Locus 776

Sequence ID 3L_DroMel_CAF1
Location 2,329,513 – 2,329,603
Length 90
Max. P 0.999008
window1194 window1195

overview

Window 4

Location 2,329,513 – 2,329,603
Length 90
Sequences 4
Columns 91
Reading direction forward
Mean pairwise identity 82.87
Mean single sequence MFE -17.82
Consensus MFE -12.76
Energy contribution -13.83
Covariance contribution 1.06
Combinations/Pair 1.06
Mean z-score -1.92
Structure conservation index 0.72
SVM decision value 0.71
SVM RNA-class probability 0.828902
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2329513 90 + 23771897
AGAAAUAUUUACUCGUCGGAGGAAAGGGAAUCCAAAACAAUAAGCAUGAGAAAUGGGCCACAAAACUUUAUGGCCAA-AACGAGCUGGGAA
.......(((((((((.(((..........)))...........(((.....)))(((((.((....)).)))))..-.))))).)))).. ( -15.50)
>DroSec_CAF1 78717 90 + 1
AGAAAUGUUUACUCGUAGAAGGAAAGGGAAUCCAAAACAAUAAGCAUGAGAAAUGGGCCAAAAAACUUUAUGGCCCA-AACGAGCUGGGAA
...........(((((....(((.......)))....................(((((((.((....)).)))))))-.)))))....... ( -19.90)
>DroSim_CAF1 78950 90 + 1
AGAAAUGUUUACUCGUAGGAGGA-AGGGAAUCCAAAACAAUAAGCAUGAGAAAUGGGCCACAAAACUUUAUGGCCCAAAACGAGCUGGGAA
...........(((((....(((-......)))....................(((((((.((....)).)))))))..)))))....... ( -20.40)
>DroAna_CAF1 76330 75 + 1
-----------CGAGUUG-AGGAAA--AAAGCUAAAACAAUAAGCAUGAGAAAUGGGCCACAAAAGUUUAUGGCCCA-UA-GAGCGGAGAA
-----------...(((.-......--...(((.........))).......((((((((.((....)).)))))))-).-.)))...... ( -15.50)
>consensus
AGAAAUGUUUACUCGUAGGAGGAAAGGGAAUCCAAAACAAUAAGCAUGAGAAAUGGGCCACAAAACUUUAUGGCCCA_AACGAGCUGGGAA
...........(((((....(((.......)))....................(((((((.((....)).)))))))..)))))....... (-12.76 = -13.83 +   1.06) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 2,329,513 – 2,329,603
Length 90
Sequences 4
Columns 91
Reading direction reverse
Mean pairwise identity 82.87
Mean single sequence MFE -21.73
Consensus MFE -16.71
Energy contribution -18.27
Covariance contribution 1.56
Combinations/Pair 1.05
Mean z-score -3.94
Structure conservation index 0.77
SVM decision value 3.32
SVM RNA-class probability 0.999008
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2329513 90 - 23771897
UUCCCAGCUCGUU-UUGGCCAUAAAGUUUUGUGGCCCAUUUCUCAUGCUUAUUGUUUUGGAUUCCCUUUCCUCCGACGAGUAAAUAUUUCU
......(((((((-..((((((((....))))))))......................(((.......)))...))))))).......... ( -21.70)
>DroSec_CAF1 78717 90 - 1
UUCCCAGCUCGUU-UGGGCCAUAAAGUUUUUUGGCCCAUUUCUCAUGCUUAUUGUUUUGGAUUCCCUUUCCUUCUACGAGUAAACAUUUCU
......((((((.-(((((((..........)))))))....................(((.......)))....)))))).......... ( -21.80)
>DroSim_CAF1 78950 90 - 1
UUCCCAGCUCGUUUUGGGCCAUAAAGUUUUGUGGCCCAUUUCUCAUGCUUAUUGUUUUGGAUUCCCU-UCCUCCUACGAGUAAACAUUUCU
......((((((..((((((((((....))))))))))....................(((......-)))....)))))).......... ( -25.70)
>DroAna_CAF1 76330 75 - 1
UUCUCCGCUC-UA-UGGGCCAUAAACUUUUGUGGCCCAUUUCUCAUGCUUAUUGUUUUAGCUUU--UUUCCU-CAACUCG-----------
......((..-.(-((((((((((....))))))))))).......))................--......-.......----------- ( -17.70)
>consensus
UUCCCAGCUCGUU_UGGGCCAUAAAGUUUUGUGGCCCAUUUCUCAUGCUUAUUGUUUUGGAUUCCCUUUCCUCCUACGAGUAAACAUUUCU
......((((((..((((((((((....))))))))))..(((...((.....))...)))..............)))))).......... (-16.71 = -18.27 +   1.56) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:55 2006