...)).))))))...))).))))))))((((((((.....)))))))).......)))).))........... ( -37.50)
>DroVir_CAF1 33989 120 - 1
GUUAUUGGAGUUGAUGGCGAAUAAAGCCAUGAAGCCACGCCAUUGGCAGCGGAUCAUGGACGUUACUCGCUACAUCUUCGAGUUCGACUCGGAGGGUUUCUCGCUCAAGAACAUACUGGA
(((....((((((.((((((.(((..((((((..((.((((...))).).)).))))))...))).))))))))((((((((.....)))))))).......))))...)))........ ( -39.80)
>DroGri_CAF1 27853 120 - 1
AUUACUGGAGUUGAUGGCGAAUAAAGCCAUGAAGCCACGCCAUUGGCAACGGAUCAUGGAUGUUACUCGCUACAUCUUCGAGUUCGACUCGGAGGGUUUCUCGCUCAAGAACAUACUGGA
....((.((((((.((((((.(((..((((((..((..(((...)))...)).))))))...))).))))))))((((((((.....)))))))).......)))).))........... ( -37.50)
>DroWil_CAF1 26000 120 - 1
GCUCCUGGAGUUGAUGGCGAAUAAAGCCAUGAAGCCACGCCAUUGGCAACGGAUCAUGGACGUUACUCGCUACAUCUUUGAAUUUGAUUCCGAGGGUUUCUCGCUCAAGAACAUUUUGGA
..(((.(((((..(((((((.(((..((((((..((..(((...)))...)).))))))...))).))))))((....))...)..)))))(((.(.....).)))...........))) ( -35.10)
>DroMoj_CAF1 33637 120 - 1
ACUAUUGGAGUUGAUGGCGAAUAAAGCCAUGAAGCCACGCCAUUGGCAACGGAUCAUGGAUGUUACUCGCUACAUCUUCGAGUUCGACUCGGAGGGUUUCUCGCUUAAGAACAUACUGGA
.(((((((((.((.((((((.(((..((((((..((..(((...)))...)).))))))...))).)))))))).))))))((((......(((.....)))......))))....))). ( -35.50)
>DroAna_CAF1 26165 120 - 1
GCUACUGGAGUUGAUGGCGAAUAAAGCCAUGAAGCCACGUCAUUGGCAACGAAUCAUGGAUGUUACUCGCUACAUCUUCGAGUUCGACUCGGAGGGUUUCUCGCUCAAGAACAUAUUGGA
....((.((((((.((((((.(((..((((((.((((......))))......))))))...))).))))))))((((((((.....)))))))).......)))).))........... ( -36.10)
>consensus
GCUACUGGAGUUGAUGGCGAAUAAAGCCAUGAAGCCACGCCAUUGGCAACGGAUCAUGGAUGUUACUCGCUACAUCUUCGAGUUCGACUCGGAGGGUUUCUCGCUCAAGAACAUACUGGA
....((.((((((.((((((.(((..((((((.((((......))))......))))))...))).))))))))((((((((.....)))))))).......)))).))........... (-34.30 = -33.83 +  -0.47)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:34 2006