Locus 658

Sequence ID 3R_DroMel_CAF1
Location 2,425,082 – 2,425,172
Length 90
Max. P 0.829115
window1040

overview

Window 0

Location 2,425,082 – 2,425,172
Length 90
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 76.53
Mean single sequence MFE -40.68
Consensus MFE -22.48
Energy contribution -25.16
Covariance contribution 2.68
Combinations/Pair 1.11
Mean z-score -1.93
Structure conservation index 0.55
SVM decision value 0.71
SVM RNA-class probability 0.829115
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2425082 90 + 27905053
GAAGCAGGA-------GCCCGGAGGUGGGUAAGACCACCUGGGCGGAGG-------------UC--CAUGCAGGGGGCGACAUAAAAGUUUCACACCCAGCCAUUUGGCCAU
...((((((-------.((((.((((((......))))))...))).).-------------))--).))).(((.(.(((......))).)...))).(((....)))... ( -34.60)
>DroSec_CAF1 138028 103 + 1
GAAGCCGGA-------GCCCGGAGGUGGGUCACACCACCUGGGCGGAGGUCCAAGCAGGGGGUC--CAUGCAGGGGGCGACAUAAAAGUUUCGCACCCAGGCAUUUGGCCAU
...((((((-------.(((..((((((......))))))((((....))))......))).))--)((((..(((((((.((....)).)))).)))..))))..)))... ( -48.90)
>DroSim_CAF1 132005 103 + 1
GAAGCCGGA-------GCCCGGAGGUGGGUCAGACCACCUGGGCGGAGGUUCAAGCAGGGGGUC--CAUGCAGGGGGCGACAUAAAAGUUUCGCACCCAGGCAUUUGGCCAU
...((((((-------.(((..((((((......))))))((((....))))......))).))--)((((..(((((((.((....)).)))).)))..))))..)))... ( -46.10)
>DroEre_CAF1 133101 99 + 1
GAGCCCGGAGCACGGAGCACGGAGGAGGGCCAGACCACCUGGCAGGUGG-------------ACCUCAUGCAAGGGGCGACAUAAAAGUUUCGCACCCCGGCAUUUGGGCAU
..(((((((((.((..(((..((((...(((((.....)))))......-------------.)))).)))..(((((((.((....)).)))).))))))).))))))).. ( -41.80)
>DroYak_CAF1 127238 96 + 1
GAGCAUGGAGCGCGGAGCAUGGAAUAGGGUCGAACCACCUGGCAGGAGG-------------UC--CAUGCAAGCGGCGACAUAAAAGU-UCGCACCCAGGCAUUUGGCCAU
.....(((..(((...(((((((...((......)).(((......)))-------------))--)))))..)))(((((......).-))))..)))(((.....))).. ( -32.00)
>consensus
GAAGCCGGA_______GCCCGGAGGUGGGUCAGACCACCUGGGCGGAGG_____________UC__CAUGCAGGGGGCGACAUAAAAGUUUCGCACCCAGGCAUUUGGCCAU
...((((((.......((((..((((((......))))))))))........................(((..(((((((.((....)).)))).)))..)))))))))... (-22.48 = -25.16 +   2.68)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:32 2006