Locus 3954

Sequence ID	X_DroMel_CAF1
Location	10,514,531 – 10,514,630
Length	99
Max. P	0.998012

overview

Window 1

Location	10,514,531 – 10,514,630
Length	99
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	88.52
Mean single sequence MFE	-36.65
Consensus MFE	-34.06
Energy contribution	-34.38
Covariance contribution	0.31
Combinations/Pair	1.03
Mean z-score	-3.09
Structure conservation index	0.93
SVM decision value	2.98
SVM RNA-class probability	0.998012
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10514531 99 + 22224390
UGUUGUUGCCGCUGCCAUUAUCCUUGUAGUGUUUCCGUACAACAGUGGCAACAGCCACCUGGCCGGUGGCAUGGGAAAGUUCCCAUCUCCC--------------AUUUCCCU
...(((((((((((.........(((((.((....))))))))))))))))))((((((.....))))))((((((....)))))).....--------------........ ( -37.00)
>DroSec_CAF1 45832 99 + 1
UGUUGUUGCCGCUGCCAUUAUCCUUGUAGUGUUUCCGUACAACAGUGGCAACAGCCACCUGGCCGGUGGCAUGGGAAAGUUCCCAUCUUCC--------------AUUUCCCU
...(((((((((((.........(((((.((....))))))))))))))))))((((((.....))))))((((((....)))))).....--------------........ ( -37.00)
>DroSim_CAF1 49169 99 + 1
UGUUGUUGCCGCUGCCAUUAUCCUUGUAGUGUUUCCGUACAACAGUGGCAACAGCCACCUGGCCGGUGGCAUGGGAAAGUUCCCAUCUUCC--------------AUUUCCCU
...(((((((((((.........(((((.((....))))))))))))))))))((((((.....))))))((((((....)))))).....--------------........ ( -37.00)
>DroEre_CAF1 46499 112 + 1
AGUUGUUGCCGCUGCCAUUAUCCUUGUAGUGUUUCCGUACAACAGUGGCAACAGC-ACCUGGCCGGCGGCAUGGGAAGGUUCCCGGUUCCCAUAUCCCAUCACCCAUCUCCCC
.(((((((((((((.........(((((.((....))))))))))))))))))))-........((.(..((((((.((...))...))))))..)))............... ( -35.60)
>consensus
UGUUGUUGCCGCUGCCAUUAUCCUUGUAGUGUUUCCGUACAACAGUGGCAACAGCCACCUGGCCGGUGGCAUGGGAAAGUUCCCAUCUCCC______________AUUUCCCU
...(((((((((((.........(((((.((....))))))))))))))))))((((((.....)))))).(((((....)))))............................ (-34.06 = -34.38 +   0.31)

alignment

secondary structure

dotplot

Window 2

Location	10,514,531 – 10,514,630
Length	99
Sequences	4
Columns	113
Reading direction	reverse
Mean pairwise identity	88.52
Mean single sequence MFE	-41.00
Consensus MFE	-36.99
Energy contribution	-37.55
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-3.56
Structure conservation index	0.90
SVM decision value	2.95
SVM RNA-class probability	0.997874
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10514531 99 - 22224390
AGGGAAAU--------------GGGAGAUGGGAACUUUCCCAUGCCACCGGCCAGGUGGCUGUUGCCACUGUUGUACGGAAACACUACAAGGAUAAUGGCAGCGGCAACAACA
......((--------------((((((.(....)))))))))((((((.....))))))(((((((.((((..(..(....).((....))...)..)))).)))))))... ( -43.60)
>DroSec_CAF1 45832 99 - 1
AGGGAAAU--------------GGAAGAUGGGAACUUUCCCAUGCCACCGGCCAGGUGGCUGUUGCCACUGUUGUACGGAAACACUACAAGGAUAAUGGCAGCGGCAACAACA
........--------------.....((((((....))))))((((((.....))))))(((((((.((((..(..(....).((....))...)..)))).)))))))... ( -39.90)
>DroSim_CAF1 49169 99 - 1
AGGGAAAU--------------GGAAGAUGGGAACUUUCCCAUGCCACCGGCCAGGUGGCUGUUGCCACUGUUGUACGGAAACACUACAAGGAUAAUGGCAGCGGCAACAACA
........--------------.....((((((....))))))((((((.....))))))(((((((.((((..(..(....).((....))...)..)))).)))))))... ( -39.90)
>DroEre_CAF1 46499 112 - 1
GGGGAGAUGGGUGAUGGGAUAUGGGAACCGGGAACCUUCCCAUGCCGCCGGCCAGGU-GCUGUUGCCACUGUUGUACGGAAACACUACAAGGAUAAUGGCAGCGGCAACAACU
.......(((.((.(((..((((((((..(....).))))))))))).)).)))(.(-((((((((((.(.(((((.(....)..))))).)....))))))))))).).... ( -40.60)
>consensus
AGGGAAAU______________GGAAGAUGGGAACUUUCCCAUGCCACCGGCCAGGUGGCUGUUGCCACUGUUGUACGGAAACACUACAAGGAUAAUGGCAGCGGCAACAACA
...........................((((((....))))))((((((.....))))))(((((((.((((..(..(....).((....))...)..)))).)))))))... (-36.99 = -37.55 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:38 2006