Locus 17

Sequence ID 2R_DroMel_CAF1
Location 1,028,329 – 1,028,448
Length 119
Max. P 0.913752
window33 window34

overview

Window 3

Location 1,028,329 – 1,028,448
Length 119
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 89.86
Mean single sequence MFE -24.75
Consensus MFE -20.91
Energy contribution -19.92
Covariance contribution -0.99
Combinations/Pair 1.16
Mean z-score -1.84
Structure conservation index 0.84
SVM decision value 0.08
SVM RNA-class probability 0.572238
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1028329 119 + 20766785
AAAUUUUAUGAACCAAUACCAAUUUUAAAGCCAAUUAUGGGAAAACUGUUUCUGGUUCGGUAAGUUCUUAAACCCAUGGACUUUAGCGAAAGUUAUCUUUCGAAUGCAAGUUUUCAUAU
......((((((............(((((((((....((((..((((....(((...)))..))))......))))))).))))))((((((....))))))..........)))))). ( -20.80)
>DroSec_CAF1 30926 117 + 1
AAAUUUUAUGAACCUAUGCU-UUCUAAAAGCCAAUUAUGGGAAAACUGUUUCUGGUUCAGUAAAUUCUUAAACCCAUAGGCUUUUGCGAAAGUAAUCUUUCGAAUGCAA-UUUCCAUAC
......((((......((((-(((((((((((...((((((......(((((((...))).)))).......)))))))))))))).))))))).......(((.....-.))))))). ( -27.22)
>DroSim_CAF1 12348 117 + 1
CAAUUUUAUGAACCUAUGCU-UUCUAAAAGCCAAUUAUGGGAAAACUGUUUCUGGUUCGGUAAAUUCUUAAACCCAUAGGCUUUUGCGAAAGUAAUCUUUUGAAUGCAA-UUUCCAUAC
......((((......((((-(((((((((((...((((((......(((((((...))).)))).......)))))))))))))).))))))).......(((.....-.))))))). ( -26.22)
>consensus
AAAUUUUAUGAACCUAUGCU_UUCUAAAAGCCAAUUAUGGGAAAACUGUUUCUGGUUCGGUAAAUUCUUAAACCCAUAGGCUUUUGCGAAAGUAAUCUUUCGAAUGCAA_UUUCCAUAC
......((((..............((((((((...((((((......(((((((...))).)))).......))))))))))))))((((((....))))))............)))). (-20.91 = -19.92 +  -0.99)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 1,028,329 – 1,028,448
Length 119
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 89.86
Mean single sequence MFE -26.21
Consensus MFE -24.72
Energy contribution -24.06
Covariance contribution -0.66
Combinations/Pair 1.15
Mean z-score -1.97
Structure conservation index 0.94
SVM decision value 1.09
SVM RNA-class probability 0.913752
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1028329 119 - 20766785
AUAUGAAAACUUGCAUUCGAAAGAUAACUUUCGCUAAAGUCCAUGGGUUUAAGAACUUACCGAACCAGAAACAGUUUUCCCAUAAUUGGCUUUAAAAUUGGUAUUGGUUCAUAAAAUUU
.((((...((((.....((((((....))))))...)))).))))(((..........)))(((((((...(((((((.(((....)))....)))))))...)))))))......... ( -25.00)
>DroSec_CAF1 30926 117 - 1
GUAUGGAAA-UUGCAUUCGAAAGAUUACUUUCGCAAAAGCCUAUGGGUUUAAGAAUUUACUGAACCAGAAACAGUUUUCCCAUAAUUGGCUUUUAGAA-AGCAUAGGUUCAUAAAAUUU
.((((((..-.(((.((((((((....)))))..(((((((((((((...........((((.........))))...))))))...))))))).)))-.)))....))))))...... ( -29.64)
>DroSim_CAF1 12348 117 - 1
GUAUGGAAA-UUGCAUUCAAAAGAUUACUUUCGCAAAAGCCUAUGGGUUUAAGAAUUUACCGAACCAGAAACAGUUUUCCCAUAAUUGGCUUUUAGAA-AGCAUAGGUUCAUAAAAUUG
.((((((..-.(((.(((....((......))..(((((((((((((....((((((...(......)....))))))))))))...))))))).)))-.)))....))))))...... ( -24.00)
>consensus
GUAUGGAAA_UUGCAUUCGAAAGAUUACUUUCGCAAAAGCCUAUGGGUUUAAGAAUUUACCGAACCAGAAACAGUUUUCCCAUAAUUGGCUUUUAGAA_AGCAUAGGUUCAUAAAAUUU
.((((((....(((...((((((....)))))).(((((((((((((....((((((...............))))))))))))...)))))))......)))....))))))...... (-24.72 = -24.06 +  -0.66)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:23:34 2006