Locus 1996

Sequence ID 3L_DroMel_CAF1
Location 5,473,966 – 5,474,077
Length 111
Max. P 0.521890
window3126

overview

Window 6

Location 5,473,966 – 5,474,077
Length 111
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 95.17
Mean single sequence MFE -23.58
Consensus MFE -19.82
Energy contribution -20.22
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.31
Structure conservation index 0.84
SVM decision value -0.02
SVM RNA-class probability 0.521890
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5473966 111 + 23771897
GAGCGCUGAAAAGAUGCCAACAAAUAACCAAUAAAAAGCAACAAGCA-------ACGAGCCAGUUGGGGGCGAAAGAAAAACAGCAUAAAGUUGUGCUUGGGAAAUUUCCCACAUUUG
(.(((((....)).))))..(((((..........(((((.(((((.-------....))..((((....(....).....))))......))))))))((((....))))..))))) ( -23.50)
>DroSec_CAF1 35470 111 + 1
GAGCGCUGAAAAGAUGCCAACAAAUAACCAAUAAAAAGCAACAAGCA-------ACGAGCCAGUUGGGGGCGAAAGAACAACAGCAUAAAGUUGUGCUUGGGAAAUUUCCCACAUUUG
((((((.......((((.....................((((..((.-------....))..)))).(..(....)..)....))))......))))))((((....))))....... ( -25.12)
>DroSim_CAF1 37147 111 + 1
GAGCGCUGAAAAGAUGCCAACAAAUAACCAAUAAAAAGCAACAAGCA-------ACGAGCCAGUUGGGGGCGAAAGAAAAACAGCAUAAAGUUGUGCUUGGGAAAUUUCCCACAUUUG
(.(((((....)).))))..(((((..........(((((.(((((.-------....))..((((....(....).....))))......))))))))((((....))))..))))) ( -23.50)
>DroEre_CAF1 34925 118 + 1
GAACGCUGAAAAGAUGCCAACAAAUAACCAAUAAAAAGCAACAAGCAACGAGCAACGAGCCAGUUGGGGGCGAAAGAAAAACAGCAUAAAGUUGUGCUUGGGAAAUUUCCCACAUUUG
....((((......(.(((((................((.....))...(.((.....))).))))).).(....).....)))).............(((((....)))))...... ( -22.90)
>DroYak_CAF1 23263 118 + 1
GAACGCUGAAAAGAUGCCAACAAAUAACCAAUAAAAAGCAACAAGCAACGAGCAACGAGCCAGUUGGGGGCGAAAGAAAAACAGCAUAAAGUUGUGCUUGGGAAAAUUCCCACAUUUG
....((((......(.(((((................((.....))...(.((.....))).))))).).(....).....)))).............(((((....)))))...... ( -22.90)
>consensus
GAGCGCUGAAAAGAUGCCAACAAAUAACCAAUAAAAAGCAACAAGCA_______ACGAGCCAGUUGGGGGCGAAAGAAAAACAGCAUAAAGUUGUGCUUGGGAAAUUUCCCACAUUUG
((((((.......((((....................((.....))............(((.......)))............))))......))))))((((....))))....... (-19.82 = -20.22 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:04 2006