Locus 1978

Sequence ID X_DroMel_CAF1
Location 5,412,148 – 5,412,265
Length 117
Max. P 0.957999
window3223

overview

Window 3

Location 5,412,148 – 5,412,265
Length 117
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 89.78
Mean single sequence MFE -26.60
Consensus MFE -25.52
Energy contribution -25.15
Covariance contribution -0.37
Combinations/Pair 1.09
Mean z-score -1.86
Structure conservation index 0.96
SVM decision value 1.48
SVM RNA-class probability 0.957999
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5412148 117 - 22224390
AUAAUAAUCAUGAUAAUAAUAAUCGCACCCACAUAUGGUUGUUUUUUUUUUUUUUACCUCGGGCCAGGGCGUUGGCGCUUGCCAGAGAAAUUCCACAAAAAAAUGUGGAAAAAAACA
.....(((((((.....................)))))))((((((...........(((.(((.((.((....)).)).))).)))...(((((((......))))))))))))). ( -26.50)
>DroSim_CAF1 19002 109 - 1
AUAAUAAUCAUGAUAAUAAUAAUCGCACCCACACAUGGU-------AUUUUUUUUACCUCGGGCCAGGGCGUUGGCGCUUGCCAGAGAAAUUCCACAAA-AAAUGUGGAAAAAAACA
......((((((.....................))))))-------...........(((.(((.((.((....)).)).))).)))...(((((((..-...)))))))....... ( -25.10)
>DroEre_CAF1 28242 106 - 1
AUAAUAAUCAUGAUAAUAAUAAUCGCACCCACACAUGGUAUUU---------UUUACCUCGGGCCAGGGCGUUGGCGCUUGCCGGAGAAAUUCCACAAA-AAAUGUGGAAA-AAGCA
........................(((((.......)))....---------.....(((.(((.((.((....)).)).))).)))...(((((((..-...))))))).-..)). ( -27.60)
>DroYak_CAF1 20371 115 - 1
AUAAUAAUCAUGAUAAUAAUAAUCGCACCCACACAUGGUAUUUUUUCUUUUUUUUACCUCGGGCCAGGGCGUUGGCGCUUGCCGGAGAAAUUCCACAAA-AAAUGUGGGAA-AACCA
...................................((((..................(((.(((.((.((....)).)).))).)))...(((((((..-...))))))).-.)))) ( -27.20)
>consensus
AUAAUAAUCAUGAUAAUAAUAAUCGCACCCACACAUGGUAUUU____UUUUUUUUACCUCGGGCCAGGGCGUUGGCGCUUGCCAGAGAAAUUCCACAAA_AAAUGUGGAAA_AAACA
......((((((.....................))))))..................(((.(((.((.((....)).)).))).)))...(((((((......)))))))....... (-25.52 = -25.15 +  -0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:23 2006