Locus 1506

Sequence ID	3L_DroMel_CAF1
Location	4,337,943 – 4,338,058
Length	115
Max. P	0.555364

overview

Window 4

Location	4,337,943 – 4,338,058
Length	115
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	90.00
Mean single sequence MFE	-30.55
Consensus MFE	-23.84
Energy contribution	-26.15
Covariance contribution	2.31
Combinations/Pair	1.03
Mean z-score	-1.46
Structure conservation index	0.78
SVM decision value	0.01
SVM RNA-class probability	0.539959
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4337943 115 + 23771897
ACUGCAAUUUCAAGUGAUUUGUGGCCGAUUUGUGUUGCCGAUUUCUUGCAAAAUGGCACACACUCCCUCUGGAAACCUAAAUCCACUCGAAACGAGAGCUCUCCAGGCAUUAACU
..(((..((((.(((((((((.((......(((((.((((.(((.....))).))))))))).(((....)))..))))))).)))).)))).(((....)))...)))...... ( -26.20)
>DroSec_CAF1 24161 102 + 1
ACUGCAAUUUCAAGUGAUUUGUGGCCG-------------AUUUCUGGCAAAAUGGCACACACUCCCGCUGGAAACCCAGAUCCACUCGAAAGGAGAGCUCUCCAGGCAUUAACU
..(((..((((.((((...((((((((-------------.(((.....))).)))).))))......((((....))))...)))).))))((((....))))..)))...... ( -29.40)
>DroSim_CAF1 24209 115 + 1
ACUGCAAUUUCAAGUGAUUUGUGGCCGAUUUGUGUUGCCGAUUUCUGGCAAAAUGGCACACACUCCCGCUGGAAACCCAGAUCCACUCGAAAGGAGAGCUCUCCAGGCAUUAACU
..(((..((((.((((...((((((((.......((((((.....))))))..)))).))))......((((....))))...)))).))))((((....))))..)))...... ( -35.60)
>DroYak_CAF1 23708 115 + 1
ACUGCAAUUUCAAGUGAUUUGUGGCCGAUUUUUGUUGCCGAUUUCUGGCAAAAUGGCACACUCUCCCUCUGCAAAUCCAGAUCCACUCGAAAGGAGGGCUCUCCAGGCAUUAACU
..(((..((((.((((....(((((((.......((((((.....))))))..)))).)))......((((......))))..)))).))))((((....))))..)))...... ( -31.00)
>consensus
ACUGCAAUUUCAAGUGAUUUGUGGCCGAUUUGUGUUGCCGAUUUCUGGCAAAAUGGCACACACUCCCGCUGGAAACCCAGAUCCACUCGAAAGGAGAGCUCUCCAGGCAUUAACU
..(((..((((.((((....(((((((.......((((((.....))))))..)))).))).......((((....))))...)))).))))((((....))))..)))...... (-23.84 = -26.15 +   2.31)

alignment

secondary structure

dotplot

Window 5

Location	4,337,943 – 4,338,058
Length	115
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	90.00
Mean single sequence MFE	-34.88
Consensus MFE	-26.26
Energy contribution	-26.82
Covariance contribution	0.56
Combinations/Pair	1.00
Mean z-score	-1.55
Structure conservation index	0.75
SVM decision value	0.04
SVM RNA-class probability	0.555364
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4337943 115 - 23771897
AGUUAAUGCCUGGAGAGCUCUCGUUUCGAGUGGAUUUAGGUUUCCAGAGGGAGUGUGUGCCAUUUUGCAAGAAAUCGGCAACACAAAUCGGCCACAAAUCACUUGAAAUUGCAGU
......(((...(((....)))((((((((((.((((.(((((((....)))((((.(((((((((....))))).)))))))).....))))..)))))))))))))).))).. ( -33.70)
>DroSec_CAF1 24161 102 - 1
AGUUAAUGCCUGGAGAGCUCUCCUUUCGAGUGGAUCUGGGUUUCCAGCGGGAGUGUGUGCCAUUUUGCCAGAAAU-------------CGGCCACAAAUCACUUGAAAUUGCAGU
......(((..((((....))))((((((((((..((((....))))......((((.((((((((....)))))-------------.)))))))..))))))))))..))).. ( -33.20)
>DroSim_CAF1 24209 115 - 1
AGUUAAUGCCUGGAGAGCUCUCCUUUCGAGUGGAUCUGGGUUUCCAGCGGGAGUGUGUGCCAUUUUGCCAGAAAUCGGCAACACAAAUCGGCCACAAAUCACUUGAAAUUGCAGU
......(((..((((....))))((((((((((..((((....))))(((...(((((((((((((....))))).))).)))))..)))........))))))))))..))).. ( -37.60)
>DroYak_CAF1 23708 115 - 1
AGUUAAUGCCUGGAGAGCCCUCCUUUCGAGUGGAUCUGGAUUUGCAGAGGGAGAGUGUGCCAUUUUGCCAGAAAUCGGCAACAAAAAUCGGCCACAAAUCACUUGAAAUUGCAGU
......(((..((((....))))((((((((((.((((......))))......(((.((((((((((((....).))))....)))).))))))...))))))))))..))).. ( -35.00)
>consensus
AGUUAAUGCCUGGAGAGCUCUCCUUUCGAGUGGAUCUGGGUUUCCAGAGGGAGUGUGUGCCAUUUUGCCAGAAAUCGGCAACACAAAUCGGCCACAAAUCACUUGAAAUUGCAGU
......(((..((((....))))((((((((((........((((....)))).(((.((((((((....))))).(....).......))))))...))))))))))..))).. (-26.26 = -26.82 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:25 2006