Locus 2010

Sequence ID X_DroMel_CAF1
Location 5,515,376 – 5,515,467
Length 91
Max. P 0.726842
window3270

overview

Window 0

Location 5,515,376 – 5,515,467
Length 91
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 71.32
Mean single sequence MFE -28.92
Consensus MFE -9.04
Energy contribution -9.84
Covariance contribution 0.80
Combinations/Pair 1.17
Mean z-score -1.81
Structure conservation index 0.31
SVM decision value 0.41
SVM RNA-class probability 0.726842
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5515376 91 + 22224390
GAAGUAGUAAGGAGAUGGGAGAGAUGCCCGUCGUGCGCAUCACUGGGGAACUGGGCGGGAGCAGG--UGCGGA-------UCCGAGGUAUC---------GAUGGAGGA
...(((.(..(((((((((.......))))))...((((((.(..(....)..)((....)).))--))))..-------)))..).))).---------......... ( -29.90)
>DroSec_CAF1 5419 86 + 1
GAAGUAGUAAGGACAUGGG----AUGCCCGUCGUGCGCAUCGCUGGGGAACUGGGCGGGAGCAGG--UGCGGA-------U-CGAGGGAUC---------GAUGGAGGA
.............(((.((----...(((.((((.((((((.(..(....)..)((....)).))--)))).)-------.-)))))).))---------.)))..... ( -29.60)
>DroSim_CAF1 5311 86 + 1
GAAGUAGUAAGGACAUGGG----AUGCCCGUCGUGCGCAUCGCUGGGGAACUGGGCGGGAGCAGG--UGCGGA-------U-CGAGGGAUC---------GAUGGAGGA
.............(((.((----...(((.((((.((((((.(..(....)..)((....)).))--)))).)-------.-)))))).))---------.)))..... ( -29.60)
>DroYak_CAF1 5400 85 + 1
GAAAUAGUA--------GG----AUGCCCGCCGUGCGCAUCCCUGGGGAACUGGGCGGGAGCAGG--UGCGGAGGUGCGAU-CAUGGGAUC---------GAUGGAGGA
.........--------..----....((.((((.((((((.(..(....)..)((....)).))--))))......((((-(....))))---------))))).)). ( -28.30)
>DroAna_CAF1 5162 89 + 1
GAAAUAGAGCGCGGAUGCA----AUACCAGC-------AAUUCC-GGGGUCAGGGCGGGAAAAAGGCUGCGGA-------U-CCAGGGAUCAUCGUGCGAGAAGAAGGA
........((((((.(((.----......))-------)(((((-.(((((...((((........)))).))-------)-)).)))))..))))))........... ( -27.20)
>consensus
GAAGUAGUAAGGACAUGGG____AUGCCCGUCGUGCGCAUCGCUGGGGAACUGGGCGGGAGCAGG__UGCGGA_______U_CGAGGGAUC_________GAUGGAGGA
...........................(((((.(((......((((....))))......))).)...))))..................................... ( -9.04 =  -9.84 +   0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:04 2006