Locus 4878

Sequence ID 3R_DroMel_CAF1
Location 12,837,286 – 12,837,388
Length 102
Max. P 0.643833
window7988

overview

Window 8

Location 12,837,286 – 12,837,388
Length 102
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 83.66
Mean single sequence MFE -39.95
Consensus MFE -28.93
Energy contribution -29.79
Covariance contribution 0.86
Combinations/Pair 1.16
Mean z-score -2.03
Structure conservation index 0.72
SVM decision value 0.23
SVM RNA-class probability 0.643833
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12837286 102 + 27905053
A------AUGGCCGGGACACGGAGUCGCUGGCCUCAAUGGCUUUGACGGAGAACGGCGGCGAGGAGGCCAUUCCUCCUCCGCUGUACCGCAACACAAUGGCCAUGUAU
.------..(((((((((.....))).))))))...(((((((((.(((...(((((((..((((((.....))))))))))))).))))))......)))))).... ( -46.30)
>DroVir_CAF1 8863 102 + 1
AAUCGGAAUGCUCGCGAUAAUGAAUCGUUGGCCUCUGUAUCUAU---GGAGAACGGAGAAGGAGAGAACAA---UAAUCCGCUUUAUCGUAAUACGAUGGCGAUGUAU
.((((((..(((.(((((.....))))).)))((((((.(((..---..))))))))).............---...)))(((..((((.....)))))))))).... ( -27.10)
>DroSec_CAF1 6648 99 + 1
A------AUGGCCGGGACACGGAGUCGCUGGUCUCGAUGGCUUUGACGGAGAACGGCGGCGAGGAGGUUAA---UCCUCCGCUGUACCGCAACACAAUGGCCAUGUAU
.------(((((((((((.(((.....))))))))..((...(((.(((...(((((((..((((......---))))))))))).))))))..))..)))))).... ( -40.40)
>DroSim_CAF1 6851 99 + 1
A------AUGGCCGGGACACGGAGUCGCUGGCCUCGAUGGCUUUGACGGAGAACGGCGGCGAGGAGGUUAA---UCCUCCGCUGUAUCGCAACACAAUGGCCAUGUAU
.------..(((((((((.....))).))))))...(((((((((...(.(((((((((..((((......---))))))))))).)).)....))).)))))).... ( -40.10)
>DroEre_CAF1 6770 99 + 1
A------AUGGCCGGGACACGGAGUCGCUGGCCUCCAUGGCUUUGACGGAGAACGGCGGCGAGGAGGUGAG---UCCUCCGCAGUACCGCAACACCAUGGCCAUGUAU
.------(((((((((...(((.(((((((..((((...........))))..)))))))(.(((((....---.))))).)....))).....)).))))))).... ( -43.90)
>DroYak_CAF1 6872 99 + 1
A------AUGGCCGGGACACGGAGUCGCUGGCCUCGAUGGCUUUGACGGAGAACGGCGGCGAGGAGGUCAA---UCCUCCGCUGUACCGCAACACCAUGGCCAUGUAU
.------(((((((((...(((.((((..((((.....)))).)))).....(((((((..((((......---))))))))))).))).....)).))))))).... ( -41.90)
>consensus
A______AUGGCCGGGACACGGAGUCGCUGGCCUCGAUGGCUUUGACGGAGAACGGCGGCGAGGAGGUCAA___UCCUCCGCUGUACCGCAACACAAUGGCCAUGUAU
.......(((((((.....(((.(((((((..(((.............)))..)))))))..(((((........)))))......)))........))))))).... (-28.93 = -29.79 +   0.86)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:03 2006