Locus 2014

Sequence ID X_DroMel_CAF1
Location 5,521,586 – 5,521,685
Length 99
Max. P 0.999597
window3275 window3276

overview

Window 5

Location 5,521,586 – 5,521,685
Length 99
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 80.84
Mean single sequence MFE -29.75
Consensus MFE -19.55
Energy contribution -19.55
Covariance contribution 0.00
Combinations/Pair 1.15
Mean z-score -3.14
Structure conservation index 0.66
SVM decision value 2.82
SVM RNA-class probability 0.997222
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5521586 99 + 22224390
GGACAGGAACAUGAGAGACGCCUGUUAUGCGCAAUUAAAAAUUUGG-GUUUAAUUGCUGUGGAAACUGUUGUUGGUGGCAUCUUAAGUUCCUGUUUAACA
((((((((((.(((((..((((......(((((((((((.......-.)))))))))...(....).))....))))...))))).)))))))))).... ( -34.80)
>DroSec_CAF1 11664 80 + 1
GGACAGGAACAUGAAAGACGCCUGUUAUGCGCAAUUAAAAAU-----------------UGGAAACUG---UUGGUGGCAUCUUAAGUUCCUGUUUAACA
((((((((((....((((.((((((.....)))......(((-----------------.(....).)---))...))).))))..)))))))))).... ( -22.10)
>DroEre_CAF1 11796 95 + 1
AGACAGGAACAUGAAGCACGCCUGUUAUGUGCAAUUAAACAUUCGGU--UUAAUUGCUGUGGAAACU---GUUGGUGGCAUCUAAAGUUCCUGUUCAACA
.(((((((((..((.((.((((........((((((((((.....))--))))))))...(....).---...)))))).))....)))))))))..... ( -33.80)
>DroYak_CAF1 11721 100 + 1
AGACAGGAACAUGAAAGGCGCCUGUUAUGUGCAAUUACAAAUUCGGUGGUUAAUUGCUGUGGCAACUAAAGUCGGUGGCAUCUUAAGUUCCUGUUCAACA
.(((((((((....(((..((((((((((.(((((((.............))))))))))))))(((......))))))..)))..)))))))))..... ( -28.32)
>consensus
AGACAGGAACAUGAAAGACGCCUGUUAUGCGCAAUUAAAAAUUCGG___UUAAUUGCUGUGGAAACUG__GUUGGUGGCAUCUUAAGUUCCUGUUCAACA
.(((((((((....((((.((((((.....)))...........................(....)..........))).))))..)))))))))..... (-19.55 = -19.55 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 5,521,586 – 5,521,685
Length 99
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 80.84
Mean single sequence MFE -27.41
Consensus MFE -19.23
Energy contribution -22.30
Covariance contribution 3.06
Combinations/Pair 1.04
Mean z-score -4.24
Structure conservation index 0.70
SVM decision value 3.77
SVM RNA-class probability 0.999597
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5521586 99 - 22224390
UGUUAAACAGGAACUUAAGAUGCCACCAACAACAGUUUCCACAGCAAUUAAAC-CCAAAUUUUUAAUUGCGCAUAACAGGCGUCUCUCAUGUUCCUGUCC
......((((((((...(((((((...(((....)))......(((((((((.-.......)))))))))........))))))).....)))))))).. ( -30.00)
>DroSec_CAF1 11664 80 - 1
UGUUAAACAGGAACUUAAGAUGCCACCAA---CAGUUUCCA-----------------AUUUUUAAUUGCGCAUAACAGGCGUCUUUCAUGUUCCUGUCC
......((((((((..((((((((.....---(((((....-----------------......))))).(.....).))))))))....)))))))).. ( -22.70)
>DroEre_CAF1 11796 95 - 1
UGUUGAACAGGAACUUUAGAUGCCACCAAC---AGUUUCCACAGCAAUUAA--ACCGAAUGUUUAAUUGCACAUAACAGGCGUGCUUCAUGUUCCUGUCU
......((((((((...(((((((......---.((....)).((((((((--((.....))))))))))........))))).))....)))))))).. ( -30.00)
>DroYak_CAF1 11721 100 - 1
UGUUGAACAGGAACUUAAGAUGCCACCGACUUUAGUUGCCACAGCAAUUAACCACCGAAUUUGUAAUUGCACAUAACAGGCGCCUUUCAUGUUCCUGUCU
......((((((((..(((.((((..((((....)))).....(((((((.............)))))))........)))).)))....)))))))).. ( -26.92)
>consensus
UGUUAAACAGGAACUUAAGAUGCCACCAAC__CAGUUUCCACAGCAAUUAA___CCGAAUUUUUAAUUGCACAUAACAGGCGUCUUUCAUGUUCCUGUCC
......((((((((..((((((((...(((....)))......(((((((.............)))))))........))))))))....)))))))).. (-19.23 = -22.30 +   3.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

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