Locus 7707

Sequence ID 3L_DroMel_CAF1
Location 20,608,108 – 20,608,244
Length 136
Max. P 0.989601
window12534 window12535

overview

Window 4

Location 20,608,108 – 20,608,208
Length 100
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 94.12
Mean single sequence MFE -25.45
Consensus MFE -23.40
Energy contribution -23.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.75
Structure conservation index 0.92
SVM decision value 2.17
SVM RNA-class probability 0.989601
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20608108 100 + 23771897
AAAGAAAAACGUGUGGAGCCGUUGCAGGCAG----ACAGGCAUUAAAUUGUAAUGAGAUCAUUGCCAUUUAAUAAAUUUACUCACAUGUCUAUUUAUAAAAUAU
........((((((((.(((.(((....)))----...)))(((((((.((((((....)))))).)))))))........))))))))............... ( -25.20)
>DroSec_CAF1 52978 100 + 1
AGAGGAAAACGUGUGGAGCCUUUGCAGGCAG----ACAGGCAUUAAAUUGUAAUGAGAUCAUUGCCAUUUAAUAAAUUUACUCACAUGUCUAUUUAUAAAAUAU
........((((((((.(((((((....)))----..))))(((((((.((((((....)))))).)))))))........))))))))............... ( -24.70)
>DroSim_CAF1 47773 100 + 1
GGAGGAAAACGUGUGGAGCCGUUGCAGGCAG----ACAGGCAUUAAAUUGUAAUGAGAUCAUUGCCAUUUAAUAAAUUUACUCACAUGUCUAUUUAUAAAAUAU
........((((((((.(((.(((....)))----...)))(((((((.((((((....)))))).)))))))........))))))))............... ( -25.20)
>DroEre_CAF1 45472 103 + 1
AAAGGA-AACGUGUGGAGCCAUUGCAGGCAGGCAGGCAGGCAUUAAAUUGUAAUGAGAUCAUUGCCAUUUAAUAAAUUUACUCACAUGUCUAUUUAUAAAAUGU
......-.((((((((.(((.((((......))))...)))(((((((.((((((....)))))).)))))))........))))))))............... ( -26.70)
>consensus
AAAGGAAAACGUGUGGAGCCGUUGCAGGCAG____ACAGGCAUUAAAUUGUAAUGAGAUCAUUGCCAUUUAAUAAAUUUACUCACAUGUCUAUUUAUAAAAUAU
........((((((((.(((......)))............(((((((.((((((....)))))).)))))))........))))))))............... (-23.40 = -23.40 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 20,608,139 – 20,608,244
Length 105
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 97.20
Mean single sequence MFE -18.30
Consensus MFE -17.73
Energy contribution -17.73
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.28
Structure conservation index 0.97
SVM decision value 1.96
SVM RNA-class probability 0.984133
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20608139 105 + 23771897
----ACAGGCAUUAAAUUGUAAUGAGAUCAUUGCCAUUUAAUAAAUUUACUCACAUGUCUAUUUAUAAAAUAUUAUGCCAUGAACCCAUAACCUUACCCAAUAAAUAAA
----.((((((((((((.((((((....)))))).)))))((((((..((......))..))))))........))))).))........................... ( -17.80)
>DroSec_CAF1 53009 105 + 1
----ACAGGCAUUAAAUUGUAAUGAGAUCAUUGCCAUUUAAUAAAUUUACUCACAUGUCUAUUUAUAAAAUAUUAUGCCAUGAACCCAUAACCUUACCCAAUAAAUAAA
----.((((((((((((.((((((....)))))).)))))((((((..((......))..))))))........))))).))........................... ( -17.80)
>DroSim_CAF1 47804 105 + 1
----ACAGGCAUUAAAUUGUAAUGAGAUCAUUGCCAUUUAAUAAAUUUACUCACAUGUCUAUUUAUAAAAUAUUAUGCCAUGAACCCAUAACCUUACCCAAUAAAUAAA
----.((((((((((((.((((((....)))))).)))))((((((..((......))..))))))........))))).))........................... ( -17.80)
>DroEre_CAF1 45502 109 + 1
GCAGGCAGGCAUUAAAUUGUAAUGAGAUCAUUGCCAUUUAAUAAAUUUACUCACAUGUCUAUUUAUAAAAUGUUAUGCCAUGAACCCAUAACCUUACCCAAUAAAUAAA
...((((((((((((((.((((((....)))))).)))).((((((..((......))..))))))..)))))).)))).............................. ( -19.80)
>consensus
____ACAGGCAUUAAAUUGUAAUGAGAUCAUUGCCAUUUAAUAAAUUUACUCACAUGUCUAUUUAUAAAAUAUUAUGCCAUGAACCCAUAACCUUACCCAAUAAAUAAA
.....((((((((((((.((((((....)))))).)))))((((((..((......))..))))))........))))).))........................... (-17.73 = -17.73 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:54:31 2006